molecular weight dna ladder  (New England Biolabs)


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    Low Molecular Weight DNA Ladder
    Description:
    Low Molecular Weight DNA Ladder 500 gel lanes
    Catalog Number:
    n3233l
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    270
    Size:
    500 gel lanes
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    DNA Ladders
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    New England Biolabs molecular weight dna ladder
    Low Molecular Weight DNA Ladder
    Low Molecular Weight DNA Ladder 500 gel lanes
    https://www.bioz.com/result/molecular weight dna ladder/product/New England Biolabs
    Average 99 stars, based on 214 article reviews
    Price from $9.99 to $1999.99
    molecular weight dna ladder - by Bioz Stars, 2020-09
    99/100 stars

    Images

    1) Product Images from "Detection of the pediocin gene pedA in strains from human faeces by real-time PCR and characterization of Pediococcus acidilactici UVA1"

    Article Title: Detection of the pediocin gene pedA in strains from human faeces by real-time PCR and characterization of Pediococcus acidilactici UVA1

    Journal: BMC Biotechnology

    doi: 10.1186/1472-6750-7-55

    Transcription analysis of pedA . pedA -reverse transcription-PCR on cDNA from P. acidilactici bac- (1, 2, 3) or UVA1 (7, 8, 9) after 1 h 30, 2 h 30 and 3 h 30 of growth, respectively, and from P. acidilactici DSM 20284 T (4) or UL5 (6) and P. pentosaceus DSM 20336 T (5) after 2 h 30 of growth. 10: water instead of DNA. lm: low molecular weight DNA ladder (in bp). h: Tridye 100-bp DNA ladder (in bp). Expected product size: 100 bp.
    Figure Legend Snippet: Transcription analysis of pedA . pedA -reverse transcription-PCR on cDNA from P. acidilactici bac- (1, 2, 3) or UVA1 (7, 8, 9) after 1 h 30, 2 h 30 and 3 h 30 of growth, respectively, and from P. acidilactici DSM 20284 T (4) or UL5 (6) and P. pentosaceus DSM 20336 T (5) after 2 h 30 of growth. 10: water instead of DNA. lm: low molecular weight DNA ladder (in bp). h: Tridye 100-bp DNA ladder (in bp). Expected product size: 100 bp.

    Techniques Used: Polymerase Chain Reaction, BAC Assay, Molecular Weight

    2) Product Images from "RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes"

    Article Title: RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes

    Journal: Methods (San Diego, Calif.)

    doi: 10.1016/j.ymeth.2013.09.013

    UV-crosslinking bias of different RBPs dictates the suitability of different approaches for identifying binding sites A. hnRNPA1:ssDNA interface. Crystal structure of two-RRM-containing UP1 domain of hnRNP A1 (PDB ID: 2UP1; blue) in complex with a target containing its AGGG preferred recognition motif (in this case, within single-stranded DNA, ssDNA; red). Black box. Enlarged view of the DNA:protein interface. Aromatic residues (Phe-17 and Phe-59 from RRM1) that stack with the nucleobases are shown in cyan. B. eIF4AIII:RNA interface. Crystal structure of eIF4AIII (PDB ID: 2J0S; blue) complexed with RNA (red) and AMP-PNP. Black box. Enlarged view of the RNA:protein interface. Note that the RNA bases are pointing away from the bound protein. ]. D. RIPiT and CLIP yield different types of information. Top: Two similar yet compositionally distinct hypothetical multi-subunit RNPs. RBPs (blue), non-RBPs (green) and proteins unique to each complex are shown (complex A: yellow; complex B: red). Left: RIPiT can reveal the binding sites of an intact multi-subunit RNP, and can also distinguish between footprints of two compositionally similar complexes (schematics on gray background). However, RIPiT does not conclusively define direct RBP-RNA interactions (crossed-out schematic). Right: On the contrary, while CLIP reveals no information regarding the complexes an RNA-bound RBP is part of (crossed-out schematics), it can unveil the sites of direct contact between an RBP and RNA (bottom schematic).
    Figure Legend Snippet: UV-crosslinking bias of different RBPs dictates the suitability of different approaches for identifying binding sites A. hnRNPA1:ssDNA interface. Crystal structure of two-RRM-containing UP1 domain of hnRNP A1 (PDB ID: 2UP1; blue) in complex with a target containing its AGGG preferred recognition motif (in this case, within single-stranded DNA, ssDNA; red). Black box. Enlarged view of the DNA:protein interface. Aromatic residues (Phe-17 and Phe-59 from RRM1) that stack with the nucleobases are shown in cyan. B. eIF4AIII:RNA interface. Crystal structure of eIF4AIII (PDB ID: 2J0S; blue) complexed with RNA (red) and AMP-PNP. Black box. Enlarged view of the RNA:protein interface. Note that the RNA bases are pointing away from the bound protein. ]. D. RIPiT and CLIP yield different types of information. Top: Two similar yet compositionally distinct hypothetical multi-subunit RNPs. RBPs (blue), non-RBPs (green) and proteins unique to each complex are shown (complex A: yellow; complex B: red). Left: RIPiT can reveal the binding sites of an intact multi-subunit RNP, and can also distinguish between footprints of two compositionally similar complexes (schematics on gray background). However, RIPiT does not conclusively define direct RBP-RNA interactions (crossed-out schematic). Right: On the contrary, while CLIP reveals no information regarding the complexes an RNA-bound RBP is part of (crossed-out schematics), it can unveil the sites of direct contact between an RBP and RNA (bottom schematic).

    Techniques Used: Binding Assay, Cross-linking Immunoprecipitation

    Biochemical analysis of proteins and RNAs from the RIPiT procedure A. Western blots showing tetracycline (Tet)-mediated induction of eIF4AIII protein with the FLAG tag at its N- or C-terminus (top and bottom panels, respectively). The Tet concentration used for induction is indicated at the top of each lane; protein identities are indicated to the right. B. Levels of proteins detected by western blots in different fractions during EJC RIPiT. The table on the top indicates the different fractions from the RIPiT procedure and the antibodies used for 1 st and 2 nd IPs. The stably expressed FLAG-tag fusion protein used in each sample is indicated directly above lane. Proteins detected by western blot are indicated to the right. C. Size distribution of EJC footprints upon RNase I titration. An autoradiogram of 26% denaturing PAGE with 5′ [ 32 P]-labeled RNA fragments from base-hydrolysis of poly U 30 oligonucleotide (lane 1) or FLAG-Magoh:eIF4AIII RIPiT (lanes 2–5). RNase I concentrations used are indicated at top of each lane; nucleotide (nt) lengths are to the left. D. Quantification of desired size RNA footprints in RIPiT elution. An autoradiogram of 20% denaturing PAGE with 5′ [ 32 P]-labeled 100 bp NEB DNA ladder (lane 1), low molecular weight ssDNA ladder (lane 2), footprints of RIPiTs indicated on top (lanes 3 and 4) and a 21 nt ssRNA oligo of known specific activity (lane 5). The signal from red rectangles is quantified in comparison to that of the 21 nt oligo to estimate the amount of RIPiT footprints in the indicated size range.
    Figure Legend Snippet: Biochemical analysis of proteins and RNAs from the RIPiT procedure A. Western blots showing tetracycline (Tet)-mediated induction of eIF4AIII protein with the FLAG tag at its N- or C-terminus (top and bottom panels, respectively). The Tet concentration used for induction is indicated at the top of each lane; protein identities are indicated to the right. B. Levels of proteins detected by western blots in different fractions during EJC RIPiT. The table on the top indicates the different fractions from the RIPiT procedure and the antibodies used for 1 st and 2 nd IPs. The stably expressed FLAG-tag fusion protein used in each sample is indicated directly above lane. Proteins detected by western blot are indicated to the right. C. Size distribution of EJC footprints upon RNase I titration. An autoradiogram of 26% denaturing PAGE with 5′ [ 32 P]-labeled RNA fragments from base-hydrolysis of poly U 30 oligonucleotide (lane 1) or FLAG-Magoh:eIF4AIII RIPiT (lanes 2–5). RNase I concentrations used are indicated at top of each lane; nucleotide (nt) lengths are to the left. D. Quantification of desired size RNA footprints in RIPiT elution. An autoradiogram of 20% denaturing PAGE with 5′ [ 32 P]-labeled 100 bp NEB DNA ladder (lane 1), low molecular weight ssDNA ladder (lane 2), footprints of RIPiTs indicated on top (lanes 3 and 4) and a 21 nt ssRNA oligo of known specific activity (lane 5). The signal from red rectangles is quantified in comparison to that of the 21 nt oligo to estimate the amount of RIPiT footprints in the indicated size range.

    Techniques Used: Western Blot, FLAG-tag, Concentration Assay, Stable Transfection, Titration, Polyacrylamide Gel Electrophoresis, Labeling, Molecular Weight, Activity Assay

    3) Product Images from "Switching the activity of Cas12a using guide RNA strand displacement circuits"

    Article Title: Switching the activity of Cas12a using guide RNA strand displacement circuits

    Journal: Nature Communications

    doi: 10.1038/s41467-019-09953-w

    Principle of strand displacement switchable gRNAs. a When the RNA trigger binds the SD gRNA, the 5′ extension domain occluding handle is displaced, thereby restoring the gRNA handle. Binding of Cas12a leads to cleavage of the gRNA, which removes the 5′ extension and creates an active Cas12a-gRNA complex. The domains are labeled as follows: s—separator, h—handle, t—target, X1—toehold. The overall nomenclature follows Zhang et al. 32 : A domain is denoted by a single letter. An upper index x denotes the first x nucleotides of a domain counting from its 5′ end. A lower index x denotes all but the first x nucleotides of a domain counting from its 5′ end. A combination of upper and lower indices includes those nucleotides that are present in both subdomains. A bar above the letter marks the reverse complement of a domain. The red star marks the position where Cas12a cleaves a successfully bound gRNA. b Agarose gel showing cutting of a target DNA by handle-based SD gRNAs with two different target sequences in the absence and presence of trigger RNA (uncut: 1190 bp, cut t1: 357 bp, cut t2: 506 bp). c Denaturing PAGE showing induced gRNA processing due to trigger binding. d Agarose gel showing activation of target cutting by varying amounts of trigger RNA (uncut: 1190 bp, cut: 357 bp). e Transfer function derived from the fraction of cut target by gels as shown in ( d ) ( N = 3, t -distribution two-sided 90% confidence interval). Source data are provided as a Source Data file
    Figure Legend Snippet: Principle of strand displacement switchable gRNAs. a When the RNA trigger binds the SD gRNA, the 5′ extension domain occluding handle is displaced, thereby restoring the gRNA handle. Binding of Cas12a leads to cleavage of the gRNA, which removes the 5′ extension and creates an active Cas12a-gRNA complex. The domains are labeled as follows: s—separator, h—handle, t—target, X1—toehold. The overall nomenclature follows Zhang et al. 32 : A domain is denoted by a single letter. An upper index x denotes the first x nucleotides of a domain counting from its 5′ end. A lower index x denotes all but the first x nucleotides of a domain counting from its 5′ end. A combination of upper and lower indices includes those nucleotides that are present in both subdomains. A bar above the letter marks the reverse complement of a domain. The red star marks the position where Cas12a cleaves a successfully bound gRNA. b Agarose gel showing cutting of a target DNA by handle-based SD gRNAs with two different target sequences in the absence and presence of trigger RNA (uncut: 1190 bp, cut t1: 357 bp, cut t2: 506 bp). c Denaturing PAGE showing induced gRNA processing due to trigger binding. d Agarose gel showing activation of target cutting by varying amounts of trigger RNA (uncut: 1190 bp, cut: 357 bp). e Transfer function derived from the fraction of cut target by gels as shown in ( d ) ( N = 3, t -distribution two-sided 90% confidence interval). Source data are provided as a Source Data file

    Techniques Used: Binding Assay, Labeling, Agarose Gel Electrophoresis, Polyacrylamide Gel Electrophoresis, Activation Assay, Derivative Assay

    4) Product Images from "Circularization restores signal recognition particle RNA functionality in Thermoproteus"

    Article Title: Circularization restores signal recognition particle RNA functionality in Thermoproteus

    Journal: eLife

    doi: 10.7554/eLife.11623

    Binding of SRP19 and SRP54 to SRP RNA variants. Proteins of flow-through (F) and elution (E) fractions of DEAE-columns are separated on 15% SDS polyacrylamide gels next to a protein marker (M). ( A ) SRP19 shows binding to the S-domain of the SRP RNA (Sd RNA). ( B ) SRP19, SRP54 and different S-domain constructs were loaded (Sd: S-domain, Open: non-circularized version of the S-domain, GNAR: point-mutation in the GNAR motif, h8b: triple mutation in the helix 8b, Ctrl: control RNA with similar length). ( C ) Loading control of the SRP S-domain RNA constructs. To verify the integrity and running behavior of the four constructed S-domain RNA variants, 100 ng of the transcripts were loaded onto a 8% denaturing polyacrylamide gel next to a DNA ladder (M1, bands marked in bp) as well as a RNA ladder (M) and SYBR Gold stained.
    Figure Legend Snippet: Binding of SRP19 and SRP54 to SRP RNA variants. Proteins of flow-through (F) and elution (E) fractions of DEAE-columns are separated on 15% SDS polyacrylamide gels next to a protein marker (M). ( A ) SRP19 shows binding to the S-domain of the SRP RNA (Sd RNA). ( B ) SRP19, SRP54 and different S-domain constructs were loaded (Sd: S-domain, Open: non-circularized version of the S-domain, GNAR: point-mutation in the GNAR motif, h8b: triple mutation in the helix 8b, Ctrl: control RNA with similar length). ( C ) Loading control of the SRP S-domain RNA constructs. To verify the integrity and running behavior of the four constructed S-domain RNA variants, 100 ng of the transcripts were loaded onto a 8% denaturing polyacrylamide gel next to a DNA ladder (M1, bands marked in bp) as well as a RNA ladder (M) and SYBR Gold stained.

    Techniques Used: Binding Assay, Flow Cytometry, Marker, Construct, Mutagenesis, Staining

    5) Product Images from "Structural diversity of supercoiled DNA"

    Article Title: Structural diversity of supercoiled DNA

    Journal: Nature Communications

    doi: 10.1038/ncomms9440

    Effect of supercoiling on the structure of minicircle DNA. ( a ) Individual 336 bp minicircle topoisomers were isolated and analysed by polyacrylamide gel electrophoresis in the presence of 10 mM CaCl 2 . Mr: 100 bp DNA ladder, L: minicircle linearized by EcoRV, N: minicircle nicked by Nb.BbvCI. ( b ) Projections of cryo-ET subtomograms of hydrated 336 bp DNA minicircles of the Lk =34 topoisomer. ( c ) Commonly observed shapes were open circle, open figure-8, figure-8, racquet, handcuffs, needle, and rod, each of which are shown in orthogonal views. ( d ) Other shapes observed, especially in the more highly supercoiled topoisomers. ( e ) Shape frequency distribution plot for each topoisomer population (n=number of minicircles analysed). A weighted average for each topoisomer, approximating the average degree of compactness, is denoted by the black triangle. The weighted average was calculated by assigning each conformation a value that increased in line with compactness. Open circles were given a value of 1, open figure-8 s a value of 2, figure-8 s as a value of 3, and so on. The relative fraction of each was subsequently used to determine the average degree of compactness. Lk , Δ Lk and superhelical density (σ) for each topoisomer are shown (see Supplementary Note 1 ).
    Figure Legend Snippet: Effect of supercoiling on the structure of minicircle DNA. ( a ) Individual 336 bp minicircle topoisomers were isolated and analysed by polyacrylamide gel electrophoresis in the presence of 10 mM CaCl 2 . Mr: 100 bp DNA ladder, L: minicircle linearized by EcoRV, N: minicircle nicked by Nb.BbvCI. ( b ) Projections of cryo-ET subtomograms of hydrated 336 bp DNA minicircles of the Lk =34 topoisomer. ( c ) Commonly observed shapes were open circle, open figure-8, figure-8, racquet, handcuffs, needle, and rod, each of which are shown in orthogonal views. ( d ) Other shapes observed, especially in the more highly supercoiled topoisomers. ( e ) Shape frequency distribution plot for each topoisomer population (n=number of minicircles analysed). A weighted average for each topoisomer, approximating the average degree of compactness, is denoted by the black triangle. The weighted average was calculated by assigning each conformation a value that increased in line with compactness. Open circles were given a value of 1, open figure-8 s a value of 2, figure-8 s as a value of 3, and so on. The relative fraction of each was subsequently used to determine the average degree of compactness. Lk , Δ Lk and superhelical density (σ) for each topoisomer are shown (see Supplementary Note 1 ).

    Techniques Used: Isolation, Polyacrylamide Gel Electrophoresis

    6) Product Images from "Improved Protocols for Illumina Sequencing"

    Article Title: Improved Protocols for Illumina Sequencing

    Journal: Current protocols in human genetics / editorial board, Jonathan L. Haines ... [et al.]

    doi: 10.1002/0471142905.hg1802s62

    Effect of AMPure XP ratios on fragment size selection. 1 μg of DNA was sheared to giver fragments from 20 to 400bp (average 160bp). Next the DNA was incubated with different AMPure ratios. The size distribution of fragments after AMPure clean up were analysed by electrophoresis using an Agilent Bioanalyzer High Sensitivity DNA chip. (A) AMPure bead to DNA ratios varying from 2.5× beads to DNA up to 1.0× beads to DNA (B) AMPure bead to DNA ratios varying from 1.5× beads to DNA up to 0.6× beads to DNA.
    Figure Legend Snippet: Effect of AMPure XP ratios on fragment size selection. 1 μg of DNA was sheared to giver fragments from 20 to 400bp (average 160bp). Next the DNA was incubated with different AMPure ratios. The size distribution of fragments after AMPure clean up were analysed by electrophoresis using an Agilent Bioanalyzer High Sensitivity DNA chip. (A) AMPure bead to DNA ratios varying from 2.5× beads to DNA up to 1.0× beads to DNA (B) AMPure bead to DNA ratios varying from 1.5× beads to DNA up to 0.6× beads to DNA.

    Techniques Used: Selection, Incubation, Electrophoresis, Chromatin Immunoprecipitation

    7) Product Images from "Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing"

    Article Title: Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp457

    Comparison of sequencing results from conventional cloning and Sanger sequencing and 454 Life Sciences FLX sequencing of MLH1 promoter PCR products from bisulfite treated DNA of an endometrial cancer and normal blood from Patient #1684. ( A ) Schematic of the MLH1 promoter is presented with arrows indicating the location of PCR primers and vertical lines representing the position of CG dinucleotides. Below the schematic are the results from cloning and bisulfite sequencing 45 molecules from the distal (left) and proximal (right) promoter in each sample (tumor and matched normal blood). Each column represents a CG dinucleotide in the sequence, and corresponds to each vertical line in the promoter schematic. Each row represents a single molecule. The color of the boxes represents the methylation state of each cytosine. Red, methylated; Black, unmethylated. ( B ) The results from the FLX single molecule sequencing of the same samples. The distance of each CpG from the transcription start site (UCSC Human Genome March 2006) is listed from distal to proximal. The Distal Amplicon: −671, −662, −654, −648, −634, −632, −630, −626, −623, −619, −609, −605, −596, −584, −576, −569, −566, −564, −560, −558, −548, −540, −537, −512, −505, −483, −470, −465, −449, −446, −421, −405, −380, −368. The Proximal Amplicon: −341, −325, −318, −286, −280, −249, −240, −226, −209, −202, −192, −190, −184, −165, −154, −139, −70, −47, −23, −15. As an additional point of reference, the translation start site (ATG) is currently annotated at +60 downstream of the transcription start site (position 0).
    Figure Legend Snippet: Comparison of sequencing results from conventional cloning and Sanger sequencing and 454 Life Sciences FLX sequencing of MLH1 promoter PCR products from bisulfite treated DNA of an endometrial cancer and normal blood from Patient #1684. ( A ) Schematic of the MLH1 promoter is presented with arrows indicating the location of PCR primers and vertical lines representing the position of CG dinucleotides. Below the schematic are the results from cloning and bisulfite sequencing 45 molecules from the distal (left) and proximal (right) promoter in each sample (tumor and matched normal blood). Each column represents a CG dinucleotide in the sequence, and corresponds to each vertical line in the promoter schematic. Each row represents a single molecule. The color of the boxes represents the methylation state of each cytosine. Red, methylated; Black, unmethylated. ( B ) The results from the FLX single molecule sequencing of the same samples. The distance of each CpG from the transcription start site (UCSC Human Genome March 2006) is listed from distal to proximal. The Distal Amplicon: −671, −662, −654, −648, −634, −632, −630, −626, −623, −619, −609, −605, −596, −584, −576, −569, −566, −564, −560, −558, −548, −540, −537, −512, −505, −483, −470, −465, −449, −446, −421, −405, −380, −368. The Proximal Amplicon: −341, −325, −318, −286, −280, −249, −240, −226, −209, −202, −192, −190, −184, −165, −154, −139, −70, −47, −23, −15. As an additional point of reference, the translation start site (ATG) is currently annotated at +60 downstream of the transcription start site (position 0).

    Techniques Used: Sequencing, Clone Assay, Polymerase Chain Reaction, Methylation Sequencing, Methylation, Amplification

    Experimental design for deep bisulfite sequencing in individual samples. ( A ) Detection of DNA methylation by sodium bisulfite treatment and PCR. ( B ) PCR amplification with sample specific DNA barcodes. ( C ) Pool PCR products for 454 sequencing.
    Figure Legend Snippet: Experimental design for deep bisulfite sequencing in individual samples. ( A ) Detection of DNA methylation by sodium bisulfite treatment and PCR. ( B ) PCR amplification with sample specific DNA barcodes. ( C ) Pool PCR products for 454 sequencing.

    Techniques Used: Methylation Sequencing, DNA Methylation Assay, Polymerase Chain Reaction, Amplification, Sequencing

    Related Articles

    Nucleic Acid Electrophoresis:

    Article Title: Dual coding potential of a 2′,5′-branched ribonucleotide in DNA
    Article Snippet: .. Single-stranded oligonucleotides synthesized by Eurofins MWG Operon or a Low Molecular Weight DNA Ladder (New England BioLabs, NEB) were used as size markers in gel electrophoresis. ..

    Synthesized:

    Article Title: Dual coding potential of a 2′,5′-branched ribonucleotide in DNA
    Article Snippet: .. Single-stranded oligonucleotides synthesized by Eurofins MWG Operon or a Low Molecular Weight DNA Ladder (New England BioLabs, NEB) were used as size markers in gel electrophoresis. ..

    Marker:

    Article Title: Circularization restores signal recognition particle RNA functionality in Thermoproteus
    Article Snippet: .. Northern blot Fractionation of 1–4 µg T. tenax total RNA was performed by electrophoretic separation on 8% denaturing-polyacrylamide gels next to an RNA and DNA marker (low molecular weight DNA ladder, NEB). .. Additionally, to verify the circularization of SRP RNA, 15 ng of full-length SRP RNA in vitro transcript and circularized SRP RNA served as a running control.

    Northern Blot:

    Article Title: Circularization restores signal recognition particle RNA functionality in Thermoproteus
    Article Snippet: .. Northern blot Fractionation of 1–4 µg T. tenax total RNA was performed by electrophoretic separation on 8% denaturing-polyacrylamide gels next to an RNA and DNA marker (low molecular weight DNA ladder, NEB). .. Additionally, to verify the circularization of SRP RNA, 15 ng of full-length SRP RNA in vitro transcript and circularized SRP RNA served as a running control.

    Purification:

    Article Title: Switching the activity of Cas12a using guide RNA strand displacement circuits
    Article Snippet: .. For both purification methods, the purified RNA was quantified by running it on an 8 M urea denaturing TBE 12% polyacrylamide (29:1 acrylamide/bis-acrylamide) gel at 120 V for 45 min and compared with an RNA ladder of known concentration (RiboRuler Low Range RNA Ladder, ThermoFisher) to determine its concentration and with a DNA ladder (Low Molecular Weight DNA Ladder, New England Biolabs) to determine its length. .. Cutting assays for gRNAs AsCas12a (containing nuclear localization sequences and C-terminal His tags) was ordered from IDT with a concentration of around 64 μM.

    Concentration Assay:

    Article Title: Switching the activity of Cas12a using guide RNA strand displacement circuits
    Article Snippet: .. For both purification methods, the purified RNA was quantified by running it on an 8 M urea denaturing TBE 12% polyacrylamide (29:1 acrylamide/bis-acrylamide) gel at 120 V for 45 min and compared with an RNA ladder of known concentration (RiboRuler Low Range RNA Ladder, ThermoFisher) to determine its concentration and with a DNA ladder (Low Molecular Weight DNA Ladder, New England Biolabs) to determine its length. .. Cutting assays for gRNAs AsCas12a (containing nuclear localization sequences and C-terminal His tags) was ordered from IDT with a concentration of around 64 μM.

    Fractionation:

    Article Title: Circularization restores signal recognition particle RNA functionality in Thermoproteus
    Article Snippet: .. Northern blot Fractionation of 1–4 µg T. tenax total RNA was performed by electrophoretic separation on 8% denaturing-polyacrylamide gels next to an RNA and DNA marker (low molecular weight DNA ladder, NEB). .. Additionally, to verify the circularization of SRP RNA, 15 ng of full-length SRP RNA in vitro transcript and circularized SRP RNA served as a running control.

    Polymerase Chain Reaction:

    Article Title: Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing
    Article Snippet: .. This was achieved by quantitatively comparing the intensity of the gel band containing the PCR product to the intensity of the similar size band in the Low Molecular Weight DNA Ladder (NEB). .. The quantity of PCR product is computed by dividing the PCR product intensity by the scaling factor, which is the ladder band intensity divided by the ladder band molecular weight.

    Molecular Weight:

    Article Title: Detection of the pediocin gene pedA in strains from human faeces by real-time PCR and characterization of Pediococcus acidilactici UVA1
    Article Snippet: .. The low molecular weight DNA ladder and Tridye 100 bp DNA-ladder (New England BioLabs, Ipswich, MA, USA) were used as size standards. ..

    Article Title: RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes
    Article Snippet: .. In separate, but otherwise identical reactions, also label 0.1 pmole of a synthetic RNA oligonucleotide of known length, 1 µl of low molecular weight ssDNA ladder and 1 µl of NEB 100 bp DNA ladder. ..

    Article Title: Dual coding potential of a 2′,5′-branched ribonucleotide in DNA
    Article Snippet: .. Single-stranded oligonucleotides synthesized by Eurofins MWG Operon or a Low Molecular Weight DNA Ladder (New England BioLabs, NEB) were used as size markers in gel electrophoresis. ..

    Article Title: Structural diversity of supercoiled DNA
    Article Snippet: .. BbvCI, EcoRV, Nb.BbvCI, NdeI, Nuclease Bal-31, T4 DNA Ligase, low molecular weight DNA ladder and 100 bp DNA ladder were purchased from New England Biolabs (Ipswich, MA). .. Proteinase K was purchased from Roche Molecular Biochemicals (Mannheim, Germany).

    Article Title: Switching the activity of Cas12a using guide RNA strand displacement circuits
    Article Snippet: .. For both purification methods, the purified RNA was quantified by running it on an 8 M urea denaturing TBE 12% polyacrylamide (29:1 acrylamide/bis-acrylamide) gel at 120 V for 45 min and compared with an RNA ladder of known concentration (RiboRuler Low Range RNA Ladder, ThermoFisher) to determine its concentration and with a DNA ladder (Low Molecular Weight DNA Ladder, New England Biolabs) to determine its length. .. Cutting assays for gRNAs AsCas12a (containing nuclear localization sequences and C-terminal His tags) was ordered from IDT with a concentration of around 64 μM.

    Article Title: Circularization restores signal recognition particle RNA functionality in Thermoproteus
    Article Snippet: .. Northern blot Fractionation of 1–4 µg T. tenax total RNA was performed by electrophoretic separation on 8% denaturing-polyacrylamide gels next to an RNA and DNA marker (low molecular weight DNA ladder, NEB). .. Additionally, to verify the circularization of SRP RNA, 15 ng of full-length SRP RNA in vitro transcript and circularized SRP RNA served as a running control.

    Article Title: Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing
    Article Snippet: .. This was achieved by quantitatively comparing the intensity of the gel band containing the PCR product to the intensity of the similar size band in the Low Molecular Weight DNA Ladder (NEB). .. The quantity of PCR product is computed by dividing the PCR product intensity by the scaling factor, which is the ladder band intensity divided by the ladder band molecular weight.

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    New England Biolabs molecular weight dna ladder
    Transcription analysis of pedA . pedA -reverse transcription-PCR on cDNA from P. acidilactici bac- (1, 2, 3) or UVA1 (7, 8, 9) after 1 h 30, 2 h 30 and 3 h 30 of growth, respectively, and from P. acidilactici DSM 20284 T (4) or UL5 (6) and P. pentosaceus DSM 20336 T (5) after 2 h 30 of growth. 10: water instead of <t>DNA.</t> lm: low molecular weight DNA ladder (in bp). h: <t>Tridye</t> 100-bp DNA ladder (in bp). Expected product size: 100 bp.
    Molecular Weight Dna Ladder, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 143 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Transcription analysis of pedA . pedA -reverse transcription-PCR on cDNA from P. acidilactici bac- (1, 2, 3) or UVA1 (7, 8, 9) after 1 h 30, 2 h 30 and 3 h 30 of growth, respectively, and from P. acidilactici DSM 20284 T (4) or UL5 (6) and P. pentosaceus DSM 20336 T (5) after 2 h 30 of growth. 10: water instead of DNA. lm: low molecular weight DNA ladder (in bp). h: Tridye 100-bp DNA ladder (in bp). Expected product size: 100 bp.

    Journal: BMC Biotechnology

    Article Title: Detection of the pediocin gene pedA in strains from human faeces by real-time PCR and characterization of Pediococcus acidilactici UVA1

    doi: 10.1186/1472-6750-7-55

    Figure Lengend Snippet: Transcription analysis of pedA . pedA -reverse transcription-PCR on cDNA from P. acidilactici bac- (1, 2, 3) or UVA1 (7, 8, 9) after 1 h 30, 2 h 30 and 3 h 30 of growth, respectively, and from P. acidilactici DSM 20284 T (4) or UL5 (6) and P. pentosaceus DSM 20336 T (5) after 2 h 30 of growth. 10: water instead of DNA. lm: low molecular weight DNA ladder (in bp). h: Tridye 100-bp DNA ladder (in bp). Expected product size: 100 bp.

    Article Snippet: The low molecular weight DNA ladder and Tridye 100 bp DNA-ladder (New England BioLabs, Ipswich, MA, USA) were used as size standards.

    Techniques: Polymerase Chain Reaction, BAC Assay, Molecular Weight

    UV-crosslinking bias of different RBPs dictates the suitability of different approaches for identifying binding sites A. hnRNPA1:ssDNA interface. Crystal structure of two-RRM-containing UP1 domain of hnRNP A1 (PDB ID: 2UP1; blue) in complex with a target containing its AGGG preferred recognition motif (in this case, within single-stranded DNA, ssDNA; red). Black box. Enlarged view of the DNA:protein interface. Aromatic residues (Phe-17 and Phe-59 from RRM1) that stack with the nucleobases are shown in cyan. B. eIF4AIII:RNA interface. Crystal structure of eIF4AIII (PDB ID: 2J0S; blue) complexed with RNA (red) and AMP-PNP. Black box. Enlarged view of the RNA:protein interface. Note that the RNA bases are pointing away from the bound protein. ]. D. RIPiT and CLIP yield different types of information. Top: Two similar yet compositionally distinct hypothetical multi-subunit RNPs. RBPs (blue), non-RBPs (green) and proteins unique to each complex are shown (complex A: yellow; complex B: red). Left: RIPiT can reveal the binding sites of an intact multi-subunit RNP, and can also distinguish between footprints of two compositionally similar complexes (schematics on gray background). However, RIPiT does not conclusively define direct RBP-RNA interactions (crossed-out schematic). Right: On the contrary, while CLIP reveals no information regarding the complexes an RNA-bound RBP is part of (crossed-out schematics), it can unveil the sites of direct contact between an RBP and RNA (bottom schematic).

    Journal: Methods (San Diego, Calif.)

    Article Title: RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes

    doi: 10.1016/j.ymeth.2013.09.013

    Figure Lengend Snippet: UV-crosslinking bias of different RBPs dictates the suitability of different approaches for identifying binding sites A. hnRNPA1:ssDNA interface. Crystal structure of two-RRM-containing UP1 domain of hnRNP A1 (PDB ID: 2UP1; blue) in complex with a target containing its AGGG preferred recognition motif (in this case, within single-stranded DNA, ssDNA; red). Black box. Enlarged view of the DNA:protein interface. Aromatic residues (Phe-17 and Phe-59 from RRM1) that stack with the nucleobases are shown in cyan. B. eIF4AIII:RNA interface. Crystal structure of eIF4AIII (PDB ID: 2J0S; blue) complexed with RNA (red) and AMP-PNP. Black box. Enlarged view of the RNA:protein interface. Note that the RNA bases are pointing away from the bound protein. ]. D. RIPiT and CLIP yield different types of information. Top: Two similar yet compositionally distinct hypothetical multi-subunit RNPs. RBPs (blue), non-RBPs (green) and proteins unique to each complex are shown (complex A: yellow; complex B: red). Left: RIPiT can reveal the binding sites of an intact multi-subunit RNP, and can also distinguish between footprints of two compositionally similar complexes (schematics on gray background). However, RIPiT does not conclusively define direct RBP-RNA interactions (crossed-out schematic). Right: On the contrary, while CLIP reveals no information regarding the complexes an RNA-bound RBP is part of (crossed-out schematics), it can unveil the sites of direct contact between an RBP and RNA (bottom schematic).

    Article Snippet: In separate, but otherwise identical reactions, also label 0.1 pmole of a synthetic RNA oligonucleotide of known length, 1 µl of low molecular weight ssDNA ladder and 1 µl of NEB 100 bp DNA ladder.

    Techniques: Binding Assay, Cross-linking Immunoprecipitation

    Biochemical analysis of proteins and RNAs from the RIPiT procedure A. Western blots showing tetracycline (Tet)-mediated induction of eIF4AIII protein with the FLAG tag at its N- or C-terminus (top and bottom panels, respectively). The Tet concentration used for induction is indicated at the top of each lane; protein identities are indicated to the right. B. Levels of proteins detected by western blots in different fractions during EJC RIPiT. The table on the top indicates the different fractions from the RIPiT procedure and the antibodies used for 1 st and 2 nd IPs. The stably expressed FLAG-tag fusion protein used in each sample is indicated directly above lane. Proteins detected by western blot are indicated to the right. C. Size distribution of EJC footprints upon RNase I titration. An autoradiogram of 26% denaturing PAGE with 5′ [ 32 P]-labeled RNA fragments from base-hydrolysis of poly U 30 oligonucleotide (lane 1) or FLAG-Magoh:eIF4AIII RIPiT (lanes 2–5). RNase I concentrations used are indicated at top of each lane; nucleotide (nt) lengths are to the left. D. Quantification of desired size RNA footprints in RIPiT elution. An autoradiogram of 20% denaturing PAGE with 5′ [ 32 P]-labeled 100 bp NEB DNA ladder (lane 1), low molecular weight ssDNA ladder (lane 2), footprints of RIPiTs indicated on top (lanes 3 and 4) and a 21 nt ssRNA oligo of known specific activity (lane 5). The signal from red rectangles is quantified in comparison to that of the 21 nt oligo to estimate the amount of RIPiT footprints in the indicated size range.

    Journal: Methods (San Diego, Calif.)

    Article Title: RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes

    doi: 10.1016/j.ymeth.2013.09.013

    Figure Lengend Snippet: Biochemical analysis of proteins and RNAs from the RIPiT procedure A. Western blots showing tetracycline (Tet)-mediated induction of eIF4AIII protein with the FLAG tag at its N- or C-terminus (top and bottom panels, respectively). The Tet concentration used for induction is indicated at the top of each lane; protein identities are indicated to the right. B. Levels of proteins detected by western blots in different fractions during EJC RIPiT. The table on the top indicates the different fractions from the RIPiT procedure and the antibodies used for 1 st and 2 nd IPs. The stably expressed FLAG-tag fusion protein used in each sample is indicated directly above lane. Proteins detected by western blot are indicated to the right. C. Size distribution of EJC footprints upon RNase I titration. An autoradiogram of 26% denaturing PAGE with 5′ [ 32 P]-labeled RNA fragments from base-hydrolysis of poly U 30 oligonucleotide (lane 1) or FLAG-Magoh:eIF4AIII RIPiT (lanes 2–5). RNase I concentrations used are indicated at top of each lane; nucleotide (nt) lengths are to the left. D. Quantification of desired size RNA footprints in RIPiT elution. An autoradiogram of 20% denaturing PAGE with 5′ [ 32 P]-labeled 100 bp NEB DNA ladder (lane 1), low molecular weight ssDNA ladder (lane 2), footprints of RIPiTs indicated on top (lanes 3 and 4) and a 21 nt ssRNA oligo of known specific activity (lane 5). The signal from red rectangles is quantified in comparison to that of the 21 nt oligo to estimate the amount of RIPiT footprints in the indicated size range.

    Article Snippet: In separate, but otherwise identical reactions, also label 0.1 pmole of a synthetic RNA oligonucleotide of known length, 1 µl of low molecular weight ssDNA ladder and 1 µl of NEB 100 bp DNA ladder.

    Techniques: Western Blot, FLAG-tag, Concentration Assay, Stable Transfection, Titration, Polyacrylamide Gel Electrophoresis, Labeling, Molecular Weight, Activity Assay

    Principle of strand displacement switchable gRNAs. a When the RNA trigger binds the SD gRNA, the 5′ extension domain occluding handle is displaced, thereby restoring the gRNA handle. Binding of Cas12a leads to cleavage of the gRNA, which removes the 5′ extension and creates an active Cas12a-gRNA complex. The domains are labeled as follows: s—separator, h—handle, t—target, X1—toehold. The overall nomenclature follows Zhang et al. 32 : A domain is denoted by a single letter. An upper index x denotes the first x nucleotides of a domain counting from its 5′ end. A lower index x denotes all but the first x nucleotides of a domain counting from its 5′ end. A combination of upper and lower indices includes those nucleotides that are present in both subdomains. A bar above the letter marks the reverse complement of a domain. The red star marks the position where Cas12a cleaves a successfully bound gRNA. b Agarose gel showing cutting of a target DNA by handle-based SD gRNAs with two different target sequences in the absence and presence of trigger RNA (uncut: 1190 bp, cut t1: 357 bp, cut t2: 506 bp). c Denaturing PAGE showing induced gRNA processing due to trigger binding. d Agarose gel showing activation of target cutting by varying amounts of trigger RNA (uncut: 1190 bp, cut: 357 bp). e Transfer function derived from the fraction of cut target by gels as shown in ( d ) ( N = 3, t -distribution two-sided 90% confidence interval). Source data are provided as a Source Data file

    Journal: Nature Communications

    Article Title: Switching the activity of Cas12a using guide RNA strand displacement circuits

    doi: 10.1038/s41467-019-09953-w

    Figure Lengend Snippet: Principle of strand displacement switchable gRNAs. a When the RNA trigger binds the SD gRNA, the 5′ extension domain occluding handle is displaced, thereby restoring the gRNA handle. Binding of Cas12a leads to cleavage of the gRNA, which removes the 5′ extension and creates an active Cas12a-gRNA complex. The domains are labeled as follows: s—separator, h—handle, t—target, X1—toehold. The overall nomenclature follows Zhang et al. 32 : A domain is denoted by a single letter. An upper index x denotes the first x nucleotides of a domain counting from its 5′ end. A lower index x denotes all but the first x nucleotides of a domain counting from its 5′ end. A combination of upper and lower indices includes those nucleotides that are present in both subdomains. A bar above the letter marks the reverse complement of a domain. The red star marks the position where Cas12a cleaves a successfully bound gRNA. b Agarose gel showing cutting of a target DNA by handle-based SD gRNAs with two different target sequences in the absence and presence of trigger RNA (uncut: 1190 bp, cut t1: 357 bp, cut t2: 506 bp). c Denaturing PAGE showing induced gRNA processing due to trigger binding. d Agarose gel showing activation of target cutting by varying amounts of trigger RNA (uncut: 1190 bp, cut: 357 bp). e Transfer function derived from the fraction of cut target by gels as shown in ( d ) ( N = 3, t -distribution two-sided 90% confidence interval). Source data are provided as a Source Data file

    Article Snippet: For both purification methods, the purified RNA was quantified by running it on an 8 M urea denaturing TBE 12% polyacrylamide (29:1 acrylamide/bis-acrylamide) gel at 120 V for 45 min and compared with an RNA ladder of known concentration (RiboRuler Low Range RNA Ladder, ThermoFisher) to determine its concentration and with a DNA ladder (Low Molecular Weight DNA Ladder, New England Biolabs) to determine its length.

    Techniques: Binding Assay, Labeling, Agarose Gel Electrophoresis, Polyacrylamide Gel Electrophoresis, Activation Assay, Derivative Assay

    Binding of SRP19 and SRP54 to SRP RNA variants. Proteins of flow-through (F) and elution (E) fractions of DEAE-columns are separated on 15% SDS polyacrylamide gels next to a protein marker (M). ( A ) SRP19 shows binding to the S-domain of the SRP RNA (Sd RNA). ( B ) SRP19, SRP54 and different S-domain constructs were loaded (Sd: S-domain, Open: non-circularized version of the S-domain, GNAR: point-mutation in the GNAR motif, h8b: triple mutation in the helix 8b, Ctrl: control RNA with similar length). ( C ) Loading control of the SRP S-domain RNA constructs. To verify the integrity and running behavior of the four constructed S-domain RNA variants, 100 ng of the transcripts were loaded onto a 8% denaturing polyacrylamide gel next to a DNA ladder (M1, bands marked in bp) as well as a RNA ladder (M) and SYBR Gold stained.

    Journal: eLife

    Article Title: Circularization restores signal recognition particle RNA functionality in Thermoproteus

    doi: 10.7554/eLife.11623

    Figure Lengend Snippet: Binding of SRP19 and SRP54 to SRP RNA variants. Proteins of flow-through (F) and elution (E) fractions of DEAE-columns are separated on 15% SDS polyacrylamide gels next to a protein marker (M). ( A ) SRP19 shows binding to the S-domain of the SRP RNA (Sd RNA). ( B ) SRP19, SRP54 and different S-domain constructs were loaded (Sd: S-domain, Open: non-circularized version of the S-domain, GNAR: point-mutation in the GNAR motif, h8b: triple mutation in the helix 8b, Ctrl: control RNA with similar length). ( C ) Loading control of the SRP S-domain RNA constructs. To verify the integrity and running behavior of the four constructed S-domain RNA variants, 100 ng of the transcripts were loaded onto a 8% denaturing polyacrylamide gel next to a DNA ladder (M1, bands marked in bp) as well as a RNA ladder (M) and SYBR Gold stained.

    Article Snippet: Northern blot Fractionation of 1–4 µg T. tenax total RNA was performed by electrophoretic separation on 8% denaturing-polyacrylamide gels next to an RNA and DNA marker (low molecular weight DNA ladder, NEB).

    Techniques: Binding Assay, Flow Cytometry, Marker, Construct, Mutagenesis, Staining