1 kb ladder  (New England Biolabs)


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    Name:
    1 kb DNA Ladder
    Description:
    1 kb DNA Ladder 1 000 gel lanes
    Catalog Number:
    n3232l
    Price:
    214
    Size:
    1 000 gel lanes
    Category:
    DNA Ladders
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    Structured Review

    New England Biolabs 1 kb ladder
    1 kb DNA Ladder
    1 kb DNA Ladder 1 000 gel lanes
    https://www.bioz.com/result/1 kb ladder/product/New England Biolabs
    Average 86 stars, based on 214 article reviews
    Price from $9.99 to $1999.99
    1 kb ladder - by Bioz Stars, 2020-09
    86/100 stars

    Images

    1) Product Images from "Edwardsiellosis Caused by Edwardsiella ictaluri in Laboratory Populations of Zebrafish Danio rerio"

    Article Title: Edwardsiellosis Caused by Edwardsiella ictaluri in Laboratory Populations of Zebrafish Danio rerio

    Journal: Journal of aquatic animal health

    doi: 10.1080/08997659.2013.782226

    Linearized plasmid profiles of Edwardsiella ictaluri isolates. Plasmid DNA from E. ictaluri isolated from Channel Catfish or Zebrafish was digested with EcoRI or BstZ17I, respectively, and separated by 0.6% agarose gel electrophoresis using a 1-kb DNA
    Figure Legend Snippet: Linearized plasmid profiles of Edwardsiella ictaluri isolates. Plasmid DNA from E. ictaluri isolated from Channel Catfish or Zebrafish was digested with EcoRI or BstZ17I, respectively, and separated by 0.6% agarose gel electrophoresis using a 1-kb DNA

    Techniques Used: Plasmid Preparation, Isolation, Agarose Gel Electrophoresis

    2) Product Images from "Human PSF binds to RAD51 and modulates its homologous-pairing and strand-exchange activities"

    Article Title: Human PSF binds to RAD51 and modulates its homologous-pairing and strand-exchange activities

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp298

    DNA-binding and RAD51-binding activities of the PSF domains. ϕX174 ssDNA (20 µM) ( A ) or ϕX174 linear dsDNA (20 µM) ( B ) was incubated with PSF, PSF(1–266) or PSF(267–468) at 37°C for 10 min. The samples were then separated by 0.8% agarose gel electrophoresis in TAE buffer and were visualized by ethidium bromide staining. The protein concentrations for panel A were 0 µM (lane 1), 0.15 µM (lanes 2, 5 and 8), 0.3 µM (lanes 3, 6 and 9) and 0.6 µM (lanes 4, 7 and 10). The protein concentrations for panel B were 0 µM (lane 1), 0.1 µM (lanes 2, 5 and 8), 0.2 µM (lanes 3, 6 and 9) and 0.4 µM (lanes 4, 7 and 10). ( C ) The pull-down assay with Ni–NTA beads. Lanes 2–5 represent purified RAD51, His 6 -tagged PSF, His 6 -tagged PSF(1–266) and His 6 -tagged PSF(267–468), respectively. His 6 -tagged PSF, His 6 -tagged PSF(1–266) or His 6 -tagged PSF(267–468) (3.8 µg) was mixed with RAD51 (7.4 µg). The RAD51 bound to the His 6 -tagged proteins was pulled down by the Ni–NTA agarose beads, and was analyzed by 12% SDS–PAGE. Bands were visualized by Coomassie Brilliant Blue staining.
    Figure Legend Snippet: DNA-binding and RAD51-binding activities of the PSF domains. ϕX174 ssDNA (20 µM) ( A ) or ϕX174 linear dsDNA (20 µM) ( B ) was incubated with PSF, PSF(1–266) or PSF(267–468) at 37°C for 10 min. The samples were then separated by 0.8% agarose gel electrophoresis in TAE buffer and were visualized by ethidium bromide staining. The protein concentrations for panel A were 0 µM (lane 1), 0.15 µM (lanes 2, 5 and 8), 0.3 µM (lanes 3, 6 and 9) and 0.6 µM (lanes 4, 7 and 10). The protein concentrations for panel B were 0 µM (lane 1), 0.1 µM (lanes 2, 5 and 8), 0.2 µM (lanes 3, 6 and 9) and 0.4 µM (lanes 4, 7 and 10). ( C ) The pull-down assay with Ni–NTA beads. Lanes 2–5 represent purified RAD51, His 6 -tagged PSF, His 6 -tagged PSF(1–266) and His 6 -tagged PSF(267–468), respectively. His 6 -tagged PSF, His 6 -tagged PSF(1–266) or His 6 -tagged PSF(267–468) (3.8 µg) was mixed with RAD51 (7.4 µg). The RAD51 bound to the His 6 -tagged proteins was pulled down by the Ni–NTA agarose beads, and was analyzed by 12% SDS–PAGE. Bands were visualized by Coomassie Brilliant Blue staining.

    Techniques Used: Binding Assay, Incubation, Agarose Gel Electrophoresis, Staining, Pull Down Assay, Purification, SDS Page

    3) Product Images from "Biochemical characterization and chemical validation of Leishmania MAP Kinase-3 as a potential drug target"

    Article Title: Biochemical characterization and chemical validation of Leishmania MAP Kinase-3 as a potential drug target

    Journal: Scientific Reports

    doi: 10.1038/s41598-019-52774-6

    Confirmation of pET28a- Ld MAPK3 construct. Lane 1 showing the amplification of Ld MAPK3 by colony PCR method; Lane 2 is indicating 1-kb DNA ladder and Lane 3 is showing the release of insert ( Ld MAPK3) at 1.2 kb and 5.369 kb as vector (pET 28a(+)) using restriction digestion.
    Figure Legend Snippet: Confirmation of pET28a- Ld MAPK3 construct. Lane 1 showing the amplification of Ld MAPK3 by colony PCR method; Lane 2 is indicating 1-kb DNA ladder and Lane 3 is showing the release of insert ( Ld MAPK3) at 1.2 kb and 5.369 kb as vector (pET 28a(+)) using restriction digestion.

    Techniques Used: Construct, Amplification, Polymerase Chain Reaction, Plasmid Preparation, Positron Emission Tomography

    4) Product Images from "Sizing femtogram amounts of dsDNA by single-molecule counting"

    Article Title: Sizing femtogram amounts of dsDNA by single-molecule counting

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkv904

    Single-molecule intensity distribution of a 1 kbp DNA ladder. ( A ) intensity distribution histogram of detected molecules (red), fitted Gaussians sum (black) and the residue of the fitting (blue). ( B ) a plot of expected DNA lengths in the ladder sample versus the centers of the fitted Gaussian peaks exhibits linear dependency with R 2 = 0.99932.
    Figure Legend Snippet: Single-molecule intensity distribution of a 1 kbp DNA ladder. ( A ) intensity distribution histogram of detected molecules (red), fitted Gaussians sum (black) and the residue of the fitting (blue). ( B ) a plot of expected DNA lengths in the ladder sample versus the centers of the fitted Gaussian peaks exhibits linear dependency with R 2 = 0.99932.

    Techniques Used:

    5) Product Images from "Contamination sources, serogroups, biofilm-forming ability and biocide resistance of Listeria monocytogenes persistent in tilapia-processing facilities"

    Article Title: Contamination sources, serogroups, biofilm-forming ability and biocide resistance of Listeria monocytogenes persistent in tilapia-processing facilities

    Journal: Journal of Food Science and Technology

    doi: 10.1007/s13197-017-2843-x

    Agarose gels showing RAPD patterns of L. monocytogenes for primers DAF4 ( a ), HLWL85 ( b ) and OPM-01 ( c ). Lane 1: DNA molecular weight marker (100 bp DNA ladder, 100–1517 bp, New England Biolabs)
    Figure Legend Snippet: Agarose gels showing RAPD patterns of L. monocytogenes for primers DAF4 ( a ), HLWL85 ( b ) and OPM-01 ( c ). Lane 1: DNA molecular weight marker (100 bp DNA ladder, 100–1517 bp, New England Biolabs)

    Techniques Used: Molecular Weight, Marker

    6) Product Images from "Homologous Pairing Activities of Two Rice RAD51 Proteins, RAD51A1 and RAD51A2"

    Article Title: Homologous Pairing Activities of Two Rice RAD51 Proteins, RAD51A1 and RAD51A2

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0075451

    The DNA-binding activities of rice RAD51A1 and RAD51A2. Circular φX174 ssDNA (20 µM) (A) or linear φX174 dsDNA (20 µM) (C) was incubated with rice RAD51A1, RAD51A2, or human RAD51 at 37°C for 10 min. The samples were then separated by 0.8% agarose gel electrophoresis in TAE buffer, and were visualized by ethidium bromide staining. Lanes 1–10 and 11–20 represent the reactions conducted with and without ATP, respectively. Lanes 1 and 11 indicate negative control experiments without protein. Lanes 2–4 and 12–14 represent the experiments conducted with RAD51A1. Lanes 5–7 and 15–17 represent the experiments conducted with RAD51A2. Lanes 8–10 and 18–20 represent the experiments conducted with human RAD51. The protein concentrations were 0.75 µM (lanes 2, 5, 8, 12, 15, and 18), 1.5 µM (lanes 3, 6, 9, 13, 16, and 19) and 3 µM (lanes 4, 7, 10, 14, 17, and 20). (B) Graphic representation of the relative migration distances of the RAD51A1- and RAD51A2-ssDNA complexes. The migration distances relative to the free DNA are plotted against the protein concentrations. (D) Competitive ssDNA- and dsDNA-binding. Circular φX174 ssDNA (20 µM) and linear φX174 dsDNA (20 µM) were incubated with rice RAD51A1, RAD51A2, or human RAD51 at 37°C for 10 min, under the 120 mM NaCl conditions. The samples were then separated by 0.8% agarose gel electrophoresis in TAE buffer, and were visualized by ethidium bromide staining. Lane 1 indicates negative control experiments without protein. Lanes 2–4, 5–7, and 8–10 represent the experiments conducted with RAD51A1, RAD51A2, and human RAD51, respectively. The protein concentrations were 0.9 µM (lanes 2, 5, and 8), 1.8 µM (lanes 3, 6, and 9), and 3.6 µM (lanes 4, 7, and 10).
    Figure Legend Snippet: The DNA-binding activities of rice RAD51A1 and RAD51A2. Circular φX174 ssDNA (20 µM) (A) or linear φX174 dsDNA (20 µM) (C) was incubated with rice RAD51A1, RAD51A2, or human RAD51 at 37°C for 10 min. The samples were then separated by 0.8% agarose gel electrophoresis in TAE buffer, and were visualized by ethidium bromide staining. Lanes 1–10 and 11–20 represent the reactions conducted with and without ATP, respectively. Lanes 1 and 11 indicate negative control experiments without protein. Lanes 2–4 and 12–14 represent the experiments conducted with RAD51A1. Lanes 5–7 and 15–17 represent the experiments conducted with RAD51A2. Lanes 8–10 and 18–20 represent the experiments conducted with human RAD51. The protein concentrations were 0.75 µM (lanes 2, 5, 8, 12, 15, and 18), 1.5 µM (lanes 3, 6, 9, 13, 16, and 19) and 3 µM (lanes 4, 7, 10, 14, 17, and 20). (B) Graphic representation of the relative migration distances of the RAD51A1- and RAD51A2-ssDNA complexes. The migration distances relative to the free DNA are plotted against the protein concentrations. (D) Competitive ssDNA- and dsDNA-binding. Circular φX174 ssDNA (20 µM) and linear φX174 dsDNA (20 µM) were incubated with rice RAD51A1, RAD51A2, or human RAD51 at 37°C for 10 min, under the 120 mM NaCl conditions. The samples were then separated by 0.8% agarose gel electrophoresis in TAE buffer, and were visualized by ethidium bromide staining. Lane 1 indicates negative control experiments without protein. Lanes 2–4, 5–7, and 8–10 represent the experiments conducted with RAD51A1, RAD51A2, and human RAD51, respectively. The protein concentrations were 0.9 µM (lanes 2, 5, and 8), 1.8 µM (lanes 3, 6, and 9), and 3.6 µM (lanes 4, 7, and 10).

    Techniques Used: Binding Assay, Incubation, Agarose Gel Electrophoresis, Staining, Negative Control, Migration

    Purification of rice RAD51A1 and RAD51A2. (A) The amino acid sequences of rice RAD51A1 and RAD51A2 from japonica cultivar group, cv. Nipponbare, rice RAD51 from indica cultivar group, cv. Pusa Basmati 1, and human RAD51, aligned with the ClustalX software [50] . Black and gray boxes indicate identical and similar amino acid residues, respectively. The L1 and L2 loops, which are important for DNA binding, are represented by red lines. (B) Purified rice RAD51A1, RAD51A2, and human RAD51. Lane 1 indicates the molecular mass markers, and lanes 2, 3, and 4 represent rice RAD51A1 (0.5 µg), RAD51A2 (0.5 µg), and human RAD51 (0.5 µg), respectively. (C) The ATPase activities of Oryza sativa RAD51A1 and RAD51A2. The reactions were conducted with φX174 circular ssDNA (left panel), linearized φX174 dsDNA (center panel), or without DNA (right panel), in the presence of 5 µM ATP. Blue circles and red squares represent the experiments with RAD51A1 and RAD51A2, respectively. The averages of three independent experiments are shown with the SD values.
    Figure Legend Snippet: Purification of rice RAD51A1 and RAD51A2. (A) The amino acid sequences of rice RAD51A1 and RAD51A2 from japonica cultivar group, cv. Nipponbare, rice RAD51 from indica cultivar group, cv. Pusa Basmati 1, and human RAD51, aligned with the ClustalX software [50] . Black and gray boxes indicate identical and similar amino acid residues, respectively. The L1 and L2 loops, which are important for DNA binding, are represented by red lines. (B) Purified rice RAD51A1, RAD51A2, and human RAD51. Lane 1 indicates the molecular mass markers, and lanes 2, 3, and 4 represent rice RAD51A1 (0.5 µg), RAD51A2 (0.5 µg), and human RAD51 (0.5 µg), respectively. (C) The ATPase activities of Oryza sativa RAD51A1 and RAD51A2. The reactions were conducted with φX174 circular ssDNA (left panel), linearized φX174 dsDNA (center panel), or without DNA (right panel), in the presence of 5 µM ATP. Blue circles and red squares represent the experiments with RAD51A1 and RAD51A2, respectively. The averages of three independent experiments are shown with the SD values.

    Techniques Used: Purification, Software, Binding Assay

    Electron microscopic images of RAD51A1 and RAD51A2 complexed with DNA. (A and B) Electron microscopic images of rice RAD51A1 (A) and RAD51A2 (B) filaments formed on the φX174 dsDNA in the presence of ATP. The average helical pitches of the RAD51A1 and RAD51A2 filaments were about 9.15 nm. The black bar denotes 100 nm.
    Figure Legend Snippet: Electron microscopic images of RAD51A1 and RAD51A2 complexed with DNA. (A and B) Electron microscopic images of rice RAD51A1 (A) and RAD51A2 (B) filaments formed on the φX174 dsDNA in the presence of ATP. The average helical pitches of the RAD51A1 and RAD51A2 filaments were about 9.15 nm. The black bar denotes 100 nm.

    Techniques Used:

    7) Product Images from "Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA"

    Article Title: Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkv415

    Plasmid cleavage by Pf Ago. ( A ) pWUR790 expression plasmid. ( B ) Pf Ago expressed at 20°C and purified in absence of Mn 2+ cleaves expression plasmid pWUR790. Agarose gels with plasmid targets incubated without protein (lane 1), with Pf AgoDM (lane 2) and with Pf Ago (lane 3). M1: 1-kb DNA ladder (New England Biolabs). M2: pWUR790 marker with open circular (OC), linearized (LIN) and supercoiled (SC) pWUR790. ( C ) pWUR704 target plasmid, target site indicated in gray. ( D ) Target region (gray) and FW and RV siDNA guides (black). Predicted cleavage sites are indicated with a black triangle. ( E ) Agarose gels with plasmid targets incubated with Pf AgoDM (lane 1), with guide free Pf Ago (lane 2) and with Pf Ago loaded with FW siDNA, RV siDNA, or both (lane 3–5) in reaction buffer with 250 mM NaCl (left panel) or 500 mM NaCl (right panel). M1: 1 kb GeneRuler marker (Thermo Scientific). M2: pWUR704 marker with open circular (OC), linearized (LIN) and supercoiled (SC) pWUR704.
    Figure Legend Snippet: Plasmid cleavage by Pf Ago. ( A ) pWUR790 expression plasmid. ( B ) Pf Ago expressed at 20°C and purified in absence of Mn 2+ cleaves expression plasmid pWUR790. Agarose gels with plasmid targets incubated without protein (lane 1), with Pf AgoDM (lane 2) and with Pf Ago (lane 3). M1: 1-kb DNA ladder (New England Biolabs). M2: pWUR790 marker with open circular (OC), linearized (LIN) and supercoiled (SC) pWUR790. ( C ) pWUR704 target plasmid, target site indicated in gray. ( D ) Target region (gray) and FW and RV siDNA guides (black). Predicted cleavage sites are indicated with a black triangle. ( E ) Agarose gels with plasmid targets incubated with Pf AgoDM (lane 1), with guide free Pf Ago (lane 2) and with Pf Ago loaded with FW siDNA, RV siDNA, or both (lane 3–5) in reaction buffer with 250 mM NaCl (left panel) or 500 mM NaCl (right panel). M1: 1 kb GeneRuler marker (Thermo Scientific). M2: pWUR704 marker with open circular (OC), linearized (LIN) and supercoiled (SC) pWUR704.

    Techniques Used: Plasmid Preparation, Expressing, Purification, Incubation, Marker

    8) Product Images from "In Situ Transfection by Controlled Release of Lipoplexes using Acoustic Droplet Vaporization"

    Article Title: In Situ Transfection by Controlled Release of Lipoplexes using Acoustic Droplet Vaporization

    Journal: Advanced healthcare materials

    doi: 10.1002/adhm.201600008

    Gel electrophoresis confirming stability of plasmid after ultrasound exposures. Lane 1) pDNA; lane 2) sonicated pDNA; lane 3) lipoplex; lane 4) sonicated lipoplex; lane 5) emulsified lipoplex released by ultrasound (3.5 MHz, mechanical index (MI) = 2.5, 10 Hz pulse repetition frequency (PRF), 30 cycles); lane 6) 1 kb linear DNA ladder marker. The mass of pDNA was equivalent in all lanes.
    Figure Legend Snippet: Gel electrophoresis confirming stability of plasmid after ultrasound exposures. Lane 1) pDNA; lane 2) sonicated pDNA; lane 3) lipoplex; lane 4) sonicated lipoplex; lane 5) emulsified lipoplex released by ultrasound (3.5 MHz, mechanical index (MI) = 2.5, 10 Hz pulse repetition frequency (PRF), 30 cycles); lane 6) 1 kb linear DNA ladder marker. The mass of pDNA was equivalent in all lanes.

    Techniques Used: Nucleic Acid Electrophoresis, Plasmid Preparation, Sonication, Marker

    9) Product Images from "Recombination Activator Function of the Novel RAD51- and RAD51B-binding Protein, Human EVL *Recombination Activator Function of the Novel RAD51- and RAD51B-binding Protein, Human EVL * S⃞"

    Article Title: Recombination Activator Function of the Novel RAD51- and RAD51B-binding Protein, Human EVL *Recombination Activator Function of the Novel RAD51- and RAD51B-binding Protein, Human EVL * S⃞

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.M807715200

    DNA binding activities of the EVL protein. φX174 ssDNA (20 μ m ) and/orφX174 linear dsDNA (20 μ m ) were each incubated with the EVL protein at 37 °C for 15 min. The samples were then separated by 0.8% agarose gel
    Figure Legend Snippet: DNA binding activities of the EVL protein. φX174 ssDNA (20 μ m ) and/orφX174 linear dsDNA (20 μ m ) were each incubated with the EVL protein at 37 °C for 15 min. The samples were then separated by 0.8% agarose gel

    Techniques Used: Binding Assay, Incubation, Agarose Gel Electrophoresis

    10) Product Images from "Two Phosphoglucomutase Paralogs Facilitate Ionophore-Triggered Secretion of the Toxoplasma Micronemes"

    Article Title: Two Phosphoglucomutase Paralogs Facilitate Ionophore-Triggered Secretion of the Toxoplasma Micronemes

    Journal: mSphere

    doi: 10.1128/mSphere.00521-17

    Subcellular localization of PRP1 through endogenous tagging. (A) Schematic representation of generating C-terminal endogenously YFP-tagged gPRP1-YFP parasites by single homologous recombination into the RHΔ ku80 parent line. (B) PCR validation of the gPRP1-YFP genotype using the primer pair shown in panel A. Lane M contains 1-kb DNA ladder (New England Biolabs). (C) Live imaging of gPRP1-YFP parasites under intracellular and extracellular conditions as indicated. PC, phase contrast. (D) Live imaging of gPRP1-YFP parasites cotransfected with markers for the IMC (IMC1-mCherry), rhoptries (TLN1-mCherry), and micronemes (MIC8-mCherry). (E) Representative images of intracellular gPRP1-YFP parasites fixed using either 100% methanol (MetOH) or 4% paraformaldehyde (PFA) stained with anti-PRP1 (αPRP1) and anti-GFP (αGFP) antisera as indicated. Note that PFA fixation destroys the costaining of GFP and PRP1 and thus destroys the PRP1 epitope(s) recognized by the specific antiserum.
    Figure Legend Snippet: Subcellular localization of PRP1 through endogenous tagging. (A) Schematic representation of generating C-terminal endogenously YFP-tagged gPRP1-YFP parasites by single homologous recombination into the RHΔ ku80 parent line. (B) PCR validation of the gPRP1-YFP genotype using the primer pair shown in panel A. Lane M contains 1-kb DNA ladder (New England Biolabs). (C) Live imaging of gPRP1-YFP parasites under intracellular and extracellular conditions as indicated. PC, phase contrast. (D) Live imaging of gPRP1-YFP parasites cotransfected with markers for the IMC (IMC1-mCherry), rhoptries (TLN1-mCherry), and micronemes (MIC8-mCherry). (E) Representative images of intracellular gPRP1-YFP parasites fixed using either 100% methanol (MetOH) or 4% paraformaldehyde (PFA) stained with anti-PRP1 (αPRP1) and anti-GFP (αGFP) antisera as indicated. Note that PFA fixation destroys the costaining of GFP and PRP1 and thus destroys the PRP1 epitope(s) recognized by the specific antiserum.

    Techniques Used: Homologous Recombination, Polymerase Chain Reaction, Imaging, Staining

    11) Product Images from "A single catalytic domain of the junction-resolving enzyme T7 endonuclease I is a non-specific nicking endonuclease"

    Article Title: A single catalytic domain of the junction-resolving enzyme T7 endonuclease I is a non-specific nicking endonuclease

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gki921

    ( A ) Determination of non-specific nuclease activity of SCD protein. Variable amounts of purified MEn–In/Ic–Ec were incubated with 1 µg of 2-log DNA ladder (NEB) in 20 µl of either Mg 2+ or Mn 2+ buffer at 37°C for 1 h. The digests were resolved on a 1.2% agarose gel. From lane 1 to 5, digests with 0.00, 0.125, 0.25, 0.5 and 1.0 µg of MEn–In/Ic–Ec in Mg 2+ buffer, respectively. From lane 6 to 10, digests are the same as from lane 1 to 5 except for using Mn 2+ buffer. ( B ) Identification of nicked strands as intermediate products of reaction by SCD protein. Plasmid pUC19 was incubated with MEn–In/Ic–Ec in Mg 2+ buffer at 37°C. At variable time point 0, 2, 5, 10, 20, 30, 40, 60, 120 and 180 min an aliquot of sample was withdrawn from the reaction and resolved on an agarose gel. L, N and S stand for linear, nicked and supercoiled plasmids, respectively.
    Figure Legend Snippet: ( A ) Determination of non-specific nuclease activity of SCD protein. Variable amounts of purified MEn–In/Ic–Ec were incubated with 1 µg of 2-log DNA ladder (NEB) in 20 µl of either Mg 2+ or Mn 2+ buffer at 37°C for 1 h. The digests were resolved on a 1.2% agarose gel. From lane 1 to 5, digests with 0.00, 0.125, 0.25, 0.5 and 1.0 µg of MEn–In/Ic–Ec in Mg 2+ buffer, respectively. From lane 6 to 10, digests are the same as from lane 1 to 5 except for using Mn 2+ buffer. ( B ) Identification of nicked strands as intermediate products of reaction by SCD protein. Plasmid pUC19 was incubated with MEn–In/Ic–Ec in Mg 2+ buffer at 37°C. At variable time point 0, 2, 5, 10, 20, 30, 40, 60, 120 and 180 min an aliquot of sample was withdrawn from the reaction and resolved on an agarose gel. L, N and S stand for linear, nicked and supercoiled plasmids, respectively.

    Techniques Used: Activity Assay, Purification, Incubation, Agarose Gel Electrophoresis, Plasmid Preparation

    Determination of the ratio of structure-specific to non-specific activity of SCD protein by agarose gel-electrophoresis. ( A ) Schematic illustration of possible linearization sites on pUC(AT) by both specific and non-specific activities of SCD protein. The long arrow represents the specific activity (Sp) that leads the plasmid to open at the cruciform site. The short arrows represent the non-specific activity (Non sp) that leads the plasmid to open at variable sites. ( B ) LP and SP stand for linear and supercoiled form plasmids, respectively; LF and SF for the large and the small fragments produced by DrdI digestion respectively. Lane 1, pUC(AT); lane 2, pUC(AT) cut by DrdI (a small amount of linear plasmid was produced by incomplete digestion); lane 3, linear pUC(AT) produced by T7 Endo I; lane 4, the DNA in lane 3 cut by DrdI; lane 5, linear pUC(AT) produced by MEn–In/Ic–Ec; lane 6, the DNA in lane 5 cut by DrdI; lane 7, linear pUC(AT) produced by MEn–In(9)/Ic–Ec; lane 8, the DNA in lane 7 cut by DrdI; lane 9, linear pUC19 produced by MEn–In/Ic–Ec (a small amount of supercoiled plasmid is co-purified with the linear form); lane 10, the DNA in lane 9 cut by DrdI. Each lane contained ∼1 µg of DNA. All the linear plasmids used in the assay were gel-purified.
    Figure Legend Snippet: Determination of the ratio of structure-specific to non-specific activity of SCD protein by agarose gel-electrophoresis. ( A ) Schematic illustration of possible linearization sites on pUC(AT) by both specific and non-specific activities of SCD protein. The long arrow represents the specific activity (Sp) that leads the plasmid to open at the cruciform site. The short arrows represent the non-specific activity (Non sp) that leads the plasmid to open at variable sites. ( B ) LP and SP stand for linear and supercoiled form plasmids, respectively; LF and SF for the large and the small fragments produced by DrdI digestion respectively. Lane 1, pUC(AT); lane 2, pUC(AT) cut by DrdI (a small amount of linear plasmid was produced by incomplete digestion); lane 3, linear pUC(AT) produced by T7 Endo I; lane 4, the DNA in lane 3 cut by DrdI; lane 5, linear pUC(AT) produced by MEn–In/Ic–Ec; lane 6, the DNA in lane 5 cut by DrdI; lane 7, linear pUC(AT) produced by MEn–In(9)/Ic–Ec; lane 8, the DNA in lane 7 cut by DrdI; lane 9, linear pUC19 produced by MEn–In/Ic–Ec (a small amount of supercoiled plasmid is co-purified with the linear form); lane 10, the DNA in lane 9 cut by DrdI. Each lane contained ∼1 µg of DNA. All the linear plasmids used in the assay were gel-purified.

    Techniques Used: Activity Assay, Agarose Gel Electrophoresis, Plasmid Preparation, Produced, Purification

    12) Product Images from "Isolation of a Novel Bacteriophage Specific for the Periodontal Pathogen Fusobacterium nucleatum ▿"

    Article Title: Isolation of a Novel Bacteriophage Specific for the Periodontal Pathogen Fusobacterium nucleatum ▿

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.01135-10

    Restriction digest patterns electrophoresed on a 1.5% agarose gel and stained with ethidium bromide. (A) FnpΦ02 genomic DNA digested with restriction enzymes. Lanes: L1, 100-bp DNA ladder marker (Fermentas Inc., Canada); L2, 1-kb ladder marker (Fermentas Inc., Canada); L3, undigested DNA; L4, DNA/HindIII; L5, DNA/DraI; L6, DNA/XbaI; and L7, lambda DNA/HindIII. (B) Higher magnification of the bands of the digestion of FnpΦ02 with HindIII used for genome size determination. Selected sizes of the marker are indicated in panel A.
    Figure Legend Snippet: Restriction digest patterns electrophoresed on a 1.5% agarose gel and stained with ethidium bromide. (A) FnpΦ02 genomic DNA digested with restriction enzymes. Lanes: L1, 100-bp DNA ladder marker (Fermentas Inc., Canada); L2, 1-kb ladder marker (Fermentas Inc., Canada); L3, undigested DNA; L4, DNA/HindIII; L5, DNA/DraI; L6, DNA/XbaI; and L7, lambda DNA/HindIII. (B) Higher magnification of the bands of the digestion of FnpΦ02 with HindIII used for genome size determination. Selected sizes of the marker are indicated in panel A.

    Techniques Used: Agarose Gel Electrophoresis, Staining, Marker, Lambda DNA Preparation

    13) Product Images from "GEMIN2 promotes accumulation of RAD51 at double-strand breaks in homologous recombination"

    Article Title: GEMIN2 promotes accumulation of RAD51 at double-strand breaks in homologous recombination

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkq271

    GEMIN2 stimulates RAD51–DNA filament formation. ( A ) Polyacrylamide gel electrophoresis to examine the formation of the RAD51–DNA filament. RAD51 (4 µM) and GEMIN2 were incubated with 10 µM 49-mer ssDNA. DNA was visualized by SYBR Gold (Invitrogen) staining. The GEMIN2 concentrations were 0 µM (lane 2), 1 µM (lane 3), 2 µM (lane 4), 4 µM (lane 5) and 8 µM (lanes 6 and 7). Under these experimental conditions, 90% of the input ssDNA was estimated as being in the RAD51-bound fraction in the absence of the GEMIN2 protein. ( B ) Quantification of experiments shown in panel A. The amounts of complexes formed were estimated from the residual free DNA substrates, and unbound ssDNA fractions relative to lane 2 of panel A were plotted. Average values of three independent experiments are shown with standard deviation values. ( C ) Polyacrylamide gel electrophoresis, as in panel A. RAD51 (2 µM) and GEMIN2 were incubated with 6 µM 49-mer dsDNA. DNA was visualized by SYBR Gold (Invitrogen) staining. The GEMIN2 concentrations were 0 µM (lane 2), 0.5 µM (lane 3), 1 µM (lane 4), 2 µM (lane 5) and 4 µM (lanes 6 and 7). ( D ) Quantification of experiments shown in panel C. The amounts of complexes formed were estimated from the residual free DNA substrates, and unbound dsDNA fractions relative to lane 2 of panel C were plotted. Average values of three independent experiments are shown with standard deviation values. ( E ) Agarose gel electrophoresis to examine the formation of the RAD51-ssDNA filament. RAD51 was incubated in the presence or absence of the GEMIN2 protein, followed by addition of ϕX174 ssDNA (20 µM). DNA was visualized by ethidium bromide staining. ( F ) Agarose gel electrophoresis to examine the formation of the RAD51–dsDNA filament. RAD51 was incubated in the presence or absence of the GEMIN2 protein, followed by addition of linear ϕX174 dsDNA (10 µM). Results presented as in panel E. ( G ) Agarose gel electrophoresis to assess the complex formation between the RAD51-dsDNA filament and GEMIN2. GEMIN2 was labeled with Cy5 and dsDNA was stained with EtBr. Note that GEMIN2 facilitated the formation of the RAD51-dsDNA filament, but did not bind to the filament.
    Figure Legend Snippet: GEMIN2 stimulates RAD51–DNA filament formation. ( A ) Polyacrylamide gel electrophoresis to examine the formation of the RAD51–DNA filament. RAD51 (4 µM) and GEMIN2 were incubated with 10 µM 49-mer ssDNA. DNA was visualized by SYBR Gold (Invitrogen) staining. The GEMIN2 concentrations were 0 µM (lane 2), 1 µM (lane 3), 2 µM (lane 4), 4 µM (lane 5) and 8 µM (lanes 6 and 7). Under these experimental conditions, 90% of the input ssDNA was estimated as being in the RAD51-bound fraction in the absence of the GEMIN2 protein. ( B ) Quantification of experiments shown in panel A. The amounts of complexes formed were estimated from the residual free DNA substrates, and unbound ssDNA fractions relative to lane 2 of panel A were plotted. Average values of three independent experiments are shown with standard deviation values. ( C ) Polyacrylamide gel electrophoresis, as in panel A. RAD51 (2 µM) and GEMIN2 were incubated with 6 µM 49-mer dsDNA. DNA was visualized by SYBR Gold (Invitrogen) staining. The GEMIN2 concentrations were 0 µM (lane 2), 0.5 µM (lane 3), 1 µM (lane 4), 2 µM (lane 5) and 4 µM (lanes 6 and 7). ( D ) Quantification of experiments shown in panel C. The amounts of complexes formed were estimated from the residual free DNA substrates, and unbound dsDNA fractions relative to lane 2 of panel C were plotted. Average values of three independent experiments are shown with standard deviation values. ( E ) Agarose gel electrophoresis to examine the formation of the RAD51-ssDNA filament. RAD51 was incubated in the presence or absence of the GEMIN2 protein, followed by addition of ϕX174 ssDNA (20 µM). DNA was visualized by ethidium bromide staining. ( F ) Agarose gel electrophoresis to examine the formation of the RAD51–dsDNA filament. RAD51 was incubated in the presence or absence of the GEMIN2 protein, followed by addition of linear ϕX174 dsDNA (10 µM). Results presented as in panel E. ( G ) Agarose gel electrophoresis to assess the complex formation between the RAD51-dsDNA filament and GEMIN2. GEMIN2 was labeled with Cy5 and dsDNA was stained with EtBr. Note that GEMIN2 facilitated the formation of the RAD51-dsDNA filament, but did not bind to the filament.

    Techniques Used: Polyacrylamide Gel Electrophoresis, Incubation, Staining, Standard Deviation, Agarose Gel Electrophoresis, Labeling

    GEMIN2 stabilizes the RAD51–DNA filament. ( A ) Complex formation of RAD51 and dsDNA was evaluated by electrophoresis of unbound free DNA in agarose gel. Increased concentrations of competitor DNA were incubated with 2 µM of RAD51 in the presence or absence of 4 µM of GEMIN2, prior to the addition of ϕX174 dsDNA. ( B ) Quantification of results from panel A. The relative amounts of RAD51-unbound DNA are shown. Closed and open circles indicate experiments with and without GEMIN2. Average values and standard deviation were calculated from three independent experiments. ( C ) Complex formation of RAD51 and dsDNA in the presence of the BRC4 polypeptide. The experiments were done as described for panel A. ( D ) Quantification of the data from panel C. ( E ) Surface plasmon resonance analysis. The RAD51- or GEMIN2-conjugated sensor chips were used. Sensorgrams of RAD51-BRC4 and GEMIN2-BRC4 interactions are presented. The BRC4 polypeptide concentration was 10 µM. Time 0 of the horizontal axis indicates the initiation time of the peptide injection.
    Figure Legend Snippet: GEMIN2 stabilizes the RAD51–DNA filament. ( A ) Complex formation of RAD51 and dsDNA was evaluated by electrophoresis of unbound free DNA in agarose gel. Increased concentrations of competitor DNA were incubated with 2 µM of RAD51 in the presence or absence of 4 µM of GEMIN2, prior to the addition of ϕX174 dsDNA. ( B ) Quantification of results from panel A. The relative amounts of RAD51-unbound DNA are shown. Closed and open circles indicate experiments with and without GEMIN2. Average values and standard deviation were calculated from three independent experiments. ( C ) Complex formation of RAD51 and dsDNA in the presence of the BRC4 polypeptide. The experiments were done as described for panel A. ( D ) Quantification of the data from panel C. ( E ) Surface plasmon resonance analysis. The RAD51- or GEMIN2-conjugated sensor chips were used. Sensorgrams of RAD51-BRC4 and GEMIN2-BRC4 interactions are presented. The BRC4 polypeptide concentration was 10 µM. Time 0 of the horizontal axis indicates the initiation time of the peptide injection.

    Techniques Used: Electrophoresis, Agarose Gel Electrophoresis, Incubation, Standard Deviation, SPR Assay, Concentration Assay, Injection

    14) Product Images from "Direct observation of single flexible polymers using single stranded DNA"

    Article Title: Direct observation of single flexible polymers using single stranded DNA

    Journal: Soft matter

    doi: 10.1039/C1SM05297G

    Direct visualization of fluorescently labelled ssDNA molecules using fluorescence microscopy. Single molecules of ssDNA and ds-λ-DNA are shown for (a) stretched and (b) coiled configurations. ssDNA (Sequence 1) with variable dye-labelling ratios are imaged.
    Figure Legend Snippet: Direct visualization of fluorescently labelled ssDNA molecules using fluorescence microscopy. Single molecules of ssDNA and ds-λ-DNA are shown for (a) stretched and (b) coiled configurations. ssDNA (Sequence 1) with variable dye-labelling ratios are imaged.

    Techniques Used: Fluorescence, Microscopy, Sequencing

    15) Product Images from "Modifications and optimization of manual methods for polymerase chain reaction and 16S rRNA gene sequencing quality community DNA extraction from goat rumen digesta"

    Article Title: Modifications and optimization of manual methods for polymerase chain reaction and 16S rRNA gene sequencing quality community DNA extraction from goat rumen digesta

    Journal: Veterinary World

    doi: 10.14202/vetworld.2018.990-1000

    (a) Community DNA extraction with Enzymatic method (EM)1, Enzymatic-Chemical method (ECM)1 and Enzymatic+Chemical+Physical method (ECPM2) methods. Community DNA extraction with > 15 Kb band on 1% agarose gel electrophoresis using (b) ECPM2, EM1, and ECM1 method, Lane 1: Ladder: 1 Kb, New England Biolabs. Community DNA extraction with ECPM2 using Lane 2-5: Solid rumen digesta, Lane 6-9: Squeezed rumen digesta, EM1 using Lane 10: Solid rumen digesta, Lane 11: Blank, ECM1 using Lane 12: Solid rumen digesta, and Lane 13: Squeezed rumen digesta. (b) Community DNA extraction with CM4 method. Community DNA extraction with > 15 Kb band on 1% agarose gel electrophoresis using (a) CM4 method, Lane 1: Ladder: 1 Kb, New England Biolabs, Lane 2: Blank, Lane 3-6: Community DNA with CM4 method, Lane 7-8: Blank, Lane 9-12: Community DNA with CM4 method, and Lane 13: Blank.
    Figure Legend Snippet: (a) Community DNA extraction with Enzymatic method (EM)1, Enzymatic-Chemical method (ECM)1 and Enzymatic+Chemical+Physical method (ECPM2) methods. Community DNA extraction with > 15 Kb band on 1% agarose gel electrophoresis using (b) ECPM2, EM1, and ECM1 method, Lane 1: Ladder: 1 Kb, New England Biolabs. Community DNA extraction with ECPM2 using Lane 2-5: Solid rumen digesta, Lane 6-9: Squeezed rumen digesta, EM1 using Lane 10: Solid rumen digesta, Lane 11: Blank, ECM1 using Lane 12: Solid rumen digesta, and Lane 13: Squeezed rumen digesta. (b) Community DNA extraction with CM4 method. Community DNA extraction with > 15 Kb band on 1% agarose gel electrophoresis using (a) CM4 method, Lane 1: Ladder: 1 Kb, New England Biolabs, Lane 2: Blank, Lane 3-6: Community DNA with CM4 method, Lane 7-8: Blank, Lane 9-12: Community DNA with CM4 method, and Lane 13: Blank.

    Techniques Used: DNA Extraction, Agarose Gel Electrophoresis

    (a and b) Standard polymerase chain reaction (PCR) using community DNA extracted using modified methods. Standard PCR using (a) universal bacterial primers with community DNA extracted using Lane 1: 1 Kb ladder (New England Biolabs), Lane 2: Enzymatic method (EM)1, Lane 3: EC1, Lane 4: Enzymatic+Chemical+Physical method (ECPM)2, Lane 5: Chemical method (CM)1, Lane 6: CM4, Lane 7: CM2 methods, Lane 9: Genomic DNA of Bacillus subtilis as a positive control and Lane 10: blank (b) Specific targeted bacterial 16S rRNA gene primers and community DNA as follows. Lane 1: 100 bp ladder (New England Biolabs), Lane 2: Blank, Lane 3-4: CM4 and ECPM2 DNA with genus Bacteroides and Prevotella (418 bp), Lane 5-6: CM4 and ECPM2 DNA with Streptococcus bovis (869 bp), Lane 7-8: CM4 and ECPM2 DNA with Ruminococcus flavefaciens (835 bp), Lane 9-10: CM4 and ECPM2 DNA with Fibrobacter succinogenes (446 bp), and Lane 11-12: CM4 and ECPM2 DNA with Selenomonas ruminantium (513 bp), and Lane 13: blank.
    Figure Legend Snippet: (a and b) Standard polymerase chain reaction (PCR) using community DNA extracted using modified methods. Standard PCR using (a) universal bacterial primers with community DNA extracted using Lane 1: 1 Kb ladder (New England Biolabs), Lane 2: Enzymatic method (EM)1, Lane 3: EC1, Lane 4: Enzymatic+Chemical+Physical method (ECPM)2, Lane 5: Chemical method (CM)1, Lane 6: CM4, Lane 7: CM2 methods, Lane 9: Genomic DNA of Bacillus subtilis as a positive control and Lane 10: blank (b) Specific targeted bacterial 16S rRNA gene primers and community DNA as follows. Lane 1: 100 bp ladder (New England Biolabs), Lane 2: Blank, Lane 3-4: CM4 and ECPM2 DNA with genus Bacteroides and Prevotella (418 bp), Lane 5-6: CM4 and ECPM2 DNA with Streptococcus bovis (869 bp), Lane 7-8: CM4 and ECPM2 DNA with Ruminococcus flavefaciens (835 bp), Lane 9-10: CM4 and ECPM2 DNA with Fibrobacter succinogenes (446 bp), and Lane 11-12: CM4 and ECPM2 DNA with Selenomonas ruminantium (513 bp), and Lane 13: blank.

    Techniques Used: Polymerase Chain Reaction, Modification, Positive Control

    16) Product Images from "Modifications and optimization of manual methods for polymerase chain reaction and 16S rRNA gene sequencing quality community DNA extraction from goat rumen digesta"

    Article Title: Modifications and optimization of manual methods for polymerase chain reaction and 16S rRNA gene sequencing quality community DNA extraction from goat rumen digesta

    Journal: Veterinary World

    doi: 10.14202/vetworld.2018.990-1000

    (a and b) Standard polymerase chain reaction (PCR) using community DNA extracted using modified methods. Standard PCR using (a) universal bacterial primers with community DNA extracted using Lane 1: 1 Kb ladder (New England Biolabs), Lane 2: Enzymatic method (EM)1, Lane 3: EC1, Lane 4: Enzymatic+Chemical+Physical method (ECPM)2, Lane 5: Chemical method (CM)1, Lane 6: CM4, Lane 7: CM2 methods, Lane 9: Genomic DNA of Bacillus subtilis as a positive control and Lane 10: blank (b) Specific targeted bacterial 16S rRNA gene primers and community DNA as follows. Lane 1: 100 bp ladder (New England Biolabs), Lane 2: Blank, Lane 3-4: CM4 and ECPM2 DNA with genus Bacteroides and Prevotella (418 bp), Lane 5-6: CM4 and ECPM2 DNA with Streptococcus bovis (869 bp), Lane 7-8: CM4 and ECPM2 DNA with Ruminococcus flavefaciens (835 bp), Lane 9-10: CM4 and ECPM2 DNA with Fibrobacter succinogenes (446 bp), and Lane 11-12: CM4 and ECPM2 DNA with Selenomonas ruminantium (513 bp), and Lane 13: blank.
    Figure Legend Snippet: (a and b) Standard polymerase chain reaction (PCR) using community DNA extracted using modified methods. Standard PCR using (a) universal bacterial primers with community DNA extracted using Lane 1: 1 Kb ladder (New England Biolabs), Lane 2: Enzymatic method (EM)1, Lane 3: EC1, Lane 4: Enzymatic+Chemical+Physical method (ECPM)2, Lane 5: Chemical method (CM)1, Lane 6: CM4, Lane 7: CM2 methods, Lane 9: Genomic DNA of Bacillus subtilis as a positive control and Lane 10: blank (b) Specific targeted bacterial 16S rRNA gene primers and community DNA as follows. Lane 1: 100 bp ladder (New England Biolabs), Lane 2: Blank, Lane 3-4: CM4 and ECPM2 DNA with genus Bacteroides and Prevotella (418 bp), Lane 5-6: CM4 and ECPM2 DNA with Streptococcus bovis (869 bp), Lane 7-8: CM4 and ECPM2 DNA with Ruminococcus flavefaciens (835 bp), Lane 9-10: CM4 and ECPM2 DNA with Fibrobacter succinogenes (446 bp), and Lane 11-12: CM4 and ECPM2 DNA with Selenomonas ruminantium (513 bp), and Lane 13: blank.

    Techniques Used: Polymerase Chain Reaction, Modification, Positive Control

    17) Product Images from "Revealing Off-Target Cleavage Specificities of Zinc Finger Nucleases by In Vitro Selection"

    Article Title: Revealing Off-Target Cleavage Specificities of Zinc Finger Nucleases by In Vitro Selection

    Journal: Nature Methods

    doi: 10.1038/nmeth.1670

    In vitro selection for ZFN-mediated cleavage Pre-selection library members are concatemers (represented by arrows) of identical ZFN target sites lacking 5′ phosphates (orange). L = left half-site; R = right half-site, S = spacer; L′, S′, R′ = complementary sequences to L, S, R. ZFN cleavage reveals a 5′ phosphate, which is required for sequencing adapter (red and blue) ligation. The only sequences that can be amplified by PCR using primers complementary to the red and blue adapters are sequences that have been cleaved twice and have adapters on both ends. DNA cleaved at adjacent sites are purified by gel electrophoresis and sequenced. A computational screening step after sequencing ensures that the filled-in spacer sequences (S and S′) are complementary and therefore from the same molecule.
    Figure Legend Snippet: In vitro selection for ZFN-mediated cleavage Pre-selection library members are concatemers (represented by arrows) of identical ZFN target sites lacking 5′ phosphates (orange). L = left half-site; R = right half-site, S = spacer; L′, S′, R′ = complementary sequences to L, S, R. ZFN cleavage reveals a 5′ phosphate, which is required for sequencing adapter (red and blue) ligation. The only sequences that can be amplified by PCR using primers complementary to the red and blue adapters are sequences that have been cleaved twice and have adapters on both ends. DNA cleaved at adjacent sites are purified by gel electrophoresis and sequenced. A computational screening step after sequencing ensures that the filled-in spacer sequences (S and S′) are complementary and therefore from the same molecule.

    Techniques Used: In Vitro, Selection, Sequencing, Ligation, Amplification, Polymerase Chain Reaction, Purification, Nucleic Acid Electrophoresis

    18) Product Images from "Two Phosphoglucomutase Paralogs Facilitate Ionophore-Triggered Secretion of the Toxoplasma Micronemes"

    Article Title: Two Phosphoglucomutase Paralogs Facilitate Ionophore-Triggered Secretion of the Toxoplasma Micronemes

    Journal: mSphere

    doi: 10.1128/mSphere.00521-17

    Subcellular localization of PRP1 through endogenous tagging. (A) Schematic representation of generating C-terminal endogenously YFP-tagged gPRP1-YFP parasites by single homologous recombination into the RHΔ ku80 parent line. (B) PCR validation of the gPRP1-YFP genotype using the primer pair shown in panel A. Lane M contains 1-kb DNA ladder (New England Biolabs). (C) Live imaging of gPRP1-YFP parasites under intracellular and extracellular conditions as indicated. PC, phase contrast. (D) Live imaging of gPRP1-YFP parasites cotransfected with markers for the IMC (IMC1-mCherry), rhoptries (TLN1-mCherry), and micronemes (MIC8-mCherry). (E) Representative images of intracellular gPRP1-YFP parasites fixed using either 100% methanol (MetOH) or 4% paraformaldehyde (PFA) stained with anti-PRP1 (αPRP1) and anti-GFP (αGFP) antisera as indicated. Note that PFA fixation destroys the costaining of GFP and PRP1 and thus destroys the PRP1 epitope(s) recognized by the specific antiserum.
    Figure Legend Snippet: Subcellular localization of PRP1 through endogenous tagging. (A) Schematic representation of generating C-terminal endogenously YFP-tagged gPRP1-YFP parasites by single homologous recombination into the RHΔ ku80 parent line. (B) PCR validation of the gPRP1-YFP genotype using the primer pair shown in panel A. Lane M contains 1-kb DNA ladder (New England Biolabs). (C) Live imaging of gPRP1-YFP parasites under intracellular and extracellular conditions as indicated. PC, phase contrast. (D) Live imaging of gPRP1-YFP parasites cotransfected with markers for the IMC (IMC1-mCherry), rhoptries (TLN1-mCherry), and micronemes (MIC8-mCherry). (E) Representative images of intracellular gPRP1-YFP parasites fixed using either 100% methanol (MetOH) or 4% paraformaldehyde (PFA) stained with anti-PRP1 (αPRP1) and anti-GFP (αGFP) antisera as indicated. Note that PFA fixation destroys the costaining of GFP and PRP1 and thus destroys the PRP1 epitope(s) recognized by the specific antiserum.

    Techniques Used: Homologous Recombination, Polymerase Chain Reaction, Imaging, Staining

    19) Product Images from "BRD4 inhibitors block telomere elongation"

    Article Title: BRD4 inhibitors block telomere elongation

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkx561

    Three additional BRD4 inhibitors block telomere inhibition in a dose-dependent manner. Mouse fibroblasts transduced with SVA lentivirus were treated with four different BRD4 inhibitors: JQ1, IBET151, MS436 OTX015. ( A ) Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post SVA transduction, grown in the presence of DMSO (lane 2–3), 10 μM KU-55933 (lane 4–5), 0.1 μM JQ1 (lane 6–7), 5 μM MS436 (lane 8–9), 0.5 μM OTX015 (lane 10–11) or 1 μM IBET151 (lane 12–13). ( B ) Dose dependence of IBET151. Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post SVA transduction, in the presence of 1 μM (lane 2–3), 0.5 μM (lane 4–5), 0.25 (lane 6–7) or 0.125 μM (lane 8–9) IBET151. ( C ) Dose dependence of OTX015 and MS436. Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post SVA transduction, in the presence of DMSO (lane 2–3), 10 μM KU-55933 (lane 4–5), 250 nM (lane 6–7), 125 nM (lane 8–9) or 62.5 nM OTX015 (lane 10–11), 5 μM (lane 12–13), 2.5 μM (lane 14–15), 1.25 μM (lane 16–17) or 0.625 μM (lane 18–19) MS436. Lane 1 in all panels shows the 2-log ladder marker (NEB), sizes marked are in kilobases. In Panel B, other lanes between the marker and IBET treated lanes were removed.
    Figure Legend Snippet: Three additional BRD4 inhibitors block telomere inhibition in a dose-dependent manner. Mouse fibroblasts transduced with SVA lentivirus were treated with four different BRD4 inhibitors: JQ1, IBET151, MS436 OTX015. ( A ) Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post SVA transduction, grown in the presence of DMSO (lane 2–3), 10 μM KU-55933 (lane 4–5), 0.1 μM JQ1 (lane 6–7), 5 μM MS436 (lane 8–9), 0.5 μM OTX015 (lane 10–11) or 1 μM IBET151 (lane 12–13). ( B ) Dose dependence of IBET151. Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post SVA transduction, in the presence of 1 μM (lane 2–3), 0.5 μM (lane 4–5), 0.25 (lane 6–7) or 0.125 μM (lane 8–9) IBET151. ( C ) Dose dependence of OTX015 and MS436. Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post SVA transduction, in the presence of DMSO (lane 2–3), 10 μM KU-55933 (lane 4–5), 250 nM (lane 6–7), 125 nM (lane 8–9) or 62.5 nM OTX015 (lane 10–11), 5 μM (lane 12–13), 2.5 μM (lane 14–15), 1.25 μM (lane 16–17) or 0.625 μM (lane 18–19) MS436. Lane 1 in all panels shows the 2-log ladder marker (NEB), sizes marked are in kilobases. In Panel B, other lanes between the marker and IBET treated lanes were removed.

    Techniques Used: Blocking Assay, Inhibition, Transduction, Southern Blot, Marker

    JQ1 blocks telomere elongation in a dose-dependent manner. Mouse fibroblasts were transduced with SVA lentivirus, encoding for mTERT and mTR and cultured for six days. ( A ) Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post-SVA transduction, grown in the presence of DMSO (lane 2–3), 10 μM KU-55933 (lane 4–5) or 0.1 μM JQ1 (lane 6–7). Lane 1 shows the 2-log ladder marker (NEB) sizes marked in kilobases. ( B ) Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post-SVA transduction, in the presence of DMSO (lane 2–3), 10 μM KU-55933 (lane 4–5) or decreasing concentrations of 33 nM JQ1 (lane 6–7), 11 nM JQ1 (lane 8–9) or 3.3 nM JQ1 (lane 10–11). Lane 1 shows the 2-log ladder marker (NEB) sizes marked are in kilobases.
    Figure Legend Snippet: JQ1 blocks telomere elongation in a dose-dependent manner. Mouse fibroblasts were transduced with SVA lentivirus, encoding for mTERT and mTR and cultured for six days. ( A ) Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post-SVA transduction, grown in the presence of DMSO (lane 2–3), 10 μM KU-55933 (lane 4–5) or 0.1 μM JQ1 (lane 6–7). Lane 1 shows the 2-log ladder marker (NEB) sizes marked in kilobases. ( B ) Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post-SVA transduction, in the presence of DMSO (lane 2–3), 10 μM KU-55933 (lane 4–5) or decreasing concentrations of 33 nM JQ1 (lane 6–7), 11 nM JQ1 (lane 8–9) or 3.3 nM JQ1 (lane 10–11). Lane 1 shows the 2-log ladder marker (NEB) sizes marked are in kilobases.

    Techniques Used: Transduction, Cell Culture, Southern Blot, Marker

    BRD4 inhibition causes telomere shortening in human and mouse cells in culture. ( A ) Southern blot of telomeric DNA from HeLa cells treated with DMSO (lane 2–5), or 2.5 μM OTX015 (lane 6–9) for 6 weeks, with samples taken at 2, 4 and 6 weeks of treatment. ( B ) Southern blot of telomeric DNA from mouse fibroblast cells, which were treated with DMSO (lane 2–5), or 0.5 μM OTX015 (lane 6–9) for 6 weeks, with samples taken at 2, 4 and 6 weeks of treatment.
    Figure Legend Snippet: BRD4 inhibition causes telomere shortening in human and mouse cells in culture. ( A ) Southern blot of telomeric DNA from HeLa cells treated with DMSO (lane 2–5), or 2.5 μM OTX015 (lane 6–9) for 6 weeks, with samples taken at 2, 4 and 6 weeks of treatment. ( B ) Southern blot of telomeric DNA from mouse fibroblast cells, which were treated with DMSO (lane 2–5), or 0.5 μM OTX015 (lane 6–9) for 6 weeks, with samples taken at 2, 4 and 6 weeks of treatment.

    Techniques Used: Inhibition, Southern Blot

    20) Product Images from "Novel ?-Lactamase Genes from Two Environmental Isolates of Vibrio harveyi"

    Article Title: Novel ?-Lactamase Genes from Two Environmental Isolates of Vibrio harveyi

    Journal: Antimicrobial Agents and Chemotherapy

    doi:

    (A) PFGE of Not I-digested DNA from nine environmental isolates of V. harveyi . (B) Southern hybridization analysis of DNA. The probe used was the 1.1-kb Hin dIII fragment containing bla VHW-1 . Lanes: 1, W3B; 2, GCB; 3, AP5; 4, HB3; 5, R. sphaeroides 2.4.1 DNA digested with Ase I (molecular size standard); 6, AP6; 7, P1B; 8, M 1 ; 9, E 2 ; 10, M3.4L.
    Figure Legend Snippet: (A) PFGE of Not I-digested DNA from nine environmental isolates of V. harveyi . (B) Southern hybridization analysis of DNA. The probe used was the 1.1-kb Hin dIII fragment containing bla VHW-1 . Lanes: 1, W3B; 2, GCB; 3, AP5; 4, HB3; 5, R. sphaeroides 2.4.1 DNA digested with Ase I (molecular size standard); 6, AP6; 7, P1B; 8, M 1 ; 9, E 2 ; 10, M3.4L.

    Techniques Used: Hybridization

    21) Product Images from "Single Molecule Hydrodynamic Separation Allows Sensitive and Quantitative Analysis of DNA Conformation and Binding Interactions in Free Solution"

    Article Title: Single Molecule Hydrodynamic Separation Allows Sensitive and Quantitative Analysis of DNA Conformation and Binding Interactions in Free Solution

    Journal: Journal of the American Chemical Society

    doi: 10.1021/jacs.5b10983

    The effects of both sodium chloride (blue) and magnesium chloride (red) on the packing density of double stranded and single stranded DNA is probed by comparing their relative mobilities in the same 1.6 μm diameter capillary. (a) HindIII digested
    Figure Legend Snippet: The effects of both sodium chloride (blue) and magnesium chloride (red) on the packing density of double stranded and single stranded DNA is probed by comparing their relative mobilities in the same 1.6 μm diameter capillary. (a) HindIII digested

    Techniques Used:

    22) Product Images from "Sizing femtogram amounts of dsDNA by single-molecule counting"

    Article Title: Sizing femtogram amounts of dsDNA by single-molecule counting

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkv904

    Single-molecule intensity distribution of a 1 kbp DNA ladder. ( A ) intensity distribution histogram of detected molecules (red), fitted Gaussians sum (black) and the residue of the fitting (blue). ( B ) a plot of expected DNA lengths in the ladder sample versus the centers of the fitted Gaussian peaks exhibits linear dependency with R 2 = 0.99932.
    Figure Legend Snippet: Single-molecule intensity distribution of a 1 kbp DNA ladder. ( A ) intensity distribution histogram of detected molecules (red), fitted Gaussians sum (black) and the residue of the fitting (blue). ( B ) a plot of expected DNA lengths in the ladder sample versus the centers of the fitted Gaussian peaks exhibits linear dependency with R 2 = 0.99932.

    Techniques Used:

    23) Product Images from "Targeted mutagenesis in a human-parasitic nematode"

    Article Title: Targeted mutagenesis in a human-parasitic nematode

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1006675

    CRISPR-mediated homology-directed repair of Ss-unc-22 . ( A ) Strategy for HDR at Ss-unc-22 target site #2. unc F 1 iL3s that displayed both the nicotine-twitching phenotype and red fluorescence were selected as candidates for HDR and were genotyped using the primer sets indicated. 5’ and 3’ integration primer pairs amplify only following successful integration of Ss-act-2 :: mRFPmars into site #2. HA = homology arm. ( B ) Representative DIC + epifluorescence overlays of unc F 1 iL3s expressing Ss-act-2 :: mRFPmars . Top, iL3 expressing mRFPmars (sparse expression indicated by the arrow) from an extrachromosomal array. Bottom, iL3 expressing mRFPmars following HDR, showing near-uniform mRFPmars expression in the body wall. For both images, anterior is to the left. Scale bar = 50 μm. ( C ) Representative genotypes of a wild-type iL3 and unc F 1 iL3s expressing mRFPmars . Genomic DNA from individual iL3s was split into four reactions: ctrl. = control reaction amplifying 416 bp of the first exon of the Ss-act-2 gene to confirm the presence of genomic DNA; wt = reaction for the wild-type locus of site #2 where primer R1 overlaps the predicted CRISPR cut site; 5’ = reaction for insertion of the 5’ border of the integrated cassette; 3’ = reaction for insertion of the 3’ border of the integrated cassette. For genotypes: array = red unc F 1 iL3s that showed no evidence of integration; integrated = red unc F 1 iL3s with successful HDR. Some integrated iL3s had putative homozygous disruptions of Ss-unc-22 site #2 ( e . g . iL3s #4 and #7, which lacked the wt band). Asterisks indicate genotypes for iL3s shown in B . Size markers = 2 kb, 1.5 kb, 1 kb, and 500 bp from top to bottom.
    Figure Legend Snippet: CRISPR-mediated homology-directed repair of Ss-unc-22 . ( A ) Strategy for HDR at Ss-unc-22 target site #2. unc F 1 iL3s that displayed both the nicotine-twitching phenotype and red fluorescence were selected as candidates for HDR and were genotyped using the primer sets indicated. 5’ and 3’ integration primer pairs amplify only following successful integration of Ss-act-2 :: mRFPmars into site #2. HA = homology arm. ( B ) Representative DIC + epifluorescence overlays of unc F 1 iL3s expressing Ss-act-2 :: mRFPmars . Top, iL3 expressing mRFPmars (sparse expression indicated by the arrow) from an extrachromosomal array. Bottom, iL3 expressing mRFPmars following HDR, showing near-uniform mRFPmars expression in the body wall. For both images, anterior is to the left. Scale bar = 50 μm. ( C ) Representative genotypes of a wild-type iL3 and unc F 1 iL3s expressing mRFPmars . Genomic DNA from individual iL3s was split into four reactions: ctrl. = control reaction amplifying 416 bp of the first exon of the Ss-act-2 gene to confirm the presence of genomic DNA; wt = reaction for the wild-type locus of site #2 where primer R1 overlaps the predicted CRISPR cut site; 5’ = reaction for insertion of the 5’ border of the integrated cassette; 3’ = reaction for insertion of the 3’ border of the integrated cassette. For genotypes: array = red unc F 1 iL3s that showed no evidence of integration; integrated = red unc F 1 iL3s with successful HDR. Some integrated iL3s had putative homozygous disruptions of Ss-unc-22 site #2 ( e . g . iL3s #4 and #7, which lacked the wt band). Asterisks indicate genotypes for iL3s shown in B . Size markers = 2 kb, 1.5 kb, 1 kb, and 500 bp from top to bottom.

    Techniques Used: CRISPR, Fluorescence, Activated Clotting Time Assay, Expressing

    CRISPR-mediated mutagenesis of Ss-unc-22 results in putative deletion of the target locus. ( A ) Representative gel of wild-type iL3s (top) or unc F 1 iL3s from RNP injections at site #3 (bottom). Genomic DNA from each iL3 was split into two reactions: ctrl. = control reaction amplifying 416 bp of the first exon of the Ss-act-2 gene to confirm the presence of genomic DNA; u22 = reaction amplifying 660 bp around site #3. Size markers = 1.5 kb, 1 kb, and 500 bp from top to bottom. ( B ) The Ss-unc-22 region is significantly depleted in unc F 1 iL3s. Left: relative quantity analysis of PCR products. All control bands and all u22 bands were quantified relative to their respective reference bands, denoted by asterisks in A . Values > 1 indicate more PCR product than the reference while values
    Figure Legend Snippet: CRISPR-mediated mutagenesis of Ss-unc-22 results in putative deletion of the target locus. ( A ) Representative gel of wild-type iL3s (top) or unc F 1 iL3s from RNP injections at site #3 (bottom). Genomic DNA from each iL3 was split into two reactions: ctrl. = control reaction amplifying 416 bp of the first exon of the Ss-act-2 gene to confirm the presence of genomic DNA; u22 = reaction amplifying 660 bp around site #3. Size markers = 1.5 kb, 1 kb, and 500 bp from top to bottom. ( B ) The Ss-unc-22 region is significantly depleted in unc F 1 iL3s. Left: relative quantity analysis of PCR products. All control bands and all u22 bands were quantified relative to their respective reference bands, denoted by asterisks in A . Values > 1 indicate more PCR product than the reference while values

    Techniques Used: CRISPR, Mutagenesis, Activated Clotting Time Assay, Polymerase Chain Reaction

    24) Product Images from "Human PSF concentrates DNA and stimulates duplex capture in DMC1-mediated homologous pairing"

    Article Title: Human PSF concentrates DNA and stimulates duplex capture in DMC1-mediated homologous pairing

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkr1229

    The DNA aggregation assay. ( A ) Schematic representation of the DNA aggregation assay. ( B ) The reaction was conducted with DMC1 (4 µM) and/or PSF (1.2 µM) in the presence of ϕX174 ssDNA (10 µM) and linearized ϕX174 dsDNA (10 µM). The samples were centrifuged for 3 min at 20 400 g at room temperature, and the ssDNA and dsDNA recovered in the upper (15 µl) and bottom (5 µl) fractions were analyzed by 0.8% agarose gel electrophoresis with ethidium bromide staining. ( C ) The reaction was conducted by the same method as in panel B, except HOP2-MND1 (1.2 µM) was used instead of PSF.
    Figure Legend Snippet: The DNA aggregation assay. ( A ) Schematic representation of the DNA aggregation assay. ( B ) The reaction was conducted with DMC1 (4 µM) and/or PSF (1.2 µM) in the presence of ϕX174 ssDNA (10 µM) and linearized ϕX174 dsDNA (10 µM). The samples were centrifuged for 3 min at 20 400 g at room temperature, and the ssDNA and dsDNA recovered in the upper (15 µl) and bottom (5 µl) fractions were analyzed by 0.8% agarose gel electrophoresis with ethidium bromide staining. ( C ) The reaction was conducted by the same method as in panel B, except HOP2-MND1 (1.2 µM) was used instead of PSF.

    Techniques Used: Agarose Gel Electrophoresis, Staining

    25) Product Images from "Escalating Association of Vibrio cholerae O139 with Cholera Outbreaks in India"

    Article Title: Escalating Association of Vibrio cholerae O139 with Cholera Outbreaks in India

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.40.7.2635-2637.2002

    RAPD profiles of outbreak strains using primer 1281. (a) Lanes 1 and 11, 1-kb ladder; lanes 2 and 3, Orissa, 1999; lanes 4 and 5, Ahmedabad, 2000; lanes 6 and 7, Karnataka, 2000; lanes 8, 9, and 10, Hyderabad, 2000. (b) Lanes 1 and 11, 1-kb ladder; lane 2, O139 reference strain ATCC 51394 (originally designated MO45); lanes 3, 4, 5, and 6, Orissa, 2000; lanes 7, 8, 9, and 10, Calcutta, 2000.
    Figure Legend Snippet: RAPD profiles of outbreak strains using primer 1281. (a) Lanes 1 and 11, 1-kb ladder; lanes 2 and 3, Orissa, 1999; lanes 4 and 5, Ahmedabad, 2000; lanes 6 and 7, Karnataka, 2000; lanes 8, 9, and 10, Hyderabad, 2000. (b) Lanes 1 and 11, 1-kb ladder; lane 2, O139 reference strain ATCC 51394 (originally designated MO45); lanes 3, 4, 5, and 6, Orissa, 2000; lanes 7, 8, 9, and 10, Calcutta, 2000.

    Techniques Used:

    26) Product Images from "S100A11 plays a role in homologous recombination and genome maintenance by influencing the persistence of RAD51 in DNA repair foci"

    Article Title: S100A11 plays a role in homologous recombination and genome maintenance by influencing the persistence of RAD51 in DNA repair foci

    Journal: Cell Cycle

    doi: 10.1080/15384101.2016.1220457

    S100A11 stimulates the strand exchange activity of RAD51. (A) left panel Scheme of the strand exchange reaction between circular ssDNA and linearized dsDNA. right panel Strand exchange by human RAD51 requires Ca 2+ . RAD51, derived from 2 distinct purification procedures, (lanes 2–3 and 5–6: 3 µM) was incubated with 24 µM circular ΦX174 ssDNA in strand exchange buffer containing 2 mM of either magnesium or calcium acetate for 15 min at 37°C followed by incubation with 2.4 µM RPA for 5 min and addition of 24 µM linearized ΦX174 dsDNA to initiate strand exchange reaction for 2 h at 37°C. Lane M: constructed joint molecule DNA product derived from ssDNA/dsDNA annealing used as marker (B) left panel S100A11 enhances RAD51-mediated strand exchange. RAD51 (lanes 4–6: 3 µM) alone or with S100A11 (lane 5: 2 µM, lane 6: 4 µM) was incubated as described in (A) in strand exchange buffer containing calcium acetate (2 mM). As negative control, S100A11 (lane 7: 4 µM) was incubated alone. The joint molecule product (jm) was visualized by GelStar staining. right panel Quantification of S100A11-stimulated joint molecule formation by RAD51. Average values of 3 independent experiments are shown with standard derivation. (C) Dialysis of S100A11 abrogated the stimulating effect of S100A11 on RAD51 activity. RAD51 (lanes 4–8 and 10) together with undialyzed S100A11 (lane 5), S100A11 dialyzed in EGTA containing buffer (lanes 7–9), or S100A11 dialyzed in buffer without EGTA (lane 10), was incubated with 24 µM circular ΦX174 ssDNA in strand exchange buffer containing 2 mM of either magnesium or calcium acetate for 15 min at 37°C followed by incubation with 2.4 µM RPA for 5 min and addition of 24 µM linearized ΦX174 dsDNA to initiate strand exchange reaction for 2 h at 37°C. * P
    Figure Legend Snippet: S100A11 stimulates the strand exchange activity of RAD51. (A) left panel Scheme of the strand exchange reaction between circular ssDNA and linearized dsDNA. right panel Strand exchange by human RAD51 requires Ca 2+ . RAD51, derived from 2 distinct purification procedures, (lanes 2–3 and 5–6: 3 µM) was incubated with 24 µM circular ΦX174 ssDNA in strand exchange buffer containing 2 mM of either magnesium or calcium acetate for 15 min at 37°C followed by incubation with 2.4 µM RPA for 5 min and addition of 24 µM linearized ΦX174 dsDNA to initiate strand exchange reaction for 2 h at 37°C. Lane M: constructed joint molecule DNA product derived from ssDNA/dsDNA annealing used as marker (B) left panel S100A11 enhances RAD51-mediated strand exchange. RAD51 (lanes 4–6: 3 µM) alone or with S100A11 (lane 5: 2 µM, lane 6: 4 µM) was incubated as described in (A) in strand exchange buffer containing calcium acetate (2 mM). As negative control, S100A11 (lane 7: 4 µM) was incubated alone. The joint molecule product (jm) was visualized by GelStar staining. right panel Quantification of S100A11-stimulated joint molecule formation by RAD51. Average values of 3 independent experiments are shown with standard derivation. (C) Dialysis of S100A11 abrogated the stimulating effect of S100A11 on RAD51 activity. RAD51 (lanes 4–8 and 10) together with undialyzed S100A11 (lane 5), S100A11 dialyzed in EGTA containing buffer (lanes 7–9), or S100A11 dialyzed in buffer without EGTA (lane 10), was incubated with 24 µM circular ΦX174 ssDNA in strand exchange buffer containing 2 mM of either magnesium or calcium acetate for 15 min at 37°C followed by incubation with 2.4 µM RPA for 5 min and addition of 24 µM linearized ΦX174 dsDNA to initiate strand exchange reaction for 2 h at 37°C. * P

    Techniques Used: Activity Assay, Derivative Assay, Purification, Incubation, Recombinase Polymerase Amplification, Construct, Marker, Negative Control, Staining

    27) Product Images from "Generating highly ordered DNA nanostrand arrays"

    Article Title: Generating highly ordered DNA nanostrand arrays

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    doi: 10.1073/pnas.0506902102

    Schematic of generating and transferring DNA nanostrand arrays.
    Figure Legend Snippet: Schematic of generating and transferring DNA nanostrand arrays.

    Techniques Used: Transferring

    Tapping-mode AFM height images and section profiles of short DNA nanostrands ( A ), long DNA nanostrands ( B ), and a long DNA nanostrand with a “thorn” on the mica surface ( C ). [Scale bars, 10 μm( A and B ) and 2 μm( C ).]
    Figure Legend Snippet: Tapping-mode AFM height images and section profiles of short DNA nanostrands ( A ), long DNA nanostrands ( B ), and a long DNA nanostrand with a “thorn” on the mica surface ( C ). [Scale bars, 10 μm( A and B ) and 2 μm( C ).]

    Techniques Used:

    28) Product Images from "Instability of the Octarepeat Region of the Human Prion Protein Gene"

    Article Title: Instability of the Octarepeat Region of the Human Prion Protein Gene

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0026635

    Mutant plasmids from octarepeat replication in DH5α are all head-to-head dimers. (A) Restriction analysis of replication-mutant plasmids with Spe I, Sac II and Sca I. pOct5 or pOct11b were transformed into DH5α. Plasmid DNAs were prepared from two mutant colonies and two control (non-mutant) colonies each for pOct5 and pOct11b, digested with Spe I, Sac II or Sca I, and separated by agarose gel electrophoresis. All mutant colonies appear to contain a minute amount of monomer plasmids. M1, 100-bp DNA ladder; M2, 1-kb DNA ladder. (B) Diagram of the head-to-head plasmid dimers. The top panel depicts the parental plasmid monomer; the bottom panel depicts the dimer where the newly generated monomer unit is highlighted in thicker lines. The boxes denote the octarepeat inserts.
    Figure Legend Snippet: Mutant plasmids from octarepeat replication in DH5α are all head-to-head dimers. (A) Restriction analysis of replication-mutant plasmids with Spe I, Sac II and Sca I. pOct5 or pOct11b were transformed into DH5α. Plasmid DNAs were prepared from two mutant colonies and two control (non-mutant) colonies each for pOct5 and pOct11b, digested with Spe I, Sac II or Sca I, and separated by agarose gel electrophoresis. All mutant colonies appear to contain a minute amount of monomer plasmids. M1, 100-bp DNA ladder; M2, 1-kb DNA ladder. (B) Diagram of the head-to-head plasmid dimers. The top panel depicts the parental plasmid monomer; the bottom panel depicts the dimer where the newly generated monomer unit is highlighted in thicker lines. The boxes denote the octarepeat inserts.

    Techniques Used: Mutagenesis, Transformation Assay, Plasmid Preparation, Agarose Gel Electrophoresis, Generated

    29) Product Images from "Functional and Structural Characterization of Novel Type of Linker Connecting Capsid and Nucleocapsid Protein Domains in Murine Leukemia Virus *"

    Article Title: Functional and Structural Characterization of Novel Type of Linker Connecting Capsid and Nucleocapsid Protein Domains in Murine Leukemia Virus *

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.M116.746461

    EMSA. The indicated proteins were incubated with a 1-kb DNA ladder, and the sample aliquots were then treated with proteinase K. All the samples were analyzed by agarose gel electrophoresis. Lanes: L : 1-kb DNA ladder; 1 : the tested proteins without the
    Figure Legend Snippet: EMSA. The indicated proteins were incubated with a 1-kb DNA ladder, and the sample aliquots were then treated with proteinase K. All the samples were analyzed by agarose gel electrophoresis. Lanes: L : 1-kb DNA ladder; 1 : the tested proteins without the

    Techniques Used: Incubation, Agarose Gel Electrophoresis

    30) Product Images from "Generating highly ordered DNA nanostrand arrays"

    Article Title: Generating highly ordered DNA nanostrand arrays

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    doi: 10.1073/pnas.0506902102

    Tapping-mode AFM height images and section profiles of short DNA nanostrands ( A ), long DNA nanostrands ( B ), and a long DNA nanostrand with a “thorn” on the mica surface ( C ). [Scale bars, 10 μm( A and B ) and 2 μm( C ).]
    Figure Legend Snippet: Tapping-mode AFM height images and section profiles of short DNA nanostrands ( A ), long DNA nanostrands ( B ), and a long DNA nanostrand with a “thorn” on the mica surface ( C ). [Scale bars, 10 μm( A and B ) and 2 μm( C ).]

    Techniques Used:

    Fluorescence micrographs of arrays of short ( A ) and long ( B ) DNA nanostrands prepared by double printing. (Scale bar, 10 μm.)
    Figure Legend Snippet: Fluorescence micrographs of arrays of short ( A ) and long ( B ) DNA nanostrands prepared by double printing. (Scale bar, 10 μm.)

    Techniques Used: Fluorescence

    31) Product Images from "In-Fusion BioBrick assembly and re-engineering"

    Article Title: In-Fusion BioBrick assembly and re-engineering

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkq179

    Part swapping: simultaneous promoter and RBS re-engineering. ( a ) R0011+E0240 and J04450 plasmids are shown with the forward and reverse primers for PCR. R0011+E0240 is amplified with the vector and J04450 is amplified as the insert. ( b ) Detailed schematic of the assembly strategy with the forward and reverse primers. Only the promoter (R0011) and RBS (B0032) are PCR-amplified from the R0011+E0240 plasmid. Only E1010 and B0010/12 are PCR-amplified from the J04450 circuit in order to change its promoter and RBS in one assembly step. ( c ) Since both plasmids used as template DNA in the PCR reaction were approximately the same size as the desired construct, two colony PCR reactions were performed on the same six colonies. The gel on the left shows six colonies amplified with VF2/VR primers and the gel on the right shows the same six colonies (#1–6) and negative control J04450 plasmid (#7) amplified with the VF2 and R0011+E0240 AR primer. Correct colonies show a PCR product of about 1.1 kb for the left gel and a PCR product of about 300 bp for the right gel (correct size indicated by arrow).
    Figure Legend Snippet: Part swapping: simultaneous promoter and RBS re-engineering. ( a ) R0011+E0240 and J04450 plasmids are shown with the forward and reverse primers for PCR. R0011+E0240 is amplified with the vector and J04450 is amplified as the insert. ( b ) Detailed schematic of the assembly strategy with the forward and reverse primers. Only the promoter (R0011) and RBS (B0032) are PCR-amplified from the R0011+E0240 plasmid. Only E1010 and B0010/12 are PCR-amplified from the J04450 circuit in order to change its promoter and RBS in one assembly step. ( c ) Since both plasmids used as template DNA in the PCR reaction were approximately the same size as the desired construct, two colony PCR reactions were performed on the same six colonies. The gel on the left shows six colonies amplified with VF2/VR primers and the gel on the right shows the same six colonies (#1–6) and negative control J04450 plasmid (#7) amplified with the VF2 and R0011+E0240 AR primer. Correct colonies show a PCR product of about 1.1 kb for the left gel and a PCR product of about 300 bp for the right gel (correct size indicated by arrow).

    Techniques Used: Polymerase Chain Reaction, Amplification, Plasmid Preparation, Construct, Negative Control

    32) Product Images from "Homologous Pairing Activities of Two Rice RAD51 Proteins, RAD51A1 and RAD51A2"

    Article Title: Homologous Pairing Activities of Two Rice RAD51 Proteins, RAD51A1 and RAD51A2

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0075451

    The DNA-binding activities of rice RAD51A1 and RAD51A2. Circular φX174 ssDNA (20 µM) (A) or linear φX174 dsDNA (20 µM) (C) was incubated with rice RAD51A1, RAD51A2, or human RAD51 at 37°C for 10 min. The samples were then separated by 0.8% agarose gel electrophoresis in TAE buffer, and were visualized by ethidium bromide staining. Lanes 1–10 and 11–20 represent the reactions conducted with and without ATP, respectively. Lanes 1 and 11 indicate negative control experiments without protein. Lanes 2–4 and 12–14 represent the experiments conducted with RAD51A1. Lanes 5–7 and 15–17 represent the experiments conducted with RAD51A2. Lanes 8–10 and 18–20 represent the experiments conducted with human RAD51. The protein concentrations were 0.75 µM (lanes 2, 5, 8, 12, 15, and 18), 1.5 µM (lanes 3, 6, 9, 13, 16, and 19) and 3 µM (lanes 4, 7, 10, 14, 17, and 20). (B) Graphic representation of the relative migration distances of the RAD51A1- and RAD51A2-ssDNA complexes. The migration distances relative to the free DNA are plotted against the protein concentrations. (D) Competitive ssDNA- and dsDNA-binding. Circular φX174 ssDNA (20 µM) and linear φX174 dsDNA (20 µM) were incubated with rice RAD51A1, RAD51A2, or human RAD51 at 37°C for 10 min, under the 120 mM NaCl conditions. The samples were then separated by 0.8% agarose gel electrophoresis in TAE buffer, and were visualized by ethidium bromide staining. Lane 1 indicates negative control experiments without protein. Lanes 2–4, 5–7, and 8–10 represent the experiments conducted with RAD51A1, RAD51A2, and human RAD51, respectively. The protein concentrations were 0.9 µM (lanes 2, 5, and 8), 1.8 µM (lanes 3, 6, and 9), and 3.6 µM (lanes 4, 7, and 10).
    Figure Legend Snippet: The DNA-binding activities of rice RAD51A1 and RAD51A2. Circular φX174 ssDNA (20 µM) (A) or linear φX174 dsDNA (20 µM) (C) was incubated with rice RAD51A1, RAD51A2, or human RAD51 at 37°C for 10 min. The samples were then separated by 0.8% agarose gel electrophoresis in TAE buffer, and were visualized by ethidium bromide staining. Lanes 1–10 and 11–20 represent the reactions conducted with and without ATP, respectively. Lanes 1 and 11 indicate negative control experiments without protein. Lanes 2–4 and 12–14 represent the experiments conducted with RAD51A1. Lanes 5–7 and 15–17 represent the experiments conducted with RAD51A2. Lanes 8–10 and 18–20 represent the experiments conducted with human RAD51. The protein concentrations were 0.75 µM (lanes 2, 5, 8, 12, 15, and 18), 1.5 µM (lanes 3, 6, 9, 13, 16, and 19) and 3 µM (lanes 4, 7, 10, 14, 17, and 20). (B) Graphic representation of the relative migration distances of the RAD51A1- and RAD51A2-ssDNA complexes. The migration distances relative to the free DNA are plotted against the protein concentrations. (D) Competitive ssDNA- and dsDNA-binding. Circular φX174 ssDNA (20 µM) and linear φX174 dsDNA (20 µM) were incubated with rice RAD51A1, RAD51A2, or human RAD51 at 37°C for 10 min, under the 120 mM NaCl conditions. The samples were then separated by 0.8% agarose gel electrophoresis in TAE buffer, and were visualized by ethidium bromide staining. Lane 1 indicates negative control experiments without protein. Lanes 2–4, 5–7, and 8–10 represent the experiments conducted with RAD51A1, RAD51A2, and human RAD51, respectively. The protein concentrations were 0.9 µM (lanes 2, 5, and 8), 1.8 µM (lanes 3, 6, and 9), and 3.6 µM (lanes 4, 7, and 10).

    Techniques Used: Binding Assay, Incubation, Agarose Gel Electrophoresis, Staining, Negative Control, Migration

    Purification of rice RAD51A1 and RAD51A2. (A) The amino acid sequences of rice RAD51A1 and RAD51A2 from japonica cultivar group, cv. Nipponbare, rice RAD51 from indica cultivar group, cv. Pusa Basmati 1, and human RAD51, aligned with the ClustalX software [50] . Black and gray boxes indicate identical and similar amino acid residues, respectively. The L1 and L2 loops, which are important for DNA binding, are represented by red lines. (B) Purified rice RAD51A1, RAD51A2, and human RAD51. Lane 1 indicates the molecular mass markers, and lanes 2, 3, and 4 represent rice RAD51A1 (0.5 µg), RAD51A2 (0.5 µg), and human RAD51 (0.5 µg), respectively. (C) The ATPase activities of Oryza sativa RAD51A1 and RAD51A2. The reactions were conducted with φX174 circular ssDNA (left panel), linearized φX174 dsDNA (center panel), or without DNA (right panel), in the presence of 5 µM ATP. Blue circles and red squares represent the experiments with RAD51A1 and RAD51A2, respectively. The averages of three independent experiments are shown with the SD values.
    Figure Legend Snippet: Purification of rice RAD51A1 and RAD51A2. (A) The amino acid sequences of rice RAD51A1 and RAD51A2 from japonica cultivar group, cv. Nipponbare, rice RAD51 from indica cultivar group, cv. Pusa Basmati 1, and human RAD51, aligned with the ClustalX software [50] . Black and gray boxes indicate identical and similar amino acid residues, respectively. The L1 and L2 loops, which are important for DNA binding, are represented by red lines. (B) Purified rice RAD51A1, RAD51A2, and human RAD51. Lane 1 indicates the molecular mass markers, and lanes 2, 3, and 4 represent rice RAD51A1 (0.5 µg), RAD51A2 (0.5 µg), and human RAD51 (0.5 µg), respectively. (C) The ATPase activities of Oryza sativa RAD51A1 and RAD51A2. The reactions were conducted with φX174 circular ssDNA (left panel), linearized φX174 dsDNA (center panel), or without DNA (right panel), in the presence of 5 µM ATP. Blue circles and red squares represent the experiments with RAD51A1 and RAD51A2, respectively. The averages of three independent experiments are shown with the SD values.

    Techniques Used: Purification, Software, Binding Assay

    Electron microscopic images of RAD51A1 and RAD51A2 complexed with DNA. (A and B) Electron microscopic images of rice RAD51A1 (A) and RAD51A2 (B) filaments formed on the φX174 dsDNA in the presence of ATP. The average helical pitches of the RAD51A1 and RAD51A2 filaments were about 9.15 nm. The black bar denotes 100 nm.
    Figure Legend Snippet: Electron microscopic images of RAD51A1 and RAD51A2 complexed with DNA. (A and B) Electron microscopic images of rice RAD51A1 (A) and RAD51A2 (B) filaments formed on the φX174 dsDNA in the presence of ATP. The average helical pitches of the RAD51A1 and RAD51A2 filaments were about 9.15 nm. The black bar denotes 100 nm.

    Techniques Used:

    33) Product Images from "Regulation of Rad51 Recombinase Presynaptic Filament Assembly via Interactions with the Rad52 Mediator and the Srs2 Anti-recombinase *"

    Article Title: Regulation of Rad51 Recombinase Presynaptic Filament Assembly via Interactions with the Rad52 Mediator and the Srs2 Anti-recombinase *

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.M109.032953

    Homologous DNA pairing and strand exchange by rad51 mutants. A , scheme of the homologous DNA pairing and strand exchange reaction. Pairing between the circular ϕX174 (+) ssDNA and linear ϕX174 dsDNA yields a joint molecule ( jm ), which
    Figure Legend Snippet: Homologous DNA pairing and strand exchange by rad51 mutants. A , scheme of the homologous DNA pairing and strand exchange reaction. Pairing between the circular ϕX174 (+) ssDNA and linear ϕX174 dsDNA yields a joint molecule ( jm ), which

    Techniques Used:

    34) Product Images from "Generating Transgenic Mice from Bacterial Artificial Chromosomes: Transgenesis Efficiency, Integration and Expression Outcomes"

    Article Title: Generating Transgenic Mice from Bacterial Artificial Chromosomes: Transgenesis Efficiency, Integration and Expression Outcomes

    Journal: Transgenic research

    doi: 10.1007/s11248-009-9271-2

    Pulsed-Field Gel Analysis of BAC DNA. 1a. Analysis of intact circular BAC DNA and sheared BAC DNA. Lane 1: Midrange PFG Marker II (New England Biolabs). Lanes 2, 3, and 4: BAC 2039 (expected size 182kb). Lane 2: Circular BAC DNA: 0.34 ug. Lane 3: Circular BAC DNA: 3.4 ug. Lane 4: Not I cut BAC DNA. Lane 5: deliberately empty. Lanes 6, 7, and 8 contain three fractions from a size exclusion column for BAC 2053. The expected size fragment is 140 kb. All three fractions contain sheared DNA smaller than 97 kb instead of intact linearized BAC DNA. 1b. Comparative analysis of sheared BAC DNA with conventional gel electrophoresis and pulsed-field gel electrophoresis. Lane 1: 2-Log DNA Ladder (New England Biolabs) separation on a conventional 0.8% agarose gel. Lane 2. Sheared BAC DNA runs as a sharp band on a conventional gel. Lane 3. Midrange PFG Marker II (New England Biolabs) separation on a pulsed-field gel. Lane 4. The same sheared BAC DNA that resolves as a sharp band on a conventional gel (Lane 2) appears as a smear upon pulsed-field gel electrophoresis. Arrow indicates expected size of BAC in Lane 4.
    Figure Legend Snippet: Pulsed-Field Gel Analysis of BAC DNA. 1a. Analysis of intact circular BAC DNA and sheared BAC DNA. Lane 1: Midrange PFG Marker II (New England Biolabs). Lanes 2, 3, and 4: BAC 2039 (expected size 182kb). Lane 2: Circular BAC DNA: 0.34 ug. Lane 3: Circular BAC DNA: 3.4 ug. Lane 4: Not I cut BAC DNA. Lane 5: deliberately empty. Lanes 6, 7, and 8 contain three fractions from a size exclusion column for BAC 2053. The expected size fragment is 140 kb. All three fractions contain sheared DNA smaller than 97 kb instead of intact linearized BAC DNA. 1b. Comparative analysis of sheared BAC DNA with conventional gel electrophoresis and pulsed-field gel electrophoresis. Lane 1: 2-Log DNA Ladder (New England Biolabs) separation on a conventional 0.8% agarose gel. Lane 2. Sheared BAC DNA runs as a sharp band on a conventional gel. Lane 3. Midrange PFG Marker II (New England Biolabs) separation on a pulsed-field gel. Lane 4. The same sheared BAC DNA that resolves as a sharp band on a conventional gel (Lane 2) appears as a smear upon pulsed-field gel electrophoresis. Arrow indicates expected size of BAC in Lane 4.

    Techniques Used: Pulsed-Field Gel, BAC Assay, Marker, Nucleic Acid Electrophoresis, Electrophoresis, Agarose Gel Electrophoresis

    35) Product Images from "Molecular and Phylogenetic analysis revealed new genotypes of Theileria annulata parasites from India"

    Article Title: Molecular and Phylogenetic analysis revealed new genotypes of Theileria annulata parasites from India

    Journal: Parasites & Vectors

    doi: 10.1186/s13071-015-1075-z

    PCR amplification in cattle DNA samples. Agarose gel electrophoresis of amplified DNA from different cattle blood DNA samples by using 18S rRNA. Lanes: 1-Negative control distill water: Lane 2- T. orientalis positive DNA sample; Lane 3 to Lane 8 positive blood DNA samples from cattle; Lane 9–100 base pairs DNA ladder
    Figure Legend Snippet: PCR amplification in cattle DNA samples. Agarose gel electrophoresis of amplified DNA from different cattle blood DNA samples by using 18S rRNA. Lanes: 1-Negative control distill water: Lane 2- T. orientalis positive DNA sample; Lane 3 to Lane 8 positive blood DNA samples from cattle; Lane 9–100 base pairs DNA ladder

    Techniques Used: Polymerase Chain Reaction, Amplification, Agarose Gel Electrophoresis, Negative Control

    36) Product Images from "Is the abundance of Faecalibacterium prausnitzii relevant to Crohn's disease?"

    Article Title: Is the abundance of Faecalibacterium prausnitzii relevant to Crohn's disease?

    Journal: Fems Microbiology Letters

    doi: 10.1111/j.1574-6968.2010.02057.x

    Relative quantity of  Faecalibacterium prausnitzii  in faecal DNA determined by PCR. Agarose gel showing bands of the  F. prausnitzii  amplicon from 22 faecal samples. The upper band of 778 bp corresponds to the M21/2 subgroup; the lower 650 bp band corresponds to the A2-165 subgroup. The same amount of template DNA was added to each PCR reaction, and so these differences indicate the relative amount of  F. prausnitzii  in each patient. Where a PCR product was present, the brightness of the band was measured using the software  quantity one  (Bio-Rad) and converted to DNA amount by reference to a 1 kb ladder (New England Biolabs: right-hand lane).
    Figure Legend Snippet: Relative quantity of Faecalibacterium prausnitzii in faecal DNA determined by PCR. Agarose gel showing bands of the F. prausnitzii amplicon from 22 faecal samples. The upper band of 778 bp corresponds to the M21/2 subgroup; the lower 650 bp band corresponds to the A2-165 subgroup. The same amount of template DNA was added to each PCR reaction, and so these differences indicate the relative amount of F. prausnitzii in each patient. Where a PCR product was present, the brightness of the band was measured using the software quantity one (Bio-Rad) and converted to DNA amount by reference to a 1 kb ladder (New England Biolabs: right-hand lane).

    Techniques Used: Polymerase Chain Reaction, Agarose Gel Electrophoresis, Amplification, Software

    37) Product Images from "DNA repair by a Rad22-Mus81-dependent pathway that is independent of Rhp51"

    Article Title: DNA repair by a Rad22-Mus81-dependent pathway that is independent of Rhp51

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkh853

    Rad22-promoted D-loop formation and D-loop cleavage by Mus81. ( A ) Schematic of D-loop formation. The asterisk indicates the position of the 5′- 32 P-end-label on the partial duplex. ( B ) Rad22-promoted D-loop formation. Reactions are described in Materials and Methods and contained Rad22 (6 nM, lanes b and e; 12 nM, lanes c and f; and 24 nM, lanes d and g) and 10 mM MgCl 2 . Rad22 was pre-incubated with partial duplex or φX174 DNA as indicated. ( C ) Dependence on homology for D-loop formation. Reactions are described in Materials and Methods. ( D ) Effect of Mus81 on Rad22-promoted φX174-based D-loop formation. Reactions contained 12 nM Rad22 and 14 nM Mus81–Eme1 as indicated. ( E ) Cleavage of purified φX174-based D-loops by Mus81–Eme1. Reactions contained 7 nM (lane c) or 14 nM (lanes d and e) Mus81–Eme1 and 10 mM MgCl 2 as indicated. The D-loop (lane a) was dissociated by heat treatment at 96°C for 2 min.
    Figure Legend Snippet: Rad22-promoted D-loop formation and D-loop cleavage by Mus81. ( A ) Schematic of D-loop formation. The asterisk indicates the position of the 5′- 32 P-end-label on the partial duplex. ( B ) Rad22-promoted D-loop formation. Reactions are described in Materials and Methods and contained Rad22 (6 nM, lanes b and e; 12 nM, lanes c and f; and 24 nM, lanes d and g) and 10 mM MgCl 2 . Rad22 was pre-incubated with partial duplex or φX174 DNA as indicated. ( C ) Dependence on homology for D-loop formation. Reactions are described in Materials and Methods. ( D ) Effect of Mus81 on Rad22-promoted φX174-based D-loop formation. Reactions contained 12 nM Rad22 and 14 nM Mus81–Eme1 as indicated. ( E ) Cleavage of purified φX174-based D-loops by Mus81–Eme1. Reactions contained 7 nM (lane c) or 14 nM (lanes d and e) Mus81–Eme1 and 10 mM MgCl 2 as indicated. The D-loop (lane a) was dissociated by heat treatment at 96°C for 2 min.

    Techniques Used: Incubation, Purification

    38) Product Images from "Defining synonymous codon compression schemes by genome recoding"

    Article Title: Defining synonymous codon compression schemes by genome recoding

    Journal: Nature

    doi: 10.1038/nature20124

    REXER enables site-specific integration of large DNA fragments into the genome. a . The use of two distinct double selection cassettes -1/+1 ( rpsL-Kan R ) and -2/+2 ( sacB-Cm R ) allows for simultaneous selection for the loss of the negative selection marker on the genome and the gain of the positive selection marker from the BAC, upon integration of synthetic DNA. b . Efficient replacement of genomic rpsL-Kan R with BAC bound sacB-Cm R using REXER 2 and REXER 4. All colonies contained the correct combination of selection markers after REXER 2 or REXER 4 as analysed by phenotyping, colony PCR, and DNA sequencing (not shown) (n = 22). c . Efficient insertion of 9 kb synthetic DNA. Genomic rpsL-Kan R was replaced with a synthetic lux operon coupled to sacB-Cm R using REXER 2 and REXER 4. All colonies on the 10-fold dilution double selection plates for REXER 2 and the 10 4 -fold plates for REXER 4 show bioluminescence. 11 colonies each from REXER 2 and REXER 4 showed correct integration by phenotyping, colony PCR, and DNA sequencing (not shown). d. Efficient insertion of 90kb synthetic DNA. The 90 kb DNA consisted of the lux operon in the middle of 80 kb DNA (previously deleted from the MDS42 genome) and followed by sacB-Cm R .
    Figure Legend Snippet: REXER enables site-specific integration of large DNA fragments into the genome. a . The use of two distinct double selection cassettes -1/+1 ( rpsL-Kan R ) and -2/+2 ( sacB-Cm R ) allows for simultaneous selection for the loss of the negative selection marker on the genome and the gain of the positive selection marker from the BAC, upon integration of synthetic DNA. b . Efficient replacement of genomic rpsL-Kan R with BAC bound sacB-Cm R using REXER 2 and REXER 4. All colonies contained the correct combination of selection markers after REXER 2 or REXER 4 as analysed by phenotyping, colony PCR, and DNA sequencing (not shown) (n = 22). c . Efficient insertion of 9 kb synthetic DNA. Genomic rpsL-Kan R was replaced with a synthetic lux operon coupled to sacB-Cm R using REXER 2 and REXER 4. All colonies on the 10-fold dilution double selection plates for REXER 2 and the 10 4 -fold plates for REXER 4 show bioluminescence. 11 colonies each from REXER 2 and REXER 4 showed correct integration by phenotyping, colony PCR, and DNA sequencing (not shown). d. Efficient insertion of 90kb synthetic DNA. The 90 kb DNA consisted of the lux operon in the middle of 80 kb DNA (previously deleted from the MDS42 genome) and followed by sacB-Cm R .

    Techniques Used: Selection, Marker, BAC Assay, Polymerase Chain Reaction, DNA Sequencing

    Simultaneous double selection and recombination enhances integration at a target locus. a. Classical recombination and double selection recombination. In classical recombination, a linear double stranded DNA with a synthetic DNA (s. DNA) sequence and a positive selection marker (+, Cm R ) flanked by homologous region 1 (HR1) and homologous region 2 (HR2) is transformed into the cell. Recombinants are selected by expression of the positive selection marker. By simultaneous double selection recombination, s. DNA containing double selection marker -2/+2 ( sacB-Cm R ) is integrated in place of the double selection marker -1/+1 ( rpsL - Kan R ) on the genome. Double selection for the gain of +2 and loss of -1 selects for simultaneous gain of s. DNA and loss of genomic sequence, and improves recombination at the target genomic locus. b. Colony PCR of clones from classical recombination and simultaneous double selection and recombination. c. All of the clones isolated by simultaneous double selection and recombination have s. DNA integrated at the target locus. The data show the mean of three independent experiments, the error bars represent the standard deviation (n=6). d . Both simultaneous double selection recombination (n = 8), and REXER 2 and REXER 4 (n = 296) result in the right combination of markers. A previously reported method integrating foreign DNA into B. subtilis , . A previously reported method replacing S. cerevisiae .
    Figure Legend Snippet: Simultaneous double selection and recombination enhances integration at a target locus. a. Classical recombination and double selection recombination. In classical recombination, a linear double stranded DNA with a synthetic DNA (s. DNA) sequence and a positive selection marker (+, Cm R ) flanked by homologous region 1 (HR1) and homologous region 2 (HR2) is transformed into the cell. Recombinants are selected by expression of the positive selection marker. By simultaneous double selection recombination, s. DNA containing double selection marker -2/+2 ( sacB-Cm R ) is integrated in place of the double selection marker -1/+1 ( rpsL - Kan R ) on the genome. Double selection for the gain of +2 and loss of -1 selects for simultaneous gain of s. DNA and loss of genomic sequence, and improves recombination at the target genomic locus. b. Colony PCR of clones from classical recombination and simultaneous double selection and recombination. c. All of the clones isolated by simultaneous double selection and recombination have s. DNA integrated at the target locus. The data show the mean of three independent experiments, the error bars represent the standard deviation (n=6). d . Both simultaneous double selection recombination (n = 8), and REXER 2 and REXER 4 (n = 296) result in the right combination of markers. A previously reported method integrating foreign DNA into B. subtilis , . A previously reported method replacing S. cerevisiae .

    Techniques Used: Selection, Sequencing, Marker, Transformation Assay, Expressing, Polymerase Chain Reaction, Clone Assay, Isolation, Standard Deviation

    39) Product Images from "PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes"

    Article Title: PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-8-135

    1% agarose gel electrophoresis of PCR products . PCR products derived from 24 PLUG primer sets were separated using a 1% agarose gel in TAE buffer. Lane numbers correspond to marker numbers indicated in Table 1. M: 2-Log DNA Ladder (New England BioLabs Inc., Ipswich, MA, USA).
    Figure Legend Snippet: 1% agarose gel electrophoresis of PCR products . PCR products derived from 24 PLUG primer sets were separated using a 1% agarose gel in TAE buffer. Lane numbers correspond to marker numbers indicated in Table 1. M: 2-Log DNA Ladder (New England BioLabs Inc., Ipswich, MA, USA).

    Techniques Used: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Derivative Assay, Marker

    40) Product Images from "Engineering BioBrick vectors from BioBrick parts"

    Article Title: Engineering BioBrick vectors from BioBrick parts

    Journal: Journal of Biological Engineering

    doi: 10.1186/1754-1611-2-5

    Using the new BioBrick vectors . To verify the function of the new BioBrick vectors, we performed a colony PCR using primers that anneal to the verification primer binding sites. To check the length of the resulting PCR products, we electrophoresed the reactions through an 0.8% agarose gel. Lanes 1–8 are the PCR products resulting from the amplification of the following BioBrick parts cloned into new BioBrick vectors. The desired PCR product lengths are in parentheses. Lane 1 is pSB4A5-I52001 (1370 bp), lane 2 is pSB4K5-T9003 (1883 bp), lane 3 is pSB4C5-E0435 (814 bp), lane 4 is pSB4T5-P20061 (2988 bp), lane 5 is pSB3K5-I52002 (1370 bp), lane 6 is pSB3C5-I52001 (1370 bp), lane 7 is pSB3T5-I6413 (867 bp), and lane 8 is BBa_I51020 (1370 bp). Lane 9 is 1 μ g of 2-log DNA ladder (New England Biolabs, Inc.). The 0.5 kb, 1 kb, and 3 kb DNA fragments in the DNA ladder are annotated.
    Figure Legend Snippet: Using the new BioBrick vectors . To verify the function of the new BioBrick vectors, we performed a colony PCR using primers that anneal to the verification primer binding sites. To check the length of the resulting PCR products, we electrophoresed the reactions through an 0.8% agarose gel. Lanes 1–8 are the PCR products resulting from the amplification of the following BioBrick parts cloned into new BioBrick vectors. The desired PCR product lengths are in parentheses. Lane 1 is pSB4A5-I52001 (1370 bp), lane 2 is pSB4K5-T9003 (1883 bp), lane 3 is pSB4C5-E0435 (814 bp), lane 4 is pSB4T5-P20061 (2988 bp), lane 5 is pSB3K5-I52002 (1370 bp), lane 6 is pSB3C5-I52001 (1370 bp), lane 7 is pSB3T5-I6413 (867 bp), and lane 8 is BBa_I51020 (1370 bp). Lane 9 is 1 μ g of 2-log DNA ladder (New England Biolabs, Inc.). The 0.5 kb, 1 kb, and 3 kb DNA fragments in the DNA ladder are annotated.

    Techniques Used: Polymerase Chain Reaction, Binding Assay, Agarose Gel Electrophoresis, Amplification, Clone Assay

    Related Articles

    Agarose Gel Electrophoresis:

    Article Title: Isolation of a Novel Bacteriophage Specific for the Periodontal Pathogen Fusobacterium nucleatum ▿
    Article Snippet: .. The DNA digestion mixtures were analyzed by electrophoresis at 50 V for 3.5 h in a 1.5% Tris-acetate-EDTA (TAE) agarose gel stained with ethidium bromide using a 1-kb DNA ladder (New England Biolabs) and lambda mix marker (New England Biolabs) as molecular size markers. ..

    Purification:

    Article Title: A single catalytic domain of the junction-resolving enzyme T7 endonuclease I is a non-specific nicking endonuclease
    Article Snippet: .. Non-specific nuclease activity of SCD protein Purified SCD protein MEn–In/Ic–Ec was incubated with a DNA mixture, the 2-log DNA ladder (NEB), in either Mg2+ or Mn2+ buffer. ..

    Electrophoresis:

    Article Title: Isolation of a Novel Bacteriophage Specific for the Periodontal Pathogen Fusobacterium nucleatum ▿
    Article Snippet: .. The DNA digestion mixtures were analyzed by electrophoresis at 50 V for 3.5 h in a 1.5% Tris-acetate-EDTA (TAE) agarose gel stained with ethidium bromide using a 1-kb DNA ladder (New England Biolabs) and lambda mix marker (New England Biolabs) as molecular size markers. ..

    Incubation:

    Article Title: A single catalytic domain of the junction-resolving enzyme T7 endonuclease I is a non-specific nicking endonuclease
    Article Snippet: .. Non-specific nuclease activity of SCD protein Purified SCD protein MEn–In/Ic–Ec was incubated with a DNA mixture, the 2-log DNA ladder (NEB), in either Mg2+ or Mn2+ buffer. ..

    Activity Assay:

    Article Title: A single catalytic domain of the junction-resolving enzyme T7 endonuclease I is a non-specific nicking endonuclease
    Article Snippet: .. Non-specific nuclease activity of SCD protein Purified SCD protein MEn–In/Ic–Ec was incubated with a DNA mixture, the 2-log DNA ladder (NEB), in either Mg2+ or Mn2+ buffer. ..

    Marker:

    Article Title: Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA
    Article Snippet: .. As marker, either a 1 kb Generuler Marker (Thermo Scientific) or 1 kb DNA ladder (New England Biolabs) and additionally a custom plasmid marker, were used. .. The custom plasmid marker consisted of non-treated pWUR704 (mostly in supercoiled conformation), Nb.BSMI (New England Biolabs) nicked pWUR704 (open circular conformation) and BcuI (Thermo Scientific) linearized pWUR704.

    Article Title: Contamination sources, serogroups, biofilm-forming ability and biocide resistance of Listeria monocytogenes persistent in tilapia-processing facilities
    Article Snippet: .. A DNA ladder of 100-1517 bp (100 bp DNA ladder, New England Biolabs, Brazil) was included as a molecular size marker. .. Gels were visualized in a Gel Doc XR+ system (Bio-Rad) using the ImageLab™ software (Bio-Rad Ltda.).

    Article Title: Isolation of a Novel Bacteriophage Specific for the Periodontal Pathogen Fusobacterium nucleatum ▿
    Article Snippet: .. The DNA digestion mixtures were analyzed by electrophoresis at 50 V for 3.5 h in a 1.5% Tris-acetate-EDTA (TAE) agarose gel stained with ethidium bromide using a 1-kb DNA ladder (New England Biolabs) and lambda mix marker (New England Biolabs) as molecular size markers. ..

    Article Title: Biochemical characterization and chemical validation of Leishmania MAP Kinase-3 as a potential drug target
    Article Snippet: .. Restriction enzymes, 1-kb DNA marker, stained and unstained protein markers were purchased from NEB. .. Cloning of recombinant construct The expression construct for the production of recombinant MAPK3 was created by using the gene encoding Ld MAPK3 from the NCBI nucleotide database with accession number (XM_003858842.1).

    Staining:

    Article Title: Isolation of a Novel Bacteriophage Specific for the Periodontal Pathogen Fusobacterium nucleatum ▿
    Article Snippet: .. The DNA digestion mixtures were analyzed by electrophoresis at 50 V for 3.5 h in a 1.5% Tris-acetate-EDTA (TAE) agarose gel stained with ethidium bromide using a 1-kb DNA ladder (New England Biolabs) and lambda mix marker (New England Biolabs) as molecular size markers. ..

    Article Title: Biochemical characterization and chemical validation of Leishmania MAP Kinase-3 as a potential drug target
    Article Snippet: .. Restriction enzymes, 1-kb DNA marker, stained and unstained protein markers were purchased from NEB. .. Cloning of recombinant construct The expression construct for the production of recombinant MAPK3 was created by using the gene encoding Ld MAPK3 from the NCBI nucleotide database with accession number (XM_003858842.1).

    Plasmid Preparation:

    Article Title: In Situ Transfection by Controlled Release of Lipoplexes using Acoustic Droplet Vaporization
    Article Snippet: .. Control samples of non-sonicated plasmid and lipoplex as well as a 1 kb linear DNA ladder (N3232S, New England BioLabs, Ipswich, MA, USA) were also run on the gel. ..

    Article Title: Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA
    Article Snippet: .. As marker, either a 1 kb Generuler Marker (Thermo Scientific) or 1 kb DNA ladder (New England Biolabs) and additionally a custom plasmid marker, were used. .. The custom plasmid marker consisted of non-treated pWUR704 (mostly in supercoiled conformation), Nb.BSMI (New England Biolabs) nicked pWUR704 (open circular conformation) and BcuI (Thermo Scientific) linearized pWUR704.

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    New England Biolabs 1 kb ladder
    Linearized plasmid profiles of Edwardsiella ictaluri isolates. Plasmid DNA from E. ictaluri isolated from Channel Catfish or Zebrafish was digested with EcoRI or BstZ17I, respectively, and separated by 0.6% agarose gel electrophoresis using a <t>1-kb</t> DNA
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    Linearized plasmid profiles of Edwardsiella ictaluri isolates. Plasmid DNA from E. ictaluri isolated from Channel Catfish or Zebrafish was digested with EcoRI or BstZ17I, respectively, and separated by 0.6% agarose gel electrophoresis using a 1-kb DNA

    Journal: Journal of aquatic animal health

    Article Title: Edwardsiellosis Caused by Edwardsiella ictaluri in Laboratory Populations of Zebrafish Danio rerio

    doi: 10.1080/08997659.2013.782226

    Figure Lengend Snippet: Linearized plasmid profiles of Edwardsiella ictaluri isolates. Plasmid DNA from E. ictaluri isolated from Channel Catfish or Zebrafish was digested with EcoRI or BstZ17I, respectively, and separated by 0.6% agarose gel electrophoresis using a 1-kb DNA

    Article Snippet: Plasmids were digested with either EcoRI or BstZ17I and were separated by 0.6% agarose gel electrophoresis with 1-kb ladder (New England Biolabs) as the size standard.

    Techniques: Plasmid Preparation, Isolation, Agarose Gel Electrophoresis

    DNA-binding and RAD51-binding activities of the PSF domains. ϕX174 ssDNA (20 µM) ( A ) or ϕX174 linear dsDNA (20 µM) ( B ) was incubated with PSF, PSF(1–266) or PSF(267–468) at 37°C for 10 min. The samples were then separated by 0.8% agarose gel electrophoresis in TAE buffer and were visualized by ethidium bromide staining. The protein concentrations for panel A were 0 µM (lane 1), 0.15 µM (lanes 2, 5 and 8), 0.3 µM (lanes 3, 6 and 9) and 0.6 µM (lanes 4, 7 and 10). The protein concentrations for panel B were 0 µM (lane 1), 0.1 µM (lanes 2, 5 and 8), 0.2 µM (lanes 3, 6 and 9) and 0.4 µM (lanes 4, 7 and 10). ( C ) The pull-down assay with Ni–NTA beads. Lanes 2–5 represent purified RAD51, His 6 -tagged PSF, His 6 -tagged PSF(1–266) and His 6 -tagged PSF(267–468), respectively. His 6 -tagged PSF, His 6 -tagged PSF(1–266) or His 6 -tagged PSF(267–468) (3.8 µg) was mixed with RAD51 (7.4 µg). The RAD51 bound to the His 6 -tagged proteins was pulled down by the Ni–NTA agarose beads, and was analyzed by 12% SDS–PAGE. Bands were visualized by Coomassie Brilliant Blue staining.

    Journal: Nucleic Acids Research

    Article Title: Human PSF binds to RAD51 and modulates its homologous-pairing and strand-exchange activities

    doi: 10.1093/nar/gkp298

    Figure Lengend Snippet: DNA-binding and RAD51-binding activities of the PSF domains. ϕX174 ssDNA (20 µM) ( A ) or ϕX174 linear dsDNA (20 µM) ( B ) was incubated with PSF, PSF(1–266) or PSF(267–468) at 37°C for 10 min. The samples were then separated by 0.8% agarose gel electrophoresis in TAE buffer and were visualized by ethidium bromide staining. The protein concentrations for panel A were 0 µM (lane 1), 0.15 µM (lanes 2, 5 and 8), 0.3 µM (lanes 3, 6 and 9) and 0.6 µM (lanes 4, 7 and 10). The protein concentrations for panel B were 0 µM (lane 1), 0.1 µM (lanes 2, 5 and 8), 0.2 µM (lanes 3, 6 and 9) and 0.4 µM (lanes 4, 7 and 10). ( C ) The pull-down assay with Ni–NTA beads. Lanes 2–5 represent purified RAD51, His 6 -tagged PSF, His 6 -tagged PSF(1–266) and His 6 -tagged PSF(267–468), respectively. His 6 -tagged PSF, His 6 -tagged PSF(1–266) or His 6 -tagged PSF(267–468) (3.8 µg) was mixed with RAD51 (7.4 µg). The RAD51 bound to the His 6 -tagged proteins was pulled down by the Ni–NTA agarose beads, and was analyzed by 12% SDS–PAGE. Bands were visualized by Coomassie Brilliant Blue staining.

    Article Snippet: The 5′ ends of the oligonucleotide were labeled with T4 polynucleotide kinase (New England Biolabs, Ipswich, MA, USA) in the presence of [γ-32 P]ATP at 37°C for 30 min. Single-stranded ϕX174 viral (+) strand DNA and double-stranded ϕX174 replicative form I DNA were purchased from New England Biolabs.

    Techniques: Binding Assay, Incubation, Agarose Gel Electrophoresis, Staining, Pull Down Assay, Purification, SDS Page

    Confirmation of pET28a- Ld MAPK3 construct. Lane 1 showing the amplification of Ld MAPK3 by colony PCR method; Lane 2 is indicating 1-kb DNA ladder and Lane 3 is showing the release of insert ( Ld MAPK3) at 1.2 kb and 5.369 kb as vector (pET 28a(+)) using restriction digestion.

    Journal: Scientific Reports

    Article Title: Biochemical characterization and chemical validation of Leishmania MAP Kinase-3 as a potential drug target

    doi: 10.1038/s41598-019-52774-6

    Figure Lengend Snippet: Confirmation of pET28a- Ld MAPK3 construct. Lane 1 showing the amplification of Ld MAPK3 by colony PCR method; Lane 2 is indicating 1-kb DNA ladder and Lane 3 is showing the release of insert ( Ld MAPK3) at 1.2 kb and 5.369 kb as vector (pET 28a(+)) using restriction digestion.

    Article Snippet: Restriction enzymes, 1-kb DNA marker, stained and unstained protein markers were purchased from NEB.

    Techniques: Construct, Amplification, Polymerase Chain Reaction, Plasmid Preparation, Positron Emission Tomography

    Single-molecule intensity distribution of a 1 kbp DNA ladder. ( A ) intensity distribution histogram of detected molecules (red), fitted Gaussians sum (black) and the residue of the fitting (blue). ( B ) a plot of expected DNA lengths in the ladder sample versus the centers of the fitted Gaussian peaks exhibits linear dependency with R 2 = 0.99932.

    Journal: Nucleic Acids Research

    Article Title: Sizing femtogram amounts of dsDNA by single-molecule counting

    doi: 10.1093/nar/gkv904

    Figure Lengend Snippet: Single-molecule intensity distribution of a 1 kbp DNA ladder. ( A ) intensity distribution histogram of detected molecules (red), fitted Gaussians sum (black) and the residue of the fitting (blue). ( B ) a plot of expected DNA lengths in the ladder sample versus the centers of the fitted Gaussian peaks exhibits linear dependency with R 2 = 0.99932.

    Article Snippet: In order to simulate analysis of an unknown sample, 0.5 ng of 1 kbp DNA ladder (NEB) were mixed with 0.5 ng of reference sample, containing the previously calibrated 3 kb and 7 kb populations.

    Techniques: