Structured Review

TaKaRa puc19
ttMutS2 preferably digested the DNA containing branched DNA structures. A , <t>pUC19</t> or pUC(AT) was incubated with or without 5 n m DNase I. B , the same experiment as in A was performed with 0, 100, and 200 n m ttMutS2. The reaction solutions were incubated
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Images

1) Product Images from "Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression *Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression * S⃞"

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression *Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression * S⃞

Journal:

doi: 10.1074/jbc.M806755200

ttMutS2 preferably digested the DNA containing branched DNA structures. A , pUC19 or pUC(AT) was incubated with or without 5 n m DNase I. B , the same experiment as in A was performed with 0, 100, and 200 n m ttMutS2. The reaction solutions were incubated
Figure Legend Snippet: ttMutS2 preferably digested the DNA containing branched DNA structures. A , pUC19 or pUC(AT) was incubated with or without 5 n m DNase I. B , the same experiment as in A was performed with 0, 100, and 200 n m ttMutS2. The reaction solutions were incubated

Techniques Used: Incubation

2) Product Images from "Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose"

Article Title: Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose

Journal: PLoS ONE

doi: 10.1371/journal.pone.0082624

Gel analysis of RNA-primed MPRCA products to detect the contaminating DNA in Phi29 DNA polymerase. ( A ) DNA amplification with Phi29 DNA polymerase prepared by our procedure. ( B ) DNA amplification with commercially available Phi29 DNA polymerase (Epicentre, Lot No. 10710). ( C ) DNA amplification with Phi29 DNA polymerase prepared by DNase-treatment. All gel images show the Bam HI/ Eco RI double digested amplification products. Black arrow indicates the specific amplification products from pUC19; M, AccuRuler 1-kb DNA RTU ladder (Maestrogen). All reactions were repeated three times or more; typical results are shown.
Figure Legend Snippet: Gel analysis of RNA-primed MPRCA products to detect the contaminating DNA in Phi29 DNA polymerase. ( A ) DNA amplification with Phi29 DNA polymerase prepared by our procedure. ( B ) DNA amplification with commercially available Phi29 DNA polymerase (Epicentre, Lot No. 10710). ( C ) DNA amplification with Phi29 DNA polymerase prepared by DNase-treatment. All gel images show the Bam HI/ Eco RI double digested amplification products. Black arrow indicates the specific amplification products from pUC19; M, AccuRuler 1-kb DNA RTU ladder (Maestrogen). All reactions were repeated three times or more; typical results are shown.

Techniques Used: Amplification

3) Product Images from "Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose"

Article Title: Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose

Journal: PLoS ONE

doi: 10.1371/journal.pone.0082624

Gel analysis of RNA-primed MPRCA products to detect the contaminating DNA in Phi29 DNA polymerase. ( A ) DNA amplification with Phi29 DNA polymerase prepared by our procedure. ( B ) DNA amplification with commercially available Phi29 DNA polymerase (Epicentre, Lot No. 10710). ( C ) DNA amplification with Phi29 DNA polymerase prepared by DNase-treatment. All gel images show the Bam HI/ Eco RI double digested amplification products. Black arrow indicates the specific amplification products from pUC19; M, AccuRuler 1-kb DNA RTU ladder (Maestrogen). All reactions were repeated three times or more; typical results are shown.
Figure Legend Snippet: Gel analysis of RNA-primed MPRCA products to detect the contaminating DNA in Phi29 DNA polymerase. ( A ) DNA amplification with Phi29 DNA polymerase prepared by our procedure. ( B ) DNA amplification with commercially available Phi29 DNA polymerase (Epicentre, Lot No. 10710). ( C ) DNA amplification with Phi29 DNA polymerase prepared by DNase-treatment. All gel images show the Bam HI/ Eco RI double digested amplification products. Black arrow indicates the specific amplification products from pUC19; M, AccuRuler 1-kb DNA RTU ladder (Maestrogen). All reactions were repeated three times or more; typical results are shown.

Techniques Used: Amplification

4) Product Images from "A reduced genome decreases the host carrying capacity for foreign DNA"

Article Title: A reduced genome decreases the host carrying capacity for foreign DNA

Journal: Microbial Cell Factories

doi: 10.1186/1475-2859-13-49

Contributions of plasmids to cell growth. A . Schematic drawing of the plasmids. All plasmids (pUC-S, pUC-M and pUC-L) were derived from pUC19. The lengths of S, M and L represent the plasmid sizes of 2,334, 6,426 and 9,573 bp, respectively. The site of initiation for replication and the ampicillin resistance gene are indicated as ori and bla , respectively. B . Cell growth rates. The exponential growth rates of E. coli strains MG1655 (upper panel) and MDS42 (lower panel) in a minimal medium are shown for different temperatures. The green, blue and red colors indicate the cells bearing the plasmids S, M and L, respectively. The strains that did not contain plasmids, which were used as controls ( i.e. , native growth fitness), are shown in black. The bars represent the standard errors of triplicates. Statistic significance is indicated (*, p
Figure Legend Snippet: Contributions of plasmids to cell growth. A . Schematic drawing of the plasmids. All plasmids (pUC-S, pUC-M and pUC-L) were derived from pUC19. The lengths of S, M and L represent the plasmid sizes of 2,334, 6,426 and 9,573 bp, respectively. The site of initiation for replication and the ampicillin resistance gene are indicated as ori and bla , respectively. B . Cell growth rates. The exponential growth rates of E. coli strains MG1655 (upper panel) and MDS42 (lower panel) in a minimal medium are shown for different temperatures. The green, blue and red colors indicate the cells bearing the plasmids S, M and L, respectively. The strains that did not contain plasmids, which were used as controls ( i.e. , native growth fitness), are shown in black. The bars represent the standard errors of triplicates. Statistic significance is indicated (*, p

Techniques Used: Derivative Assay, Plasmid Preparation

5) Product Images from "Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression *Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression * S⃞"

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression *Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression * S⃞

Journal:

doi: 10.1074/jbc.M806755200

ttMutS2 preferably digested the DNA containing branched DNA structures. A , pUC19 or pUC(AT) was incubated with or without 5 n m DNase I. B , the same experiment as in A was performed with 0, 100, and 200 n m ttMutS2. The reaction solutions were incubated
Figure Legend Snippet: ttMutS2 preferably digested the DNA containing branched DNA structures. A , pUC19 or pUC(AT) was incubated with or without 5 n m DNase I. B , the same experiment as in A was performed with 0, 100, and 200 n m ttMutS2. The reaction solutions were incubated

Techniques Used: Incubation

6) Product Images from "Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V"

Article Title: Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V

Journal: BMC Biotechnology

doi: 10.1186/1472-6750-13-81

mRFP1-positive clones obtained by cloning an RFP-coding device into pUC19. Recombinant E. coli colonies expressing mRFP1. Detection was facilitated via excitation at 505 nm. Manual counting yielded a positive fraction (dark blue markers) of about 92.4% (233 of 252 colonies), cyan markers present negative colonies with poor or no fluorescence.
Figure Legend Snippet: mRFP1-positive clones obtained by cloning an RFP-coding device into pUC19. Recombinant E. coli colonies expressing mRFP1. Detection was facilitated via excitation at 505 nm. Manual counting yielded a positive fraction (dark blue markers) of about 92.4% (233 of 252 colonies), cyan markers present negative colonies with poor or no fluorescence.

Techniques Used: Clone Assay, Recombinant, Expressing, Fluorescence

7) Product Images from "Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression *Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression * S⃞"

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression *Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression * S⃞

Journal:

doi: 10.1074/jbc.M806755200

ttMutS2 preferably digested the DNA containing branched DNA structures. A , pUC19 or pUC(AT) was incubated with or without 5 n m DNase I. B , the same experiment as in A was performed with 0, 100, and 200 n m ttMutS2. The reaction solutions were incubated
Figure Legend Snippet: ttMutS2 preferably digested the DNA containing branched DNA structures. A , pUC19 or pUC(AT) was incubated with or without 5 n m DNase I. B , the same experiment as in A was performed with 0, 100, and 200 n m ttMutS2. The reaction solutions were incubated

Techniques Used: Incubation

8) Product Images from "Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose"

Article Title: Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose

Journal: PLoS ONE

doi: 10.1371/journal.pone.0082624

Gel analysis of RNA-primed MPRCA products to detect the contaminating DNA in Phi29 DNA polymerase. ( A ) DNA amplification with Phi29 DNA polymerase prepared by our procedure. ( B ) DNA amplification with commercially available Phi29 DNA polymerase (Epicentre, Lot No. 10710). ( C ) DNA amplification with Phi29 DNA polymerase prepared by DNase-treatment. All gel images show the Bam HI/ Eco RI double digested amplification products. Black arrow indicates the specific amplification products from pUC19; M, AccuRuler 1-kb DNA RTU ladder (Maestrogen). All reactions were repeated three times or more; typical results are shown.
Figure Legend Snippet: Gel analysis of RNA-primed MPRCA products to detect the contaminating DNA in Phi29 DNA polymerase. ( A ) DNA amplification with Phi29 DNA polymerase prepared by our procedure. ( B ) DNA amplification with commercially available Phi29 DNA polymerase (Epicentre, Lot No. 10710). ( C ) DNA amplification with Phi29 DNA polymerase prepared by DNase-treatment. All gel images show the Bam HI/ Eco RI double digested amplification products. Black arrow indicates the specific amplification products from pUC19; M, AccuRuler 1-kb DNA RTU ladder (Maestrogen). All reactions were repeated three times or more; typical results are shown.

Techniques Used: Amplification

9) Product Images from "An A-Factor-Dependent Extracytoplasmic Function Sigma Factor (?AdsA) That Is Essential for Morphological Development in Streptomyces griseus"

Article Title: An A-Factor-Dependent Extracytoplasmic Function Sigma Factor (?AdsA) That Is Essential for Morphological Development in Streptomyces griseus

Journal: Journal of Bacteriology

doi:

Gel mobility shift-PCR for isolation of DNA fragments recognized and bound by AdpA-H (A) and gel mobility shift of AdBS1 caused by AdpA-H (B). (A) The S. griseus chromosomal DNA of 300 to 500 bp obtained after Hae III digestion was sandwiched by the catch linkers, 32 P-labeled, mixed and incubated with AdpA-H, and run on a polyacrylamide gel. The amounts of AdpA-H used were 0.02 μg (lane 2), 0.2 μg (lane 3), and 1 μg (lane 4). Lane 1 is a control lane in which there was no AdpA-H. The DNA fragments retarded were recovered and subjected to a second cycle and further cycles. The mobility shift patterns after the second and third cycles are presented, showing the presence of retarded signals. The opposing arrows show the area from which DNA was extracted; the upper position was determined with a 500-bp DNA fragment, including the AdpA-binding site for strR , and the lower position was determined with a 300-bp fragment including the same AdpA-binding site, as described in Materials and Methods. (B) AdBS1 was excised by Eco RI digestion of the recombinant pUC19 plasmid, 32 P-labeled, and subjected to gel mobility shift assay. In the presence of AdpA-H (0.2 μg), AdBS1 is shifted. The positions of AdpA-H-bound (solid triangle) and free (open triangle) probes are shown.
Figure Legend Snippet: Gel mobility shift-PCR for isolation of DNA fragments recognized and bound by AdpA-H (A) and gel mobility shift of AdBS1 caused by AdpA-H (B). (A) The S. griseus chromosomal DNA of 300 to 500 bp obtained after Hae III digestion was sandwiched by the catch linkers, 32 P-labeled, mixed and incubated with AdpA-H, and run on a polyacrylamide gel. The amounts of AdpA-H used were 0.02 μg (lane 2), 0.2 μg (lane 3), and 1 μg (lane 4). Lane 1 is a control lane in which there was no AdpA-H. The DNA fragments retarded were recovered and subjected to a second cycle and further cycles. The mobility shift patterns after the second and third cycles are presented, showing the presence of retarded signals. The opposing arrows show the area from which DNA was extracted; the upper position was determined with a 500-bp DNA fragment, including the AdpA-binding site for strR , and the lower position was determined with a 300-bp fragment including the same AdpA-binding site, as described in Materials and Methods. (B) AdBS1 was excised by Eco RI digestion of the recombinant pUC19 plasmid, 32 P-labeled, and subjected to gel mobility shift assay. In the presence of AdpA-H (0.2 μg), AdBS1 is shifted. The positions of AdpA-H-bound (solid triangle) and free (open triangle) probes are shown.

Techniques Used: Mobility Shift, Polymerase Chain Reaction, Isolation, Labeling, Incubation, Binding Assay, Recombinant, Plasmid Preparation

10) Product Images from "Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose"

Article Title: Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose

Journal: PLoS ONE

doi: 10.1371/journal.pone.0082624

Gel analysis of RNA-primed MPRCA products to detect the contaminating DNA in Phi29 DNA polymerase. ( A ) DNA amplification with Phi29 DNA polymerase prepared by our procedure. ( B ) DNA amplification with commercially available Phi29 DNA polymerase (Epicentre, Lot No. 10710). ( C ) DNA amplification with Phi29 DNA polymerase prepared by DNase-treatment. All gel images show the Bam HI/ Eco RI double digested amplification products. Black arrow indicates the specific amplification products from pUC19; M, AccuRuler 1-kb DNA RTU ladder (Maestrogen). All reactions were repeated three times or more; typical results are shown.
Figure Legend Snippet: Gel analysis of RNA-primed MPRCA products to detect the contaminating DNA in Phi29 DNA polymerase. ( A ) DNA amplification with Phi29 DNA polymerase prepared by our procedure. ( B ) DNA amplification with commercially available Phi29 DNA polymerase (Epicentre, Lot No. 10710). ( C ) DNA amplification with Phi29 DNA polymerase prepared by DNase-treatment. All gel images show the Bam HI/ Eco RI double digested amplification products. Black arrow indicates the specific amplification products from pUC19; M, AccuRuler 1-kb DNA RTU ladder (Maestrogen). All reactions were repeated three times or more; typical results are shown.

Techniques Used: Amplification

11) Product Images from "Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose"

Article Title: Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose

Journal: PLoS ONE

doi: 10.1371/journal.pone.0082624

Gel analysis of RNA-primed MPRCA products to detect the contaminating DNA in Phi29 DNA polymerase. ( A ) DNA amplification with Phi29 DNA polymerase prepared by our procedure. ( B ) DNA amplification with commercially available Phi29 DNA polymerase (Epicentre, Lot No. 10710). ( C ) DNA amplification with Phi29 DNA polymerase prepared by DNase-treatment. All gel images show the Bam HI/ Eco RI double digested amplification products. Black arrow indicates the specific amplification products from pUC19; M, AccuRuler 1-kb DNA RTU ladder (Maestrogen). All reactions were repeated three times or more; typical results are shown.
Figure Legend Snippet: Gel analysis of RNA-primed MPRCA products to detect the contaminating DNA in Phi29 DNA polymerase. ( A ) DNA amplification with Phi29 DNA polymerase prepared by our procedure. ( B ) DNA amplification with commercially available Phi29 DNA polymerase (Epicentre, Lot No. 10710). ( C ) DNA amplification with Phi29 DNA polymerase prepared by DNase-treatment. All gel images show the Bam HI/ Eco RI double digested amplification products. Black arrow indicates the specific amplification products from pUC19; M, AccuRuler 1-kb DNA RTU ladder (Maestrogen). All reactions were repeated three times or more; typical results are shown.

Techniques Used: Amplification

12) Product Images from "BLV-CoCoMo-qPCR: Quantitation of bovine leukemia virus proviral load using the CoCoMo algorithm"

Article Title: BLV-CoCoMo-qPCR: Quantitation of bovine leukemia virus proviral load using the CoCoMo algorithm

Journal: Retrovirology

doi: 10.1186/1742-4690-7-91

Evaluation of the specificity of the BLV-CoCoMo-qPCR primers . (A) Real-time PCR using the CoCoMo 6 and CoCoMo 81 primers from the BLV-CoCoMo-qPCR was performed using 0.3 ng of the following infectious molecular clones: BLV (pBLV-IF, lane 2); HTLV-1 (pK30, lane 3); HIV-1 (pNL4-3, lane 4); SIV (pSIVmac239/WT, lane 5); MMTV (hybrid MMTV, lane 6); M-MLV (pL-4, lane 7); and the plasmids pUC18 (lane 8), pUC19 (lane 9), pBR322 (lane 10), and pBluescript SK(+) (lane 11). PCR products were subjected to 3% agarose gel electrophoresis. Lane 1, DNA marker Φ × 174- Hae III digest. A PCR product 168 bp in length is indicated by an arrow. (B) The number of BLV provirus copies in 1 μg of DNA from each DNA sample is indicated by lowercase. Values represent the mean ± standard deviation (SD) of the results of three independent experiments.
Figure Legend Snippet: Evaluation of the specificity of the BLV-CoCoMo-qPCR primers . (A) Real-time PCR using the CoCoMo 6 and CoCoMo 81 primers from the BLV-CoCoMo-qPCR was performed using 0.3 ng of the following infectious molecular clones: BLV (pBLV-IF, lane 2); HTLV-1 (pK30, lane 3); HIV-1 (pNL4-3, lane 4); SIV (pSIVmac239/WT, lane 5); MMTV (hybrid MMTV, lane 6); M-MLV (pL-4, lane 7); and the plasmids pUC18 (lane 8), pUC19 (lane 9), pBR322 (lane 10), and pBluescript SK(+) (lane 11). PCR products were subjected to 3% agarose gel electrophoresis. Lane 1, DNA marker Φ × 174- Hae III digest. A PCR product 168 bp in length is indicated by an arrow. (B) The number of BLV provirus copies in 1 μg of DNA from each DNA sample is indicated by lowercase. Values represent the mean ± standard deviation (SD) of the results of three independent experiments.

Techniques Used: Real-time Polymerase Chain Reaction, Clone Assay, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Marker, Standard Deviation

13) Product Images from "Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose"

Article Title: Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose

Journal: PLoS ONE

doi: 10.1371/journal.pone.0082624

Gel analysis of RNA-primed MPRCA products to detect the contaminating DNA in Phi29 DNA polymerase. ( A ) DNA amplification with Phi29 DNA polymerase prepared by our procedure. ( B ) DNA amplification with commercially available Phi29 DNA polymerase (Epicentre, Lot No. 10710). ( C ) DNA amplification with Phi29 DNA polymerase prepared by DNase-treatment. All gel images show the Bam HI/ Eco RI double digested amplification products. Black arrow indicates the specific amplification products from pUC19; M, AccuRuler 1-kb DNA RTU ladder (Maestrogen). All reactions were repeated three times or more; typical results are shown.
Figure Legend Snippet: Gel analysis of RNA-primed MPRCA products to detect the contaminating DNA in Phi29 DNA polymerase. ( A ) DNA amplification with Phi29 DNA polymerase prepared by our procedure. ( B ) DNA amplification with commercially available Phi29 DNA polymerase (Epicentre, Lot No. 10710). ( C ) DNA amplification with Phi29 DNA polymerase prepared by DNase-treatment. All gel images show the Bam HI/ Eco RI double digested amplification products. Black arrow indicates the specific amplification products from pUC19; M, AccuRuler 1-kb DNA RTU ladder (Maestrogen). All reactions were repeated three times or more; typical results are shown.

Techniques Used: Amplification

14) Product Images from "A reduced genome decreases the host carrying capacity for foreign DNA"

Article Title: A reduced genome decreases the host carrying capacity for foreign DNA

Journal: Microbial Cell Factories

doi: 10.1186/1475-2859-13-49

Contributions of plasmids to cell growth. A . Schematic drawing of the plasmids. All plasmids (pUC-S, pUC-M and pUC-L) were derived from pUC19. The lengths of S, M and L represent the plasmid sizes of 2,334, 6,426 and 9,573 bp, respectively. The site of initiation for replication and the ampicillin resistance gene are indicated as ori and bla , respectively. B . Cell growth rates. The exponential growth rates of E. coli strains MG1655 (upper panel) and MDS42 (lower panel) in a minimal medium are shown for different temperatures. The green, blue and red colors indicate the cells bearing the plasmids S, M and L, respectively. The strains that did not contain plasmids, which were used as controls ( i.e. , native growth fitness), are shown in black. The bars represent the standard errors of triplicates. Statistic significance is indicated (*, p
Figure Legend Snippet: Contributions of plasmids to cell growth. A . Schematic drawing of the plasmids. All plasmids (pUC-S, pUC-M and pUC-L) were derived from pUC19. The lengths of S, M and L represent the plasmid sizes of 2,334, 6,426 and 9,573 bp, respectively. The site of initiation for replication and the ampicillin resistance gene are indicated as ori and bla , respectively. B . Cell growth rates. The exponential growth rates of E. coli strains MG1655 (upper panel) and MDS42 (lower panel) in a minimal medium are shown for different temperatures. The green, blue and red colors indicate the cells bearing the plasmids S, M and L, respectively. The strains that did not contain plasmids, which were used as controls ( i.e. , native growth fitness), are shown in black. The bars represent the standard errors of triplicates. Statistic significance is indicated (*, p

Techniques Used: Derivative Assay, Plasmid Preparation

15) Product Images from "The Probiotic Escherichia coli Strain Nissle 1917 Combats Lambdoid Bacteriophages stx and λ"

Article Title: The Probiotic Escherichia coli Strain Nissle 1917 Combats Lambdoid Bacteriophages stx and λ

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2018.00929

Determination of the protection in MG1655 recombinant strains toward lambdoid phage infection. MG1655 was transformed with pUC19 (MG1655R) with or without the phage repressor ( pr ) gene sequence of EcN (MG1655R pr ). Serial dilutions of stx -phages (A) or lambda-phages (B) in 0.9% saline were dropped on EcN, MG1655 or MG1655 recombinants lawns. Lysis of the respective bacterial strain is visible as lysis zone or individual plaques. UD, undiluted, −1 to −7, 1:10 dilution series.
Figure Legend Snippet: Determination of the protection in MG1655 recombinant strains toward lambdoid phage infection. MG1655 was transformed with pUC19 (MG1655R) with or without the phage repressor ( pr ) gene sequence of EcN (MG1655R pr ). Serial dilutions of stx -phages (A) or lambda-phages (B) in 0.9% saline were dropped on EcN, MG1655 or MG1655 recombinants lawns. Lysis of the respective bacterial strain is visible as lysis zone or individual plaques. UD, undiluted, −1 to −7, 1:10 dilution series.

Techniques Used: Recombinant, Infection, Transformation Assay, Sequencing, Lysis

Related Articles

Clone Assay:

Article Title: BLV-CoCoMo-qPCR: Quantitation of bovine leukemia virus proviral load using the CoCoMo algorithm
Article Snippet: .. Additional clones used included a BLV infectious clone, pBLV-IF [ ]; a HTLV-1 infectious clone, pK30 [ ]; a HIV-1 infectious clone, pNL4-3 [ ]; a SIV infectious clone, SIVmac239/WT [ ]; a hybrid MMTV provirus plasmid [ ]; a M-MLV infectious clone, pL-4 [ ] and plasmids including pUC18 (Takara Bio Inc., Tokyo, Japan), pUC19 (Takara Bio Inc.), and pBR322 (Promega). .. Calculation of copy number by the serial dilution method pBLV-LTR/SK and pBoLA-DRA/SK were digested with Sca I and purified using a Sephadex G-50 column (GE Healthcare Japan, Tokyo, Japan).

Article Title: A reduced genome decreases the host carrying capacity for foreign DNA
Article Snippet: .. The lacZ region of pUC19 was also removed using the In-Fusion HD Cloning Kit (Clontech) but with a different primer set (pUC19_del_lacZ_linearize_Fw and pUC19_del_lacZ_linearize_Rv2) , resulting in a 2,334-bp-long fragment, the same length as pUC-S. .. The two fragments were ligated using the In-Fusion HD Cloning Kit.

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression *Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression * S⃞
Article Snippet: .. First, a plasmid DNA, pUC(AT), containing a cruciform structure was digested with ttMutS2. pUC(AT) was made by replacing the multiple cloning site sequence of pUC19 with 40-bp A/T repeats and used to assay the junction-resolving or structure-specific nicking endonuclease activity ( ). .. As shown in , ttMutS2 digested pUC(AT) more preferably than pUC19, a normal plasmid DNA, whereas a negative control DNase I equally digested the two kinds of plasmid DNAs ( ).

Article Title: A reduced genome decreases the host carrying capacity for foreign DNA
Article Snippet: .. Plasmid construction The lacZ region of pUC19 was removed using the In-Fusion HD Cloning Kit (Clontech) and the pUC19_del_lacZ_Fw and pUC19_del_lacZ_Rv primers. .. Both colony PCR and blue-white selection were performed to verify the deletion.

Article Title: The Probiotic Escherichia coli Strain Nissle 1917 Combats Lambdoid Bacteriophages stx and λ
Article Snippet: .. The amplicons were cloned into pUC19 using the In-fusion cloning Kit (Takara Bio Europe, France). .. The E. coli K-12 strain MG1655 was transformed with pUC19 and the pUC19 harboring the phage repressor (pUC19_ pr ).

Negative Control:

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression *Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression * S⃞
Article Snippet: .. As shown in , ttMutS2 digested pUC(AT) more preferably than pUC19, a normal plasmid DNA, whereas a negative control DNase I equally digested the two kinds of plasmid DNAs ( ). .. Second, three kinds of branched DNA structures, the immobile Holliday junction, and the D-loop and loop structures, were incubated with ttMutS2.

Amplification:

Article Title: Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose
Article Snippet: Verification of Contaminating DNA by RNA-primed MPRCA To detect contaminating DNA in the polymerase, RNA-primed MPRCA was carried out with 10–104 copies of pUC19 (Takara) or without the DNA template (Ultra PURE™ dDW). .. Then, 2× amplification premix (10 µL) was added, yielding a final concentration of 35 mM Tris-HCl (pH 7.5), 50 mM KCl, 14 mM MgCl2 , 20 mM (NH4 )2 SO4 , 5 mM DTT, 1 mM dNTPs, 0.002 U of inorganic pyrophosphatase (Roche) and 100 ng of the purified Phi29 polymerases or RepliPhi™ Phi29 DNA polymerase (Lot No. 10710).

Article Title: Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose
Article Snippet: .. The amplification products were confirmed by agarose gel electrophoresis after Bam HI/Eco RI double-digestion because specifically amplified products from pUC19 would be found as an obvious band corresponding to the linear form of pUC19 (approximately 2.7 kb) by the digestion , . .. However, non-specific amplification products emerge as fragments with other sizes, or are migrated at over 20 kbp , .

Article Title: Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose
Article Snippet: .. Moreover, the limit of specific amplification using our DNase-treated polymerase was reduced to 103 copies of pUC19 (approximately 3 femtograms, ). .. This result also indicates that contaminating DNA in the polymerase reduces the efficiency of the amplification of the target DNA.

Article Title: Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose
Article Snippet: .. As a result, no amplification product were found in plural NTCs using the purified Phi29 DNA polymerase, while 2.7 kb fragment was found in all positive controls using pUC19 as a template DNA ( ). .. This result indicates that this purified Phi29 DNA polymerase contains little amplifiable DNA, and that RNA-primed MPRCA using this purified Phi29 DNA polymerase has the potential to reproducibly amplify ten copies of pUC19 (approximately 30 attograms, ) without any byproducts and reducing reaction volume as previously reported .

Article Title: A reduced genome decreases the host carrying capacity for foreign DNA
Article Snippet: A GFP sequence that includes the promoter Ptet was amplified from the pBRgalKGR plasmid (a pBR322 derivative) [ , ] using the pBR_gfp_kanR_Fw and pBR_gfp_kanR_Rv primers. .. The lacZ region of pUC19 was also removed using the In-Fusion HD Cloning Kit (Clontech) but with a different primer set (pUC19_del_lacZ_linearize_Fw and pUC19_del_lacZ_linearize_Rv2) , resulting in a 2,334-bp-long fragment, the same length as pUC-S.

Article Title: A reduced genome decreases the host carrying capacity for foreign DNA
Article Snippet: Plasmid construction The lacZ region of pUC19 was removed using the In-Fusion HD Cloning Kit (Clontech) and the pUC19_del_lacZ_Fw and pUC19_del_lacZ_Rv primers. .. The resultant plasmid had a length of 2,334 bp and was named pUC-S. A DNA sequence (4,092 bp) of pSC101 was amplified with the pSC101_seq_Fw and pSC101_seq_Rv primers.

Article Title: The Probiotic Escherichia coli Strain Nissle 1917 Combats Lambdoid Bacteriophages stx and λ
Article Snippet: The pr was amplified from the EcN genome using the primers PR_P2_fwd/PR_P1_rev (Table ). .. The amplicons were cloned into pUC19 using the In-fusion cloning Kit (Takara Bio Europe, France).

Agarose Gel Electrophoresis:

Article Title: Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose
Article Snippet: .. The amplification products were confirmed by agarose gel electrophoresis after Bam HI/Eco RI double-digestion because specifically amplified products from pUC19 would be found as an obvious band corresponding to the linear form of pUC19 (approximately 2.7 kb) by the digestion , . .. However, non-specific amplification products emerge as fragments with other sizes, or are migrated at over 20 kbp , .

Plaque Assay:

Article Title: The Probiotic Escherichia coli Strain Nissle 1917 Combats Lambdoid Bacteriophages stx and λ
Article Snippet: The amplicons were cloned into pUC19 using the In-fusion cloning Kit (Takara Bio Europe, France). .. The transformants were screened with pUC19_M13 fwd/rev primers (Table ) and the importance of this gene in the protection of MG1655 phage infection was determined with the phage plaque assay.

Mutagenesis:

Article Title: An A-Factor-Dependent Extracytoplasmic Function Sigma Factor (?AdsA) That Is Essential for Morphological Development in Streptomyces griseus
Article Snippet: The wild-type strain S. griseus IFO13350 and an A-factor-deficient mutant strain HH1 were described previously ( ). .. Escherichia coli JM109 and pUC19 ( ) for DNA manipulation were purchased from Takara Shuzo.

Sequencing:

Article Title: Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V
Article Snippet: .. Plasmids and strains Target plasmid vectors suitable for propagation in E. coli were pUC18 and pUC19 [ ], pIRES2-EGFP (Clontech, Mountain View, CA, USA) and pBluescript II KS(+) [GenBank: X52327.1]. pSB1C3 and the RFP coding device BBa_J04450 were obtained from the Registry of Standard Biological Parts [ ]. pAR200d-Mitf_FL is a derivative of pQE16 (Qiagen, Hilden, Germany) containing the coding sequence of the Mus musculus microphthalmia-associated transcription factor (Mitf)[GenBank: Z23066.1]. .. Competent Escherichia coli XL-1 Blue (Stratagene; now Agilent Technologies, Böblingen, Germany) and BL21-cells (Novagen, Darmstadt, Germany) were prepared by standard CaCl2 protocol.

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression *Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression * S⃞
Article Snippet: The length of the DNA product was subsequently determined by analysis on an 11% polyacrylamide sequencing gel containing 8 m urea and 1× TBE buffer. .. The 5 ng/μl pUC19 (Takara) or pUC(AT) (New England Biolabs) plasmid DNA was incubated with or without freshly prepared ttMutS2 or bovine DNase I (Takara) in 50 m m Tris-HCl, pH 7.5, 100 m m KCl, 5 m m MgCl2 , 0.1 mg/ml BSA, and 1 m m dithiothreitol at 37 °C.

Article Title: BLV-CoCoMo-qPCR: Quantitation of bovine leukemia virus proviral load using the CoCoMo algorithm
Article Snippet: The Xba I-Xba I fragment including the MR1 sequence was then subcloned into pBluescript II SK (+) (Stratagene). .. Additional clones used included a BLV infectious clone, pBLV-IF [ ]; a HTLV-1 infectious clone, pK30 [ ]; a HIV-1 infectious clone, pNL4-3 [ ]; a SIV infectious clone, SIVmac239/WT [ ]; a hybrid MMTV provirus plasmid [ ]; a M-MLV infectious clone, pL-4 [ ] and plasmids including pUC18 (Takara Bio Inc., Tokyo, Japan), pUC19 (Takara Bio Inc.), and pBR322 (Promega).

Article Title: A reduced genome decreases the host carrying capacity for foreign DNA
Article Snippet: A GFP sequence that includes the promoter Ptet was amplified from the pBRgalKGR plasmid (a pBR322 derivative) [ , ] using the pBR_gfp_kanR_Fw and pBR_gfp_kanR_Rv primers. .. The lacZ region of pUC19 was also removed using the In-Fusion HD Cloning Kit (Clontech) but with a different primer set (pUC19_del_lacZ_linearize_Fw and pUC19_del_lacZ_linearize_Rv2) , resulting in a 2,334-bp-long fragment, the same length as pUC-S.

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression *Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression * S⃞
Article Snippet: .. First, a plasmid DNA, pUC(AT), containing a cruciform structure was digested with ttMutS2. pUC(AT) was made by replacing the multiple cloning site sequence of pUC19 with 40-bp A/T repeats and used to assay the junction-resolving or structure-specific nicking endonuclease activity ( ). .. As shown in , ttMutS2 digested pUC(AT) more preferably than pUC19, a normal plasmid DNA, whereas a negative control DNase I equally digested the two kinds of plasmid DNAs ( ).

Article Title: A reduced genome decreases the host carrying capacity for foreign DNA
Article Snippet: Plasmid construction The lacZ region of pUC19 was removed using the In-Fusion HD Cloning Kit (Clontech) and the pUC19_del_lacZ_Fw and pUC19_del_lacZ_Rv primers. .. The resultant plasmid had a length of 2,334 bp and was named pUC-S. A DNA sequence (4,092 bp) of pSC101 was amplified with the pSC101_seq_Fw and pSC101_seq_Rv primers.

Infection:

Article Title: The Probiotic Escherichia coli Strain Nissle 1917 Combats Lambdoid Bacteriophages stx and λ
Article Snippet: The amplicons were cloned into pUC19 using the In-fusion cloning Kit (Takara Bio Europe, France). .. The transformants were screened with pUC19_M13 fwd/rev primers (Table ) and the importance of this gene in the protection of MG1655 phage infection was determined with the phage plaque assay.

Purification:

Article Title: Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose
Article Snippet: Verification of Contaminating DNA by RNA-primed MPRCA To detect contaminating DNA in the polymerase, RNA-primed MPRCA was carried out with 10–104 copies of pUC19 (Takara) or without the DNA template (Ultra PURE™ dDW). .. Then, 2× amplification premix (10 µL) was added, yielding a final concentration of 35 mM Tris-HCl (pH 7.5), 50 mM KCl, 14 mM MgCl2 , 20 mM (NH4 )2 SO4 , 5 mM DTT, 1 mM dNTPs, 0.002 U of inorganic pyrophosphatase (Roche) and 100 ng of the purified Phi29 polymerases or RepliPhi™ Phi29 DNA polymerase (Lot No. 10710).

Article Title: Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose
Article Snippet: .. As a result, no amplification product were found in plural NTCs using the purified Phi29 DNA polymerase, while 2.7 kb fragment was found in all positive controls using pUC19 as a template DNA ( ). .. This result indicates that this purified Phi29 DNA polymerase contains little amplifiable DNA, and that RNA-primed MPRCA using this purified Phi29 DNA polymerase has the potential to reproducibly amplify ten copies of pUC19 (approximately 30 attograms, ) without any byproducts and reducing reaction volume as previously reported .

Article Title: Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose
Article Snippet: .. This result indicates that this purified Phi29 DNA polymerase contains little amplifiable DNA, and that RNA-primed MPRCA using this purified Phi29 DNA polymerase has the potential to reproducibly amplify ten copies of pUC19 (approximately 30 attograms, ) without any byproducts and reducing reaction volume as previously reported . .. By contrast, non-specific amplification products were found in all NTCs and positive controls using the commercially available Phi29 DNA polymerases (Epicentre Lot.No.

Produced:

Article Title: A reduced genome decreases the host carrying capacity for foreign DNA
Article Snippet: Thus, all three plasmids that were produced had a common site of initiation for replication derived from pUC19, and carried a single gene for ampicillin resistance. .. The lacZ region of pUC19 was also removed using the In-Fusion HD Cloning Kit (Clontech) but with a different primer set (pUC19_del_lacZ_linearize_Fw and pUC19_del_lacZ_linearize_Rv2) , resulting in a 2,334-bp-long fragment, the same length as pUC-S.

Concentration Assay:

Article Title: Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose
Article Snippet: Verification of Contaminating DNA by RNA-primed MPRCA To detect contaminating DNA in the polymerase, RNA-primed MPRCA was carried out with 10–104 copies of pUC19 (Takara) or without the DNA template (Ultra PURE™ dDW). .. Then, 2× amplification premix (10 µL) was added, yielding a final concentration of 35 mM Tris-HCl (pH 7.5), 50 mM KCl, 14 mM MgCl2 , 20 mM (NH4 )2 SO4 , 5 mM DTT, 1 mM dNTPs, 0.002 U of inorganic pyrophosphatase (Roche) and 100 ng of the purified Phi29 polymerases or RepliPhi™ Phi29 DNA polymerase (Lot No. 10710).

Incubation:

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression *Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression * S⃞
Article Snippet: .. The 5 ng/μl pUC19 (Takara) or pUC(AT) (New England Biolabs) plasmid DNA was incubated with or without freshly prepared ttMutS2 or bovine DNase I (Takara) in 50 m m Tris-HCl, pH 7.5, 100 m m KCl, 5 m m MgCl2 , 0.1 mg/ml BSA, and 1 m m dithiothreitol at 37 °C. ..

Selection:

Article Title: A reduced genome decreases the host carrying capacity for foreign DNA
Article Snippet: Plasmid construction The lacZ region of pUC19 was removed using the In-Fusion HD Cloning Kit (Clontech) and the pUC19_del_lacZ_Fw and pUC19_del_lacZ_Rv primers. .. Both colony PCR and blue-white selection were performed to verify the deletion.

Activity Assay:

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression *Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression * S⃞
Article Snippet: .. First, a plasmid DNA, pUC(AT), containing a cruciform structure was digested with ttMutS2. pUC(AT) was made by replacing the multiple cloning site sequence of pUC19 with 40-bp A/T repeats and used to assay the junction-resolving or structure-specific nicking endonuclease activity ( ). .. As shown in , ttMutS2 digested pUC(AT) more preferably than pUC19, a normal plasmid DNA, whereas a negative control DNase I equally digested the two kinds of plasmid DNAs ( ).

Plasmid Preparation:

Article Title: Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V
Article Snippet: .. Plasmids and strains Target plasmid vectors suitable for propagation in E. coli were pUC18 and pUC19 [ ], pIRES2-EGFP (Clontech, Mountain View, CA, USA) and pBluescript II KS(+) [GenBank: X52327.1]. pSB1C3 and the RFP coding device BBa_J04450 were obtained from the Registry of Standard Biological Parts [ ]. pAR200d-Mitf_FL is a derivative of pQE16 (Qiagen, Hilden, Germany) containing the coding sequence of the Mus musculus microphthalmia-associated transcription factor (Mitf)[GenBank: Z23066.1]. .. Competent Escherichia coli XL-1 Blue (Stratagene; now Agilent Technologies, Böblingen, Germany) and BL21-cells (Novagen, Darmstadt, Germany) were prepared by standard CaCl2 protocol.

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression *Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression * S⃞
Article Snippet: .. The 5 ng/μl pUC19 (Takara) or pUC(AT) (New England Biolabs) plasmid DNA was incubated with or without freshly prepared ttMutS2 or bovine DNase I (Takara) in 50 m m Tris-HCl, pH 7.5, 100 m m KCl, 5 m m MgCl2 , 0.1 mg/ml BSA, and 1 m m dithiothreitol at 37 °C. ..

Article Title: BLV-CoCoMo-qPCR: Quantitation of bovine leukemia virus proviral load using the CoCoMo algorithm
Article Snippet: .. Additional clones used included a BLV infectious clone, pBLV-IF [ ]; a HTLV-1 infectious clone, pK30 [ ]; a HIV-1 infectious clone, pNL4-3 [ ]; a SIV infectious clone, SIVmac239/WT [ ]; a hybrid MMTV provirus plasmid [ ]; a M-MLV infectious clone, pL-4 [ ] and plasmids including pUC18 (Takara Bio Inc., Tokyo, Japan), pUC19 (Takara Bio Inc.), and pBR322 (Promega). .. Calculation of copy number by the serial dilution method pBLV-LTR/SK and pBoLA-DRA/SK were digested with Sca I and purified using a Sephadex G-50 column (GE Healthcare Japan, Tokyo, Japan).

Article Title: A reduced genome decreases the host carrying capacity for foreign DNA
Article Snippet: Paragraph title: Plasmid construction ... The lacZ region of pUC19 was also removed using the In-Fusion HD Cloning Kit (Clontech) but with a different primer set (pUC19_del_lacZ_linearize_Fw and pUC19_del_lacZ_linearize_Rv2) , resulting in a 2,334-bp-long fragment, the same length as pUC-S.

Article Title: An A-Factor-Dependent Extracytoplasmic Function Sigma Factor (?AdsA) That Is Essential for Morphological Development in Streptomyces griseus
Article Snippet: Escherichia coli JM109 and pUC19 ( ) for DNA manipulation were purchased from Takara Shuzo. .. Plasmid pET26b(+) and E. coli BL21(DE3) (Novagen) were used for producing histidine-tagged AdpA.

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression *Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression * S⃞
Article Snippet: .. First, a plasmid DNA, pUC(AT), containing a cruciform structure was digested with ttMutS2. pUC(AT) was made by replacing the multiple cloning site sequence of pUC19 with 40-bp A/T repeats and used to assay the junction-resolving or structure-specific nicking endonuclease activity ( ). .. As shown in , ttMutS2 digested pUC(AT) more preferably than pUC19, a normal plasmid DNA, whereas a negative control DNase I equally digested the two kinds of plasmid DNAs ( ).

Article Title: A reduced genome decreases the host carrying capacity for foreign DNA
Article Snippet: .. Plasmid construction The lacZ region of pUC19 was removed using the In-Fusion HD Cloning Kit (Clontech) and the pUC19_del_lacZ_Fw and pUC19_del_lacZ_Rv primers. .. Both colony PCR and blue-white selection were performed to verify the deletion.

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression *Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression * S⃞
Article Snippet: .. As shown in , ttMutS2 digested pUC(AT) more preferably than pUC19, a normal plasmid DNA, whereas a negative control DNase I equally digested the two kinds of plasmid DNAs ( ). .. Second, three kinds of branched DNA structures, the immobile Holliday junction, and the D-loop and loop structures, were incubated with ttMutS2.

Expressing:

Article Title: BLV-CoCoMo-qPCR: Quantitation of bovine leukemia virus proviral load using the CoCoMo algorithm
Article Snippet: To generate pBoLA-DRA/SK, which includes a full-length bovine DRA gene, we digested MR1 from the mammalian expression vector pCDM8 [ ] with Xba I. .. Additional clones used included a BLV infectious clone, pBLV-IF [ ]; a HTLV-1 infectious clone, pK30 [ ]; a HIV-1 infectious clone, pNL4-3 [ ]; a SIV infectious clone, SIVmac239/WT [ ]; a hybrid MMTV provirus plasmid [ ]; a M-MLV infectious clone, pL-4 [ ] and plasmids including pUC18 (Takara Bio Inc., Tokyo, Japan), pUC19 (Takara Bio Inc.), and pBR322 (Promega).

Nuclease Assay:

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression *Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression * S⃞
Article Snippet: Nuclease Assay Using Plasmid DNA —The assay was performed as described previously ( ). .. The 5 ng/μl pUC19 (Takara) or pUC(AT) (New England Biolabs) plasmid DNA was incubated with or without freshly prepared ttMutS2 or bovine DNase I (Takara) in 50 m m Tris-HCl, pH 7.5, 100 m m KCl, 5 m m MgCl2 , 0.1 mg/ml BSA, and 1 m m dithiothreitol at 37 °C.

Polymerase Chain Reaction:

Article Title: BLV-CoCoMo-qPCR: Quantitation of bovine leukemia virus proviral load using the CoCoMo algorithm
Article Snippet: PCR products were cloned into pBluescript II SK (+) (Stratagene, La Jolla, CA). .. Additional clones used included a BLV infectious clone, pBLV-IF [ ]; a HTLV-1 infectious clone, pK30 [ ]; a HIV-1 infectious clone, pNL4-3 [ ]; a SIV infectious clone, SIVmac239/WT [ ]; a hybrid MMTV provirus plasmid [ ]; a M-MLV infectious clone, pL-4 [ ] and plasmids including pUC18 (Takara Bio Inc., Tokyo, Japan), pUC19 (Takara Bio Inc.), and pBR322 (Promega).

Article Title: A reduced genome decreases the host carrying capacity for foreign DNA
Article Snippet: Plasmid construction The lacZ region of pUC19 was removed using the In-Fusion HD Cloning Kit (Clontech) and the pUC19_del_lacZ_Fw and pUC19_del_lacZ_Rv primers. .. Both colony PCR and blue-white selection were performed to verify the deletion.

Transformation Assay:

Article Title: Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V
Article Snippet: Plasmids and strains Target plasmid vectors suitable for propagation in E. coli were pUC18 and pUC19 [ ], pIRES2-EGFP (Clontech, Mountain View, CA, USA) and pBluescript II KS(+) [GenBank: X52327.1]. pSB1C3 and the RFP coding device BBa_J04450 were obtained from the Registry of Standard Biological Parts [ ]. pAR200d-Mitf_FL is a derivative of pQE16 (Qiagen, Hilden, Germany) containing the coding sequence of the Mus musculus microphthalmia-associated transcription factor (Mitf)[GenBank: Z23066.1]. .. Transformation efficiencies determined as cfu per μg pUC18 plasmid DNA reached 1–3 × 106 for XL-1 Blue and 3–4 × 106 for BL21.

Article Title: The Probiotic Escherichia coli Strain Nissle 1917 Combats Lambdoid Bacteriophages stx and λ
Article Snippet: The amplicons were cloned into pUC19 using the In-fusion cloning Kit (Takara Bio Europe, France). .. The E. coli K-12 strain MG1655 was transformed with pUC19 and the pUC19 harboring the phage repressor (pUC19_ pr ).

Derivative Assay:

Article Title: A reduced genome decreases the host carrying capacity for foreign DNA
Article Snippet: Thus, all three plasmids that were produced had a common site of initiation for replication derived from pUC19, and carried a single gene for ampicillin resistance. .. The lacZ region of pUC19 was also removed using the In-Fusion HD Cloning Kit (Clontech) but with a different primer set (pUC19_del_lacZ_linearize_Fw and pUC19_del_lacZ_linearize_Rv2) , resulting in a 2,334-bp-long fragment, the same length as pUC-S.

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  • 77
    TaKaRa puc18 dna
    Topological inactivation activities. Lane 1 indicated <t>pUC18</t> as a control; Lane 2 indicated the products of pUC18 <t>DNA</t> treated with α-MMC; Lane M indicated DNA ladder; Lane 3 indicated the products of pUC18 DNA treated with MAP30.
    Puc18 Dna, supplied by TaKaRa, used in various techniques. Bioz Stars score: 77/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/puc18 dna/product/TaKaRa
    Average 77 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    puc18 dna - by Bioz Stars, 2020-02
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    90
    TaKaRa materials plasmid puc19 dna
    Histograms and electropherograms (the right side figure) representing cleavage of <t>pUC19</t> plasmid <t>DNA</t> (0.008 µg/µL) by different concentrations of 1b (pH = 7.4) and 1c (pH = 7.4) in buffer (5 mM Tris-HCl/10 mM NaCl) at 37 °C for 6 h. ( A ) Complex 1b ; Lanes 1–6: 6.25 × 10 − 5 , 3.13 × 10 − 5 , 6.25 × 10 − 6 , 3.13 × 10 − 6 , 6.25 × 10 − 7 , 3.13 × 10 − 7 mol/L, Lane 7 = DNA control, respectively; ( B ) Complex 1c ; Lanes 1–6: 6.25 × 10 − 5 , 3.13 × 10 − 5 , 6.25 × 10 − 6 , 3.13 × 10 − 6 , 6.25 × 10 − 7 , 3.13 × 10 − 7 mol/L, Lane 7 = DNA control, respectively.
    Materials Plasmid Puc19 Dna, supplied by TaKaRa, used in various techniques. Bioz Stars score: 90/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/materials plasmid puc19 dna/product/TaKaRa
    Average 90 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    materials plasmid puc19 dna - by Bioz Stars, 2020-02
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    79
    TaKaRa puc19 replication origin
    Design of Level 0 vectors. The backbone is a yeast shuttle vector with a <t>pUC19</t> replication origin, the kanamycin resistance gene nptII for selection in Escherichia coli , a high-copy 2-micron origin for replication and the URA3 marker gene for selection in Saccharomyces cerevisiae . Each Level 0 vector possesses a different combination of homology regions (HR). HR1 gives homology to the Level 1 vector backbone or to the HR2 of the adjacent Level 0 vector. HR2 gives homology to the next Level 0 vector or to the Level 1 vector backbone. These regions are separated by a HindIII-flanked ccdB expression cassette. The HindIII sites are used to release the ccdB cassette and to allow the subsequent insertion of the individual subunits in-between the homology regions by scar-free, overlap-based cloning. The homology regions are flanked by two multiple cloning sites (MCS), containing the five 8-base cutters AscI, SbfI, SwaI, FseI, PmeI to release Level 0 constructs for further cloning into Level 1.
    Puc19 Replication Origin, supplied by TaKaRa, used in various techniques. Bioz Stars score: 79/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 79 stars, based on 1 article reviews
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    Image Search Results


    Topological inactivation activities. Lane 1 indicated pUC18 as a control; Lane 2 indicated the products of pUC18 DNA treated with α-MMC; Lane M indicated DNA ladder; Lane 3 indicated the products of pUC18 DNA treated with MAP30.

    Journal: PLoS ONE

    Article Title: A Novel Method for Simultaneous Production of Two Ribosome-Inactivating Proteins, ?-MMC and MAP30, from Momordica charantia L

    doi: 10.1371/journal.pone.0101998

    Figure Lengend Snippet: Topological inactivation activities. Lane 1 indicated pUC18 as a control; Lane 2 indicated the products of pUC18 DNA treated with α-MMC; Lane M indicated DNA ladder; Lane 3 indicated the products of pUC18 DNA treated with MAP30.

    Article Snippet: LMW Calibration Kit was supplied by SIBAS (Shanghai, China). pUC18 DNA used in detection of topological activity was obtained from TAKARA (Dalian, China).

    Techniques:

    Histograms and electropherograms (the right side figure) representing cleavage of pUC19 plasmid DNA (0.008 µg/µL) by different concentrations of 1b (pH = 7.4) and 1c (pH = 7.4) in buffer (5 mM Tris-HCl/10 mM NaCl) at 37 °C for 6 h. ( A ) Complex 1b ; Lanes 1–6: 6.25 × 10 − 5 , 3.13 × 10 − 5 , 6.25 × 10 − 6 , 3.13 × 10 − 6 , 6.25 × 10 − 7 , 3.13 × 10 − 7 mol/L, Lane 7 = DNA control, respectively; ( B ) Complex 1c ; Lanes 1–6: 6.25 × 10 − 5 , 3.13 × 10 − 5 , 6.25 × 10 − 6 , 3.13 × 10 − 6 , 6.25 × 10 − 7 , 3.13 × 10 − 7 mol/L, Lane 7 = DNA control, respectively.

    Journal: Molecules

    Article Title: DNA Cleavage and Condensation Activities of Mono- and Binuclear Hybrid Complexes and Regulation by Graphene Oxide

    doi: 10.3390/molecules21070920

    Figure Lengend Snippet: Histograms and electropherograms (the right side figure) representing cleavage of pUC19 plasmid DNA (0.008 µg/µL) by different concentrations of 1b (pH = 7.4) and 1c (pH = 7.4) in buffer (5 mM Tris-HCl/10 mM NaCl) at 37 °C for 6 h. ( A ) Complex 1b ; Lanes 1–6: 6.25 × 10 − 5 , 3.13 × 10 − 5 , 6.25 × 10 − 6 , 3.13 × 10 − 6 , 6.25 × 10 − 7 , 3.13 × 10 − 7 mol/L, Lane 7 = DNA control, respectively; ( B ) Complex 1c ; Lanes 1–6: 6.25 × 10 − 5 , 3.13 × 10 − 5 , 6.25 × 10 − 6 , 3.13 × 10 − 6 , 6.25 × 10 − 7 , 3.13 × 10 − 7 mol/L, Lane 7 = DNA control, respectively.

    Article Snippet: Materials Plasmid pUC19 DNA (TaKaRa Biotechnology, Dalian, China), 50 × TAE, 6× loading buffer, gold view dye, and agarose were purchased from Beijing Changsheng Biotechnology Co., Ltd. (Beijing, China).

    Techniques: Plasmid Preparation

    Histograms and electropherograms (the right side figure) representing cleavage of pUC19 plasmid DNA (0.008 µg/µL) in different pH buffer of 2a (6.25 × 10 −7 mol/L), 2b (3.13 × 10 −7 mol/L) and 2d (6.25 × 10 −7 mol/L) (5 mM Tris-HCl/10 mM NaCl) at 37 °C for 6 h. ( A ) Complex 2a; Lanes 1–8: pH = 6.5, 6.8, 7.0, 7.2, 7.4, 7.6, 7.8, 8.0; Lane 9 = DNA control, respectively. ( B ) Complex 2b and Lanes 1–8: pH = 6.5, 6.8, 7.0, 7.2, 7.4, 7.6, 7.8, 8.0 Lane 9 = DNA control, respectively; ( C ) complex 2d; Lanes 1–8: pH = 6.5, 6.8, 7.0, 7.2, 7.4, 7.6, 7.8, 8.0; Lane 9 = DNA control, respectively.

    Journal: Molecules

    Article Title: DNA Cleavage and Condensation Activities of Mono- and Binuclear Hybrid Complexes and Regulation by Graphene Oxide

    doi: 10.3390/molecules21070920

    Figure Lengend Snippet: Histograms and electropherograms (the right side figure) representing cleavage of pUC19 plasmid DNA (0.008 µg/µL) in different pH buffer of 2a (6.25 × 10 −7 mol/L), 2b (3.13 × 10 −7 mol/L) and 2d (6.25 × 10 −7 mol/L) (5 mM Tris-HCl/10 mM NaCl) at 37 °C for 6 h. ( A ) Complex 2a; Lanes 1–8: pH = 6.5, 6.8, 7.0, 7.2, 7.4, 7.6, 7.8, 8.0; Lane 9 = DNA control, respectively. ( B ) Complex 2b and Lanes 1–8: pH = 6.5, 6.8, 7.0, 7.2, 7.4, 7.6, 7.8, 8.0 Lane 9 = DNA control, respectively; ( C ) complex 2d; Lanes 1–8: pH = 6.5, 6.8, 7.0, 7.2, 7.4, 7.6, 7.8, 8.0; Lane 9 = DNA control, respectively.

    Article Snippet: Materials Plasmid pUC19 DNA (TaKaRa Biotechnology, Dalian, China), 50 × TAE, 6× loading buffer, gold view dye, and agarose were purchased from Beijing Changsheng Biotechnology Co., Ltd. (Beijing, China).

    Techniques: Plasmid Preparation

    Electropherograms representing cleavage of pUC19 plasmid DNA (0.008 µg/µL) in buffer of different weight ratios of GO to complex 2c (6.25 × 10 −7 mol/L, 5 mM Tris-HCl/10 mM NaCl, pH = 6.0) at 37 °C for 8 h. Lanes 1–7: complex 2c alone, 0.5, 1.0, 2.0, 3.0, 4.0, 5.0, respectively and Lane 8 is DNA control with GO (0.67 μg/μL), respectively.

    Journal: Molecules

    Article Title: DNA Cleavage and Condensation Activities of Mono- and Binuclear Hybrid Complexes and Regulation by Graphene Oxide

    doi: 10.3390/molecules21070920

    Figure Lengend Snippet: Electropherograms representing cleavage of pUC19 plasmid DNA (0.008 µg/µL) in buffer of different weight ratios of GO to complex 2c (6.25 × 10 −7 mol/L, 5 mM Tris-HCl/10 mM NaCl, pH = 6.0) at 37 °C for 8 h. Lanes 1–7: complex 2c alone, 0.5, 1.0, 2.0, 3.0, 4.0, 5.0, respectively and Lane 8 is DNA control with GO (0.67 μg/μL), respectively.

    Article Snippet: Materials Plasmid pUC19 DNA (TaKaRa Biotechnology, Dalian, China), 50 × TAE, 6× loading buffer, gold view dye, and agarose were purchased from Beijing Changsheng Biotechnology Co., Ltd. (Beijing, China).

    Techniques: Plasmid Preparation

    Electropherograms representing condensation and release of pUC19 plasmid DNA (0.008 µg/µL) in buffer of different weight ratios of GO to complex 2c (5 mM Tris-HCl/10 mM NaCl, pH = 7.4) at 37 °C. Lane 1 is DNA control, Lanes 2–8: 2c (6.25 × 10 −5 mol/L), 2c (3.13 × 10 −5 mol/L), 2c (6.25 × 10 −5 mol/L)/GO (0.67 μg/μL), 2c (6.25 × 10 −5 mol/L)/GO (1.34 μg/μL), 2c (3.13 × 10 −5 mol/L)/GO (0.67 μg/μL), 2c (3.13 × 10 −5 mol/L)/GO (1.34 μg/μL), respectively.

    Journal: Molecules

    Article Title: DNA Cleavage and Condensation Activities of Mono- and Binuclear Hybrid Complexes and Regulation by Graphene Oxide

    doi: 10.3390/molecules21070920

    Figure Lengend Snippet: Electropherograms representing condensation and release of pUC19 plasmid DNA (0.008 µg/µL) in buffer of different weight ratios of GO to complex 2c (5 mM Tris-HCl/10 mM NaCl, pH = 7.4) at 37 °C. Lane 1 is DNA control, Lanes 2–8: 2c (6.25 × 10 −5 mol/L), 2c (3.13 × 10 −5 mol/L), 2c (6.25 × 10 −5 mol/L)/GO (0.67 μg/μL), 2c (6.25 × 10 −5 mol/L)/GO (1.34 μg/μL), 2c (3.13 × 10 −5 mol/L)/GO (0.67 μg/μL), 2c (3.13 × 10 −5 mol/L)/GO (1.34 μg/μL), respectively.

    Article Snippet: Materials Plasmid pUC19 DNA (TaKaRa Biotechnology, Dalian, China), 50 × TAE, 6× loading buffer, gold view dye, and agarose were purchased from Beijing Changsheng Biotechnology Co., Ltd. (Beijing, China).

    Techniques: Plasmid Preparation

    Histograms and electropherograms (the right side figure) representing cleavage of pUC19 plasmid DNA (0.008 µg/µL) by different concentrations of 2b (pH = 7.4), 2c (pH = 7.4) and 2d (pH = 7.4) in buffer (5 mM Tris-HCl/10 mM NaCl) at 37°C for 6 h. ( A ) Complex 2b ; Lanes 1–6: 6.25 × 10 − 5 , 3.13 × 10 − 5 , 6.25 × 10 − 6 , 3.13 × 10 − 6 , 6.25 × 10 − 7 , 3.13 × 10 − 7 mol/L, Lane 7 = DNA control, respectively; ( B ) Complex 2c; Lanes 1–6: 6.25 × 10 − 5 , 3.13 × 10 − 5 , 6.25 × 10 − 6 , 3.13 × 10 − 6 , 6.25 × 10 − 7 , 3.13 × 10 − 7 mol/L, Lane 7 = DNA control, respectively; ( C ) Complex 2d ; Lanes 1–6: 6.25 × 10 − 5 , 3.13 × 10 − 5 , 6.25 × 10 − 6 , 3.13 × 10 − 6 , 6.25 × 10 − 7 , 3.13 × 10 − 7 mol/L, Lane 7 = DNA control, respectively.

    Journal: Molecules

    Article Title: DNA Cleavage and Condensation Activities of Mono- and Binuclear Hybrid Complexes and Regulation by Graphene Oxide

    doi: 10.3390/molecules21070920

    Figure Lengend Snippet: Histograms and electropherograms (the right side figure) representing cleavage of pUC19 plasmid DNA (0.008 µg/µL) by different concentrations of 2b (pH = 7.4), 2c (pH = 7.4) and 2d (pH = 7.4) in buffer (5 mM Tris-HCl/10 mM NaCl) at 37°C for 6 h. ( A ) Complex 2b ; Lanes 1–6: 6.25 × 10 − 5 , 3.13 × 10 − 5 , 6.25 × 10 − 6 , 3.13 × 10 − 6 , 6.25 × 10 − 7 , 3.13 × 10 − 7 mol/L, Lane 7 = DNA control, respectively; ( B ) Complex 2c; Lanes 1–6: 6.25 × 10 − 5 , 3.13 × 10 − 5 , 6.25 × 10 − 6 , 3.13 × 10 − 6 , 6.25 × 10 − 7 , 3.13 × 10 − 7 mol/L, Lane 7 = DNA control, respectively; ( C ) Complex 2d ; Lanes 1–6: 6.25 × 10 − 5 , 3.13 × 10 − 5 , 6.25 × 10 − 6 , 3.13 × 10 − 6 , 6.25 × 10 − 7 , 3.13 × 10 − 7 mol/L, Lane 7 = DNA control, respectively.

    Article Snippet: Materials Plasmid pUC19 DNA (TaKaRa Biotechnology, Dalian, China), 50 × TAE, 6× loading buffer, gold view dye, and agarose were purchased from Beijing Changsheng Biotechnology Co., Ltd. (Beijing, China).

    Techniques: Plasmid Preparation

    Time course of pUC19 DNA (0.008 µg/µL) cleavage promoted by 1b (6.25 × 10 −7 mol/L) in pH = 7.4 buffers (5 mM Tris-HCl/10 mM NaCl) at 37 °C. Lanes 1–6, reaction time 6, 5, 4, 3, 2, 1 h, respectively.

    Journal: Molecules

    Article Title: DNA Cleavage and Condensation Activities of Mono- and Binuclear Hybrid Complexes and Regulation by Graphene Oxide

    doi: 10.3390/molecules21070920

    Figure Lengend Snippet: Time course of pUC19 DNA (0.008 µg/µL) cleavage promoted by 1b (6.25 × 10 −7 mol/L) in pH = 7.4 buffers (5 mM Tris-HCl/10 mM NaCl) at 37 °C. Lanes 1–6, reaction time 6, 5, 4, 3, 2, 1 h, respectively.

    Article Snippet: Materials Plasmid pUC19 DNA (TaKaRa Biotechnology, Dalian, China), 50 × TAE, 6× loading buffer, gold view dye, and agarose were purchased from Beijing Changsheng Biotechnology Co., Ltd. (Beijing, China).

    Techniques:

    Time course of pUC19 DNA (0.008 µg/µL) cleavage promoted by 2c (3.13 × 10 −7 mol/L) in pH = 6.0 buffers (5 mM Tris-HCl/10 mM NaCl) at 37 °C. Lanes 1–6, 6, 5, 4, 3, 2, 1 h reaction time, respectively.

    Journal: Molecules

    Article Title: DNA Cleavage and Condensation Activities of Mono- and Binuclear Hybrid Complexes and Regulation by Graphene Oxide

    doi: 10.3390/molecules21070920

    Figure Lengend Snippet: Time course of pUC19 DNA (0.008 µg/µL) cleavage promoted by 2c (3.13 × 10 −7 mol/L) in pH = 6.0 buffers (5 mM Tris-HCl/10 mM NaCl) at 37 °C. Lanes 1–6, 6, 5, 4, 3, 2, 1 h reaction time, respectively.

    Article Snippet: Materials Plasmid pUC19 DNA (TaKaRa Biotechnology, Dalian, China), 50 × TAE, 6× loading buffer, gold view dye, and agarose were purchased from Beijing Changsheng Biotechnology Co., Ltd. (Beijing, China).

    Techniques:

    Time course of pUC19 DNA (0.008 µg/µL) cleavage promoted by 2b (3.13 × 10 −7 mol/L) in pH = 7.4 buffers (5 mM Tris-HCl/10 mM NaCl) at 37 °C. Lanes 1–6, reaction time 6, 5, 4, 3, 2, 1 h, respectively.

    Journal: Molecules

    Article Title: DNA Cleavage and Condensation Activities of Mono- and Binuclear Hybrid Complexes and Regulation by Graphene Oxide

    doi: 10.3390/molecules21070920

    Figure Lengend Snippet: Time course of pUC19 DNA (0.008 µg/µL) cleavage promoted by 2b (3.13 × 10 −7 mol/L) in pH = 7.4 buffers (5 mM Tris-HCl/10 mM NaCl) at 37 °C. Lanes 1–6, reaction time 6, 5, 4, 3, 2, 1 h, respectively.

    Article Snippet: Materials Plasmid pUC19 DNA (TaKaRa Biotechnology, Dalian, China), 50 × TAE, 6× loading buffer, gold view dye, and agarose were purchased from Beijing Changsheng Biotechnology Co., Ltd. (Beijing, China).

    Techniques:

    Histograms representing cleavage of pUC19 plasmid DNA (0.008 µg/µL) by compound 2a typical radical scavengers (6.25 × 10 −7 mol/L, pH = 7.4). Lane 1: DNA control, Lane 2: no inhibitor, Lane 3: NaN 3 , Lane 4: KI, Lane 5: DMSO, Lane 6: t -BuOH.

    Journal: Molecules

    Article Title: DNA Cleavage and Condensation Activities of Mono- and Binuclear Hybrid Complexes and Regulation by Graphene Oxide

    doi: 10.3390/molecules21070920

    Figure Lengend Snippet: Histograms representing cleavage of pUC19 plasmid DNA (0.008 µg/µL) by compound 2a typical radical scavengers (6.25 × 10 −7 mol/L, pH = 7.4). Lane 1: DNA control, Lane 2: no inhibitor, Lane 3: NaN 3 , Lane 4: KI, Lane 5: DMSO, Lane 6: t -BuOH.

    Article Snippet: Materials Plasmid pUC19 DNA (TaKaRa Biotechnology, Dalian, China), 50 × TAE, 6× loading buffer, gold view dye, and agarose were purchased from Beijing Changsheng Biotechnology Co., Ltd. (Beijing, China).

    Techniques: Plasmid Preparation

    Histograms representing cleavage of pUC19 plasmid DNA (0.008 µg/µL) by compound 1a with different typical radical scavengers (6.25 × 10 −7 mol/L, pH = 8.0). Lane 1: DNA control, Lane 2: no inhibitor, Lane 3: NaN 3 , Lane 4: KI, Lane 5: DMSO, Lane 6: t -BuOH.

    Journal: Molecules

    Article Title: DNA Cleavage and Condensation Activities of Mono- and Binuclear Hybrid Complexes and Regulation by Graphene Oxide

    doi: 10.3390/molecules21070920

    Figure Lengend Snippet: Histograms representing cleavage of pUC19 plasmid DNA (0.008 µg/µL) by compound 1a with different typical radical scavengers (6.25 × 10 −7 mol/L, pH = 8.0). Lane 1: DNA control, Lane 2: no inhibitor, Lane 3: NaN 3 , Lane 4: KI, Lane 5: DMSO, Lane 6: t -BuOH.

    Article Snippet: Materials Plasmid pUC19 DNA (TaKaRa Biotechnology, Dalian, China), 50 × TAE, 6× loading buffer, gold view dye, and agarose were purchased from Beijing Changsheng Biotechnology Co., Ltd. (Beijing, China).

    Techniques: Plasmid Preparation

    Histograms representing cleavage of pUC19 plasmid DNA (0.008 µg/µL) by compound 1b typical radical scavengers (3.13 × 10 −4 mol/L, pH = 7.4). Lane 1: DNA control, Lane 2: no inhibitor, Lane 3: NaN 3 , Lane 4: KI, Lane 5: t -BuOH, Lane 6: DMSO.

    Journal: Molecules

    Article Title: DNA Cleavage and Condensation Activities of Mono- and Binuclear Hybrid Complexes and Regulation by Graphene Oxide

    doi: 10.3390/molecules21070920

    Figure Lengend Snippet: Histograms representing cleavage of pUC19 plasmid DNA (0.008 µg/µL) by compound 1b typical radical scavengers (3.13 × 10 −4 mol/L, pH = 7.4). Lane 1: DNA control, Lane 2: no inhibitor, Lane 3: NaN 3 , Lane 4: KI, Lane 5: t -BuOH, Lane 6: DMSO.

    Article Snippet: Materials Plasmid pUC19 DNA (TaKaRa Biotechnology, Dalian, China), 50 × TAE, 6× loading buffer, gold view dye, and agarose were purchased from Beijing Changsheng Biotechnology Co., Ltd. (Beijing, China).

    Techniques: Plasmid Preparation

    Histograms and electropherograms (the right side figure) representing cleavage of pUC19 plasmid DNA (0.008 µg/µL) in different pH buffer of 1a (6.25 × 10 −7 mol/L), 1b (3.13 × 10 −6 mol/L) and 1c (6.25 × 10 −7 mol/L) (5 mM Tris-HCl/10 mM NaCl) at 37 °C for 6 h. ( A ) Complex 1a ; Lanes 1−5: pH = 6.5, 7.0, 7.4, 8.0, 8.3, Lane 6 = DNA control, respectively; ( B ) Complex 1b; Lanes 1–7: pH = 6.8, 7.0, 7.2, 7.4, 7.6, 7.8, 8.0; Lane 8 = DNA control, respectively; ( C ) Complex 1c; Lanes 1–8: pH = 6.5, 6.8, 7.0, 7.2, 7.4, 7.6, 7.8, 8.0; Lane 9 = DNA control, respectively.

    Journal: Molecules

    Article Title: DNA Cleavage and Condensation Activities of Mono- and Binuclear Hybrid Complexes and Regulation by Graphene Oxide

    doi: 10.3390/molecules21070920

    Figure Lengend Snippet: Histograms and electropherograms (the right side figure) representing cleavage of pUC19 plasmid DNA (0.008 µg/µL) in different pH buffer of 1a (6.25 × 10 −7 mol/L), 1b (3.13 × 10 −6 mol/L) and 1c (6.25 × 10 −7 mol/L) (5 mM Tris-HCl/10 mM NaCl) at 37 °C for 6 h. ( A ) Complex 1a ; Lanes 1−5: pH = 6.5, 7.0, 7.4, 8.0, 8.3, Lane 6 = DNA control, respectively; ( B ) Complex 1b; Lanes 1–7: pH = 6.8, 7.0, 7.2, 7.4, 7.6, 7.8, 8.0; Lane 8 = DNA control, respectively; ( C ) Complex 1c; Lanes 1–8: pH = 6.5, 6.8, 7.0, 7.2, 7.4, 7.6, 7.8, 8.0; Lane 9 = DNA control, respectively.

    Article Snippet: Materials Plasmid pUC19 DNA (TaKaRa Biotechnology, Dalian, China), 50 × TAE, 6× loading buffer, gold view dye, and agarose were purchased from Beijing Changsheng Biotechnology Co., Ltd. (Beijing, China).

    Techniques: Plasmid Preparation

    Effect of different ligands and complexes on the interaction with pUC19 DNA (7 μg/ml) with the existence of DNaseI in a Tris-HCl buffer (100 mM, pH 7.4) at 37 ºC for 0.5 h. Agarose gel electrophoresis diagram: lane 1, DNA control ; lane 2 DNA+ DNaseI; lane 3 DNA+ DNaseI + 6a ; lane 4 DNA + DNaseI + 6b ; lane 5 DNA + DNaseI +1a ; lane 6 DNA+ DNaseI + 1b .

    Journal: International Journal of Molecular Sciences

    Article Title: Dinuclear Zinc (II) Complexes of Macrocyclic Polyamine Ligands Containing an Imidazolium Bridge: Synthesis, Characterization, and Their Interaction with Plasmid DNA

    doi:

    Figure Lengend Snippet: Effect of different ligands and complexes on the interaction with pUC19 DNA (7 μg/ml) with the existence of DNaseI in a Tris-HCl buffer (100 mM, pH 7.4) at 37 ºC for 0.5 h. Agarose gel electrophoresis diagram: lane 1, DNA control ; lane 2 DNA+ DNaseI; lane 3 DNA+ DNaseI + 6a ; lane 4 DNA + DNaseI + 6b ; lane 5 DNA + DNaseI +1a ; lane 6 DNA+ DNaseI + 1b .

    Article Snippet: Electrophoresis grade agarose and plasmid DNA (pUC19) were purchased from Takara Biotechnology Company.

    Techniques: Agarose Gel Electrophoresis

    Effect of different concentration of 1-ethyl-3-methylimidazolium bromide (EMI) on the interaction with pUC19 DNA (7 μg/ml) in a Tris-HCl buffer (100 mM, pH 7.4) at 37 ºC for 0.5 h. Agarose gel electrophoresis diagram: lane 1, DNA control ; lanes 2–5, ligand: [EMI] = 5.6, 11.2, 22.4, 44.8, 89.6 mM.

    Journal: International Journal of Molecular Sciences

    Article Title: Dinuclear Zinc (II) Complexes of Macrocyclic Polyamine Ligands Containing an Imidazolium Bridge: Synthesis, Characterization, and Their Interaction with Plasmid DNA

    doi:

    Figure Lengend Snippet: Effect of different concentration of 1-ethyl-3-methylimidazolium bromide (EMI) on the interaction with pUC19 DNA (7 μg/ml) in a Tris-HCl buffer (100 mM, pH 7.4) at 37 ºC for 0.5 h. Agarose gel electrophoresis diagram: lane 1, DNA control ; lanes 2–5, ligand: [EMI] = 5.6, 11.2, 22.4, 44.8, 89.6 mM.

    Article Snippet: Electrophoresis grade agarose and plasmid DNA (pUC19) were purchased from Takara Biotechnology Company.

    Techniques: Concentration Assay, Agarose Gel Electrophoresis

    Effect of different ligands and complexes on the interaction with pUC19 DNA (7 μg/ml) in a Tris-HCl buffer (100 mM, pH 7.4) at 37 ºC for 0.5 h. Agarose gel electrophoresis diagram: lane 1, DNA control ; lanes 2–6, ligand: [ 6a ] = 1.40, 0.70, 0.35, 0.18, 0.09 mM; lanes 7–12 ligand: [ 6b ] = 1.40, 0.70, 0.35, 0.18, 0.09, 0.05 mM; lanes 13–18 complex: [ 1a ] = 0.144, 0.072, 0.036, 0.018, 0.009, 0.005 mM; lanes 19–24 complex: [ 1b ] = 0.144, 0.072, 0.036, 0.018, 0.009, 0.005 mM.

    Journal: International Journal of Molecular Sciences

    Article Title: Dinuclear Zinc (II) Complexes of Macrocyclic Polyamine Ligands Containing an Imidazolium Bridge: Synthesis, Characterization, and Their Interaction with Plasmid DNA

    doi:

    Figure Lengend Snippet: Effect of different ligands and complexes on the interaction with pUC19 DNA (7 μg/ml) in a Tris-HCl buffer (100 mM, pH 7.4) at 37 ºC for 0.5 h. Agarose gel electrophoresis diagram: lane 1, DNA control ; lanes 2–6, ligand: [ 6a ] = 1.40, 0.70, 0.35, 0.18, 0.09 mM; lanes 7–12 ligand: [ 6b ] = 1.40, 0.70, 0.35, 0.18, 0.09, 0.05 mM; lanes 13–18 complex: [ 1a ] = 0.144, 0.072, 0.036, 0.018, 0.009, 0.005 mM; lanes 19–24 complex: [ 1b ] = 0.144, 0.072, 0.036, 0.018, 0.009, 0.005 mM.

    Article Snippet: Electrophoresis grade agarose and plasmid DNA (pUC19) were purchased from Takara Biotechnology Company.

    Techniques: Agarose Gel Electrophoresis

    Effect of different concentration of ligands 6a on the interaction with pUC19 DNA (7 μg/ml) in a Tris-HCl buffer (100 mM, pH 7.4) at 37 ºC for 0.5 h. Agarose gel electrophoresis diagram: lane 1, DNA control ; lanes 2–4, ligand: [ 6a ] = 5.6, 4.2, 2.8 mM.

    Journal: International Journal of Molecular Sciences

    Article Title: Dinuclear Zinc (II) Complexes of Macrocyclic Polyamine Ligands Containing an Imidazolium Bridge: Synthesis, Characterization, and Their Interaction with Plasmid DNA

    doi:

    Figure Lengend Snippet: Effect of different concentration of ligands 6a on the interaction with pUC19 DNA (7 μg/ml) in a Tris-HCl buffer (100 mM, pH 7.4) at 37 ºC for 0.5 h. Agarose gel electrophoresis diagram: lane 1, DNA control ; lanes 2–4, ligand: [ 6a ] = 5.6, 4.2, 2.8 mM.

    Article Snippet: Electrophoresis grade agarose and plasmid DNA (pUC19) were purchased from Takara Biotechnology Company.

    Techniques: Concentration Assay, Agarose Gel Electrophoresis

    Design of Level 0 vectors. The backbone is a yeast shuttle vector with a pUC19 replication origin, the kanamycin resistance gene nptII for selection in Escherichia coli , a high-copy 2-micron origin for replication and the URA3 marker gene for selection in Saccharomyces cerevisiae . Each Level 0 vector possesses a different combination of homology regions (HR). HR1 gives homology to the Level 1 vector backbone or to the HR2 of the adjacent Level 0 vector. HR2 gives homology to the next Level 0 vector or to the Level 1 vector backbone. These regions are separated by a HindIII-flanked ccdB expression cassette. The HindIII sites are used to release the ccdB cassette and to allow the subsequent insertion of the individual subunits in-between the homology regions by scar-free, overlap-based cloning. The homology regions are flanked by two multiple cloning sites (MCS), containing the five 8-base cutters AscI, SbfI, SwaI, FseI, PmeI to release Level 0 constructs for further cloning into Level 1.

    Journal: Nucleic Acids Research

    Article Title: AssemblX: a user-friendly toolkit for rapid and reliable multi-gene assemblies

    doi: 10.1093/nar/gkx034

    Figure Lengend Snippet: Design of Level 0 vectors. The backbone is a yeast shuttle vector with a pUC19 replication origin, the kanamycin resistance gene nptII for selection in Escherichia coli , a high-copy 2-micron origin for replication and the URA3 marker gene for selection in Saccharomyces cerevisiae . Each Level 0 vector possesses a different combination of homology regions (HR). HR1 gives homology to the Level 1 vector backbone or to the HR2 of the adjacent Level 0 vector. HR2 gives homology to the next Level 0 vector or to the Level 1 vector backbone. These regions are separated by a HindIII-flanked ccdB expression cassette. The HindIII sites are used to release the ccdB cassette and to allow the subsequent insertion of the individual subunits in-between the homology regions by scar-free, overlap-based cloning. The homology regions are flanked by two multiple cloning sites (MCS), containing the five 8-base cutters AscI, SbfI, SwaI, FseI, PmeI to release Level 0 constructs for further cloning into Level 1.

    Article Snippet: Assembly of Level 0 vector sets To generate the Level 0 vector backbone, the pUC19 replication origin and the nptII kanamycin resistance gene from plasmid pHis2.1 (Takara Bio, Saint-Germain-en-Laye, France) were amplified by PCR using primer combinations P094/P095 and P096/P097, respectively.

    Techniques: Plasmid Preparation, Selection, Marker, Expressing, Clone Assay, Construct