Structured Review

TaKaRa puc19
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 <t>pUC19;</t> M, AccuRuler 1-kb DNA RTU ladder (Maestrogen). All reactions were repeated three times or more; typical results are shown.
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Images

1) 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

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 "Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression"

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

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

4) Product Images from "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 * 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

5) Product Images from "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 * 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 "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

7) 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

8) Product Images from "Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein"

Article Title: Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkl350

Effect of Tth SSB-255 protein on the efficiency and specificity of RCA. ( a ) Top: RCAs were performed in the absence of the SSB proteins using pUC19 DNA as template and phi29 DNA polymerase for the indicated reaction times. Bottom: Signals of spot hybridization of the same samples. ( b ) Top and Bottom: same as (a), except for the absence of template DNA. ( c ) Top and Bottom: same as (a), except for the presence of the Tth SSB protein (3.0 µg/20 µl reaction volume). ( d ) Top and Bottom: same as (c), except for the absence of template DNA. ( e ) Top and Bottom: same as (a), except for the presence of the Tth SSB-255 protein (3.0 µg/20 µl reaction volume). ( f ) Top and Bottom: same as (e), except for the absence of template DNA.
Figure Legend Snippet: Effect of Tth SSB-255 protein on the efficiency and specificity of RCA. ( a ) Top: RCAs were performed in the absence of the SSB proteins using pUC19 DNA as template and phi29 DNA polymerase for the indicated reaction times. Bottom: Signals of spot hybridization of the same samples. ( b ) Top and Bottom: same as (a), except for the absence of template DNA. ( c ) Top and Bottom: same as (a), except for the presence of the Tth SSB protein (3.0 µg/20 µl reaction volume). ( d ) Top and Bottom: same as (c), except for the absence of template DNA. ( e ) Top and Bottom: same as (a), except for the presence of the Tth SSB-255 protein (3.0 µg/20 µl reaction volume). ( f ) Top and Bottom: same as (e), except for the absence of template DNA.

Techniques Used: Hybridization

Effect of Tth SSB-255 protein on RCA assays. ( a ) RCAs were carried out in the absence or presence of the indicated SSB proteins using pUC19 DNA as a template and phi29 DNA polymerase. ( b ) Same as (a), except for using linearized ( Eco RI) pUC19 DNA as the template. ( c ) Same as (a), except that the amplifications were carried out in the absence of template DNA. Lane M: molecular weight markers (100 and 12 kb).
Figure Legend Snippet: Effect of Tth SSB-255 protein on RCA assays. ( a ) RCAs were carried out in the absence or presence of the indicated SSB proteins using pUC19 DNA as a template and phi29 DNA polymerase. ( b ) Same as (a), except for using linearized ( Eco RI) pUC19 DNA as the template. ( c ) Same as (a), except that the amplifications were carried out in the absence of template DNA. Lane M: molecular weight markers (100 and 12 kb).

Techniques Used: Molecular Weight

9) Product Images from "Vpu Augments the Initial Burst Phase of HIV-1 Propagation and Downregulates BST2 and CD4 in Humanized Mice"

Article Title: Vpu Augments the Initial Burst Phase of HIV-1 Propagation and Downregulates BST2 and CD4 in Humanized Mice

Journal:

doi: 10.1128/JVI.07062-11

Different potentials of CD4 and BST2 in the production of infectious cell-free virions and cell-to-cell HIV-1 transmission. A total of 800 ng of pAD8 + (WT HIV-1-producing plasmid), pAD8-U DEL2 ( vpu -deficient HIV-1-producing plasmid), or pUC19 (parental
Figure Legend Snippet: Different potentials of CD4 and BST2 in the production of infectious cell-free virions and cell-to-cell HIV-1 transmission. A total of 800 ng of pAD8 + (WT HIV-1-producing plasmid), pAD8-U DEL2 ( vpu -deficient HIV-1-producing plasmid), or pUC19 (parental

Techniques Used: Transmission Assay, 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

Related Articles

Clone Assay:

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). .. 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: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression
Article Snippet: Such junction-specific protection was not detected when a mismatch-recognition protein, ttMutS1, was used ( ). ttMutS2 Preferably Digested Branched DNA Structures —Because competition experiments and DNase I footprinting assays revealed that ttMutS2 preferably binds to branched DNA structures, nuclease activity assays of ttMutS2 were carried out using branched DNA structures as substrates. .. 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: Establishment of a novel hepatic steatosis cell model by Cas9/sgRNA-mediated DGKθ gene knockout
Article Snippet: The sgRNAs were synthesized at the Beijing Genomics Institute (Beijing, China). .. According to a previously described method , the human U6 promoter and sgRNA backbone were sequentially cloned into pUC19 (Clontech Laboratories, Inc., Mountain view, CA, USA), the obtained plasmid was called the pUC19/U6-BsaI-sgRNA backbone vector. .. The synthesized oligos were annealed, and ligated into the BsaI sites of the pUC19/U6-BsaI-sgRNA backbone vector under the control of the U6 promoter.

Article Title: Enzymatic improvement of mitochondrial thiol oxidase Erv1 for oxidized glutathione fermentation by Saccharomyces cerevisiae
Article Snippet: The cDNA was prepared by reverse transcription PCR using a PrimeScrip RT-PCR Kit (Takara Bio, Otsu, Japan) from total RNA extracted from S. cerevisiae YPH499 cells using NucleoSpin RNA (Takara Bio). .. The PCR product was cloned between Sph I and Bam HI sites of pUC19 (Takara Bio). .. After the sequence was checked, the ERV1 gene was subcloned between Nde I and Xho I sites of pET-22b (Novagen) to give pET-ERV1 . pET-ERV1 was used for Erv1 protein preparation.

Article Title: Improved sugar-free succinate production by Synechocystis sp. PCC 6803 following identification of the limiting steps in glycogen catabolism
Article Snippet: The upstream region of slr0168 was amplified from Synechocystis 6803 genomic DNA by PCR using the primer set 5′-TATAGGGCGAATTGGGTACCATGACTATTCAATACACCCCCCTAG-3′/5′-TACCGTCGACCTCGAGCACCAGACCAAAGCCGGGAATTTC-3′ and then integrated into the Kpn I and Xho I sites of pBluescript-Kmr -PrbcL-TrbcL-slr0168 using an In-Fusion HD Cloning Kit to yield pBluescript-slr0168-Kmr -PrbcL-TrbcL-slr0168. .. The Nde I site (CATATG) of pUC19 (Takara Bio) was replaced with CACATG by digesting Aat II and Eco RI and inserting the synthetic DNA.

Article Title: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues
Article Snippet: A gene coding for PmDAP IV (residues 1–745) was cloned from a P . mexicana WO24 genomic DNA library by a cultivation plate assay based on DPP IV activity, the hydrolysis of Gly-Pro-β-naphthylamide . .. An E . coli JM109 (Takara Bio) transformant harbouring the full-length PmDAP IV M12I mutant sequence inserted into the pUC19 (Takara Bio) expression plasmid was used to produce the periplasmic form of PmDAP IV.

Centrifugation:

Article Title: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues
Article Snippet: An E . coli JM109 (Takara Bio) transformant harbouring the full-length PmDAP IV M12I mutant sequence inserted into the pUC19 (Takara Bio) expression plasmid was used to produce the periplasmic form of PmDAP IV. .. Cells were grown in 2 x YT media at 310 K. Overproduction of PmDAP IV was performed by IPTG induction (final concentration, 0.1 mM) at an OD600 of approximately 0.6.

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: In addition, since MPRCA and MDA use the same DNA amplification machinery, RNA-primed MPRCA can also amplify DNA fragments, (e.g., from the E. coli genome) contaminating in the polymerase. .. 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: 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). .. 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).

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: However, non-specific amplification products emerge as fragments with other sizes, or are migrated at over 20 kbp , . .. 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: Furthermore, these results also suggest that DNA might be additionally contaminated by DNase-treatment, as observed in previous reports on PCR-decontamination procedures , , . .. 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: Establishment of a novel hepatic steatosis cell model by Cas9/sgRNA-mediated DGKθ gene knockout
Article Snippet: According to a previously described method , the human U6 promoter and sgRNA backbone were sequentially cloned into pUC19 (Clontech Laboratories, Inc., Mountain view, CA, USA), the obtained plasmid was called the pUC19/U6-BsaI-sgRNA backbone vector. .. According to a previously described method , the human U6 promoter and sgRNA backbone were sequentially cloned into pUC19 (Clontech Laboratories, Inc., Mountain view, CA, USA), the obtained plasmid was called the pUC19/U6-BsaI-sgRNA backbone vector.

Article Title: GAPDH-A Recruits a Plant Virus Movement Protein to Cortical Virus Replication Complexes to Facilitate Viral Cell-to-Cell Movement
Article Snippet: A DNA fragment containing T7 promoter and the 5′ half of RNA2 and HA was amplified from pRC2|G using primers 11 and 12. .. Eco RI/Hin dIII fragment of pBE2113 that contains a 35S promoter-∧ sequence-nos terminator cassette was inserted to the same sites of pUC19 (Takara Bio Inc.) producing pUC2113.

Article Title: Enzymatic improvement of mitochondrial thiol oxidase Erv1 for oxidized glutathione fermentation by Saccharomyces cerevisiae
Article Snippet: The ERV1 gene was amplified by polymerase chain reaction (PCR) from complementary DNA (cDNA) of S. cerevisiae YPH499 using primers ERV1F1 and ERV1R1. .. The PCR product was cloned between Sph I and Bam HI sites of pUC19 (Takara Bio).

Article Title: Improved sugar-free succinate production by Synechocystis sp. PCC 6803 following identification of the limiting steps in glycogen catabolism
Article Snippet: The upstream region of slr0168 was amplified from Synechocystis 6803 genomic DNA by PCR using the primer set 5′-TATAGGGCGAATTGGGTACCATGACTATTCAATACACCCCCCTAG-3′/5′-TACCGTCGACCTCGAGCACCAGACCAAAGCCGGGAATTTC-3′ and then integrated into the Kpn I and Xho I sites of pBluescript-Kmr -PrbcL-TrbcL-slr0168 using an In-Fusion HD Cloning Kit to yield pBluescript-slr0168-Kmr -PrbcL-TrbcL-slr0168. .. The Nde I site (CATATG) of pUC19 (Takara Bio) was replaced with CACATG by digesting Aat II and Eco RI and inserting the synthetic DNA.

Article Title: Generation of Circularly Permuted Fluorescent-Protein-Based Indicators for In Vitro and In Vivo Detection of Citrate
Article Snippet: The two fragments amplified with Pr3/Pr4 and Pr5/Pr6 were mixed, annealed, and elongated by PCR with Pr3 and Pr6. .. The resulting fragment encoding a circularly permuted cpFP was amplified by PCR with Pr3 and Pr6, digested with Pst I and Kpn I, and the restriction fragment covering the coding region for cpFP was inserted into pUC19 (Takara Bio). .. Since the mutation (F46L) was essential for accelerating the chromophore maturation in accordance with the report of the fluorescent protein Venus and the mutations (T65G, V68L, S72A, H148D, T203F) were optimized for the ratiometric Pericam , several mutations (F46L, T65G, V68L, S72A, H148D, T203F) were introduced into the cpFP coding sequence by site-directed mutagenesis with primers Pr7-12 ( ).

Synthesized:

Article Title: Establishment of a novel hepatic steatosis cell model by Cas9/sgRNA-mediated DGKθ gene knockout
Article Snippet: The sgRNAs were synthesized at the Beijing Genomics Institute (Beijing, China). .. According to a previously described method , the human U6 promoter and sgRNA backbone were sequentially cloned into pUC19 (Clontech Laboratories, Inc., Mountain view, CA, USA), the obtained plasmid was called the pUC19/U6-BsaI-sgRNA backbone vector.

Nuclease Assay:

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

Construct:

Article Title: Establishment of a novel hepatic steatosis cell model by Cas9/sgRNA-mediated DGKθ gene knockout
Article Snippet: According to a previously described method , the human U6 promoter and sgRNA backbone were sequentially cloned into pUC19 (Clontech Laboratories, Inc., Mountain view, CA, USA), the obtained plasmid was called the pUC19/U6-BsaI-sgRNA backbone vector. .. According to a previously described method , the human U6 promoter and sgRNA backbone were sequentially cloned into pUC19 (Clontech Laboratories, Inc., Mountain view, CA, USA), the obtained plasmid was called the pUC19/U6-BsaI-sgRNA backbone vector.

Article Title: Precisely controlling endogenous protein dosage in hPSCs and derivatives to model FOXG1 syndrome
Article Snippet: Cas9 sequence was obtained from PX458 (Addgene 48138) . pCMV-intron-spCas9 (Supplementary Data ) was constructed by replacing GFP in pmaxGFP with Cas9 cDNA. .. U6-sgRNA sequence was also obtained from PX458. pMini-sgRNA was built based on puc19 (Takara, 3219) using Gibson Assembly (NEB, E2611L).

Article Title: Enzymatic improvement of mitochondrial thiol oxidase Erv1 for oxidized glutathione fermentation by Saccharomyces cerevisiae
Article Snippet: The PCR product was cloned between Sph I and Bam HI sites of pUC19 (Takara Bio). .. After the sequence was checked, the ERV1 gene was subcloned between Nde I and Xho I sites of pET-22b (Novagen) to give pET-ERV1 . pET-ERV1 was used for Erv1 protein preparation.

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: In addition, since MPRCA and MDA use the same DNA amplification machinery, RNA-primed MPRCA can also amplify DNA fragments, (e.g., from the E. coli genome) contaminating in the polymerase. .. 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 , .

Incubation:

Article Title: Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein
Article Snippet: The membrane was incubated for 2 h at 68°C in 20 ml of prehybridization solution in a hybridization chamber. .. The radiolabeled probes were prepared with [γ-32 P]dCTP (6000 Ci/mmol, Amersham Pharmacia Biotech, Buckinghamshire, UK), a kit (BcaBEST™ Labeling kit, Takara Bio) and pUC19 or a human gene site (3121 bp).

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression
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. .. Crystal Structure of the ttMutS2 Endonuclease Domain —We prepared ttSmr663 for x-ray crystallographic analysis.

Activity Assay:

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression
Article Snippet: Such junction-specific protection was not detected when a mismatch-recognition protein, ttMutS1, was used ( ). ttMutS2 Preferably Digested Branched DNA Structures —Because competition experiments and DNase I footprinting assays revealed that ttMutS2 preferably binds to branched DNA structures, nuclease activity assays of ttMutS2 were carried out using branched DNA structures as substrates. .. 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: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues
Article Snippet: A gene coding for PmDAP IV (residues 1–745) was cloned from a P . mexicana WO24 genomic DNA library by a cultivation plate assay based on DPP IV activity, the hydrolysis of Gly-Pro-β-naphthylamide . .. An E . coli JM109 (Takara Bio) transformant harbouring the full-length PmDAP IV M12I mutant sequence inserted into the pUC19 (Takara Bio) expression plasmid was used to produce the periplasmic form of PmDAP IV.

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).

Article Title: Precisely controlling endogenous protein dosage in hPSCs and derivatives to model FOXG1 syndrome
Article Snippet: Mammal codon-optimized Streptococcus pyogenes wild-type Cas9 expressing plasmid was built base on pmaxGFP (LONZA). .. U6-sgRNA sequence was also obtained from PX458. pMini-sgRNA was built based on puc19 (Takara, 3219) using Gibson Assembly (NEB, E2611L).

Article Title: GAPDH-A Recruits a Plant Virus Movement Protein to Cortical Virus Replication Complexes to Facilitate Viral Cell-to-Cell Movement
Article Snippet: Paragraph title: Construction of plasmids expressing recombinant virus RNAs ... Eco RI/Hin dIII fragment of pBE2113 that contains a 35S promoter-∧ sequence-nos terminator cassette was inserted to the same sites of pUC19 (Takara Bio Inc.) producing pUC2113.

Article Title: Enzymatic improvement of mitochondrial thiol oxidase Erv1 for oxidized glutathione fermentation by Saccharomyces cerevisiae
Article Snippet: The PCR product was cloned between Sph I and Bam HI sites of pUC19 (Takara Bio). .. The plasmids for preparation of Erv1 variant proteins were constructed by inverse PCR using corresponding primer pairs and templates (Additional file : Table S1).

Article Title: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues
Article Snippet: The periplasmic form of PmDAP IV comprised 723 amino acids, with a theoretical molecular weight of 79981.58 and a theoretical isoelectric point of 5.80. .. An E . coli JM109 (Takara Bio) transformant harbouring the full-length PmDAP IV M12I mutant sequence inserted into the pUC19 (Takara Bio) expression plasmid was used to produce the periplasmic form of PmDAP IV. .. Cells were grown in 2 x YT media at 310 K. Overproduction of PmDAP IV was performed by IPTG induction (final concentration, 0.1 mM) at an OD600 of approximately 0.6.

Bradford Assay:

Article Title: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues
Article Snippet: An E . coli JM109 (Takara Bio) transformant harbouring the full-length PmDAP IV M12I mutant sequence inserted into the pUC19 (Takara Bio) expression plasmid was used to produce the periplasmic form of PmDAP IV. .. An E . coli JM109 (Takara Bio) transformant harbouring the full-length PmDAP IV M12I mutant sequence inserted into the pUC19 (Takara Bio) expression plasmid was used to produce the periplasmic form of PmDAP IV.

Western Blot:

Article Title: Vpu Augments the Initial Burst Phase of HIV-1 Propagation and Downregulates BST2 and CD4 in Humanized Mice
Article Snippet: Paragraph title: Transfection, Western blotting, and TZM-bl assay. ... For in vitro transfection experiments shown in , 1 μg of pAD8+ (a molecular clone of HIV-1 strain AD8 [HIV-1AD8 ]) , pAD8-UDEL2 , which is a derivative of AD8 carrying an 81-bp deletion and an 8-bp irrelevant insertion in the vpu region ( , ), or pUC19 (for mock control [TaKaRa]; shown as “vector” on the figures) was transfected into 293T and HeLa cells by using Lipofectamine 2000 (Life Technologies) according to the manufacturer's protocol.

Over Expression:

Article Title: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues
Article Snippet: Paragraph title: Overexpression and purification of PmDAPIV ... An E . coli JM109 (Takara Bio) transformant harbouring the full-length PmDAP IV M12I mutant sequence inserted into the pUC19 (Takara Bio) expression plasmid was used to produce the periplasmic form of PmDAP IV.

Hybridization:

Article Title: Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein
Article Snippet: Paragraph title: DNA spot hybridization ... The radiolabeled probes were prepared with [γ-32 P]dCTP (6000 Ci/mmol, Amersham Pharmacia Biotech, Buckinghamshire, UK), a kit (BcaBEST™ Labeling kit, Takara Bio) and pUC19 or a human gene site (3121 bp).

Transfection:

Article Title: Vpu Augments the Initial Burst Phase of HIV-1 Propagation and Downregulates BST2 and CD4 in Humanized Mice
Article Snippet: The activated human CD4+ T cells were maintained in RPMI 1640 medium containing 10% fetal calf serum, 100 U/ml interleukin-2, 100 U/ml penicillin, and 100 μg/ml streptomycin. .. For in vitro transfection experiments shown in , 1 μg of pAD8+ (a molecular clone of HIV-1 strain AD8 [HIV-1AD8 ]) , pAD8-UDEL2 , which is a derivative of AD8 carrying an 81-bp deletion and an 8-bp irrelevant insertion in the vpu region ( , ), or pUC19 (for mock control [TaKaRa]; shown as “vector” on the figures) was transfected into 293T and HeLa cells by using Lipofectamine 2000 (Life Technologies) according to the manufacturer's protocol. .. At 48 h posttransfection, the culture supernatant was harvested, centrifuged, and then filtered through a 0.45-μm-pore-size filter (Millipore) to produce virus solutions.

Sequencing:

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: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression
Article Snippet: Such junction-specific protection was not detected when a mismatch-recognition protein, ttMutS1, was used ( ). ttMutS2 Preferably Digested Branched DNA Structures —Because competition experiments and DNase I footprinting assays revealed that ttMutS2 preferably binds to branched DNA structures, nuclease activity assays of ttMutS2 were carried out using branched DNA structures as substrates. .. 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: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression
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: Precisely controlling endogenous protein dosage in hPSCs and derivatives to model FOXG1 syndrome
Article Snippet: Cas9 sequence was obtained from PX458 (Addgene 48138) . pCMV-intron-spCas9 (Supplementary Data ) was constructed by replacing GFP in pmaxGFP with Cas9 cDNA. .. U6-sgRNA sequence was also obtained from PX458. pMini-sgRNA was built based on puc19 (Takara, 3219) using Gibson Assembly (NEB, E2611L). .. The pmini-sgRNA vector includes two BbsI restriction sites for rapid cloning of sgRNA.

Article Title: GAPDH-A Recruits a Plant Virus Movement Protein to Cortical Virus Replication Complexes to Facilitate Viral Cell-to-Cell Movement
Article Snippet: The generated PCR product was digested with Eco RI/Sma I and inserted into the same site of pUC119, producing pUCR2MP-HA ( ). .. Eco RI/Hin dIII fragment of pBE2113 that contains a 35S promoter-∧ sequence-nos terminator cassette was inserted to the same sites of pUC19 (Takara Bio Inc.) producing pUC2113. .. The Xba I site downstream of ∧ sequence in pUC2113 was digested and filled in with T4-polymerase, and the linker sequence containing Sac I site was ligated, producing pUC2113(Sac I).

Article Title: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues
Article Snippet: The periplasmic form of PmDAP IV comprised 723 amino acids, with a theoretical molecular weight of 79981.58 and a theoretical isoelectric point of 5.80. .. An E . coli JM109 (Takara Bio) transformant harbouring the full-length PmDAP IV M12I mutant sequence inserted into the pUC19 (Takara Bio) expression plasmid was used to produce the periplasmic form of PmDAP IV. .. Cells were grown in 2 x YT media at 310 K. Overproduction of PmDAP IV was performed by IPTG induction (final concentration, 0.1 mM) at an OD600 of approximately 0.6.

Article Title: Generation of Circularly Permuted Fluorescent-Protein-Based Indicators for In Vitro and In Vivo Detection of Citrate
Article Snippet: The primers Pr4 and Pr5 have a sequence coding for a linker (-VDGGSGGTG- between the original C and N termini), allowing complementary fragment annealing in the following elongation reactions. .. The resulting fragment encoding a circularly permuted cpFP was amplified by PCR with Pr3 and Pr6, digested with Pst I and Kpn I, and the restriction fragment covering the coding region for cpFP was inserted into pUC19 (Takara Bio).

Inverse PCR:

Article Title: Enzymatic improvement of mitochondrial thiol oxidase Erv1 for oxidized glutathione fermentation by Saccharomyces cerevisiae
Article Snippet: The PCR product was cloned between Sph I and Bam HI sites of pUC19 (Takara Bio). .. After the sequence was checked, the ERV1 gene was subcloned between Nde I and Xho I sites of pET-22b (Novagen) to give pET-ERV1 . pET-ERV1 was used for Erv1 protein preparation.

Hemagglutination Assay:

Article Title: GAPDH-A Recruits a Plant Virus Movement Protein to Cortical Virus Replication Complexes to Facilitate Viral Cell-to-Cell Movement
Article Snippet: A DNA fragment containing T7 promoter and the 5′ half of RNA2 and HA was amplified from pRC2|G using primers 11 and 12. .. Eco RI/Hin dIII fragment of pBE2113 that contains a 35S promoter-∧ sequence-nos terminator cassette was inserted to the same sites of pUC19 (Takara Bio Inc.) producing pUC2113.

Generated:

Article Title: GAPDH-A Recruits a Plant Virus Movement Protein to Cortical Virus Replication Complexes to Facilitate Viral Cell-to-Cell Movement
Article Snippet: The generated PCR product was digested with Eco RI/Sma I and inserted into the same site of pUC119, producing pUCR2MP-HA ( ). .. Eco RI/Hin dIII fragment of pBE2113 that contains a 35S promoter-∧ sequence-nos terminator cassette was inserted to the same sites of pUC19 (Takara Bio Inc.) producing pUC2113.

Imaging:

Article Title: Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein
Article Snippet: The radiolabeled probes were prepared with [γ-32 P]dCTP (6000 Ci/mmol, Amersham Pharmacia Biotech, Buckinghamshire, UK), a kit (BcaBEST™ Labeling kit, Takara Bio) and pUC19 or a human gene site (3121 bp). .. Following addition of the radiolabeled probes, the membrane was incubated at 68°C for a further 12 h. After hybridization, the membrane was washed with 200 ml 0.5× SSC (7.5 mM sodium citrate pH 7.0 and 75 mM NaCl), 0.1% SDS at 68°C.

Protein Concentration:

Article Title: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues
Article Snippet: An E . coli JM109 (Takara Bio) transformant harbouring the full-length PmDAP IV M12I mutant sequence inserted into the pUC19 (Takara Bio) expression plasmid was used to produce the periplasmic form of PmDAP IV. .. An E . coli JM109 (Takara Bio) transformant harbouring the full-length PmDAP IV M12I mutant sequence inserted into the pUC19 (Takara Bio) expression plasmid was used to produce the periplasmic form of PmDAP IV.

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: Establishment of a novel hepatic steatosis cell model by Cas9/sgRNA-mediated DGKθ gene knockout
Article Snippet: According to a previously described method , the human U6 promoter and sgRNA backbone were sequentially cloned into pUC19 (Clontech Laboratories, Inc., Mountain view, CA, USA), the obtained plasmid was called the pUC19/U6-BsaI-sgRNA backbone vector. .. According to a previously described method , the human U6 promoter and sgRNA backbone were sequentially cloned into pUC19 (Clontech Laboratories, Inc., Mountain view, CA, USA), the obtained plasmid was called the pUC19/U6-BsaI-sgRNA backbone vector.

Article Title: GAPDH-A Recruits a Plant Virus Movement Protein to Cortical Virus Replication Complexes to Facilitate Viral Cell-to-Cell Movement
Article Snippet: The generated PCR product was digested with Eco RI/Sma I and inserted into the same site of pUC119, producing pUCR2MP-HA ( ). .. Eco RI/Hin dIII fragment of pBE2113 that contains a 35S promoter-∧ sequence-nos terminator cassette was inserted to the same sites of pUC19 (Takara Bio Inc.) producing pUC2113.

Article Title: Enzymatic improvement of mitochondrial thiol oxidase Erv1 for oxidized glutathione fermentation by Saccharomyces cerevisiae
Article Snippet: The cDNA was prepared by reverse transcription PCR using a PrimeScrip RT-PCR Kit (Takara Bio, Otsu, Japan) from total RNA extracted from S. cerevisiae YPH499 cells using NucleoSpin RNA (Takara Bio). .. The PCR product was cloned between Sph I and Bam HI sites of pUC19 (Takara Bio). .. After the sequence was checked, the ERV1 gene was subcloned between Nde I and Xho I sites of pET-22b (Novagen) to give pET-ERV1 . pET-ERV1 was used for Erv1 protein preparation.

Article Title: Improved sugar-free succinate production by Synechocystis sp. PCC 6803 following identification of the limiting steps in glycogen catabolism
Article Snippet: The upstream region of slr0168 was amplified from Synechocystis 6803 genomic DNA by PCR using the primer set 5′-TATAGGGCGAATTGGGTACCATGACTATTCAATACACCCCCCTAG-3′/5′-TACCGTCGACCTCGAGCACCAGACCAAAGCCGGGAATTTC-3′ and then integrated into the Kpn I and Xho I sites of pBluescript-Kmr -PrbcL-TrbcL-slr0168 using an In-Fusion HD Cloning Kit to yield pBluescript-slr0168-Kmr -PrbcL-TrbcL-slr0168. .. The Nde I site (CATATG) of pUC19 (Takara Bio) was replaced with CACATG by digesting Aat II and Eco RI and inserting the synthetic DNA.

Article Title: Generation of Circularly Permuted Fluorescent-Protein-Based Indicators for In Vitro and In Vivo Detection of Citrate
Article Snippet: The two fragments amplified with Pr3/Pr4 and Pr5/Pr6 were mixed, annealed, and elongated by PCR with Pr3 and Pr6. .. The resulting fragment encoding a circularly permuted cpFP was amplified by PCR with Pr3 and Pr6, digested with Pst I and Kpn I, and the restriction fragment covering the coding region for cpFP was inserted into pUC19 (Takara Bio). .. Since the mutation (F46L) was essential for accelerating the chromophore maturation in accordance with the report of the fluorescent protein Venus and the mutations (T65G, V68L, S72A, H148D, T203F) were optimized for the ratiometric Pericam , several mutations (F46L, T65G, V68L, S72A, H148D, T203F) were introduced into the cpFP coding sequence by site-directed mutagenesis with primers Pr7-12 ( ).

Recombinant:

Article Title: GAPDH-A Recruits a Plant Virus Movement Protein to Cortical Virus Replication Complexes to Facilitate Viral Cell-to-Cell Movement
Article Snippet: Paragraph title: Construction of plasmids expressing recombinant virus RNAs ... Eco RI/Hin dIII fragment of pBE2113 that contains a 35S promoter-∧ sequence-nos terminator cassette was inserted to the same sites of pUC19 (Takara Bio Inc.) producing pUC2113.

Article Title: Improved sugar-free succinate production by Synechocystis sp. PCC 6803 following identification of the limiting steps in glycogen catabolism
Article Snippet: Paragraph title: Construction of recombinant strains ... The Nde I site (CATATG) of pUC19 (Takara Bio) was replaced with CACATG by digesting Aat II and Eco RI and inserting the synthetic DNA.

Molecular Weight:

Article Title: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues
Article Snippet: The periplasmic form of PmDAP IV comprised 723 amino acids, with a theoretical molecular weight of 79981.58 and a theoretical isoelectric point of 5.80. .. An E . coli JM109 (Takara Bio) transformant harbouring the full-length PmDAP IV M12I mutant sequence inserted into the pUC19 (Takara Bio) expression plasmid was used to produce the periplasmic form of PmDAP IV.

Mutagenesis:

Article Title: Engineering of a thermostable esterase Est816 to improve its quorum-quenching activity and the underlying structural basis
Article Snippet: Taken together, the mutagenesis and structural studies provided useful information about the enzymatic properties, and will guide our next-round rational design to further develop Est816 as an efficient quorum-quenching reagent for pathogen outbreak prevention. .. Escherichia coli (E. coli ) DH5α and pUC19 (TaKaRa, Dalian, China) were used for the construction of random mutagenesis libraries. .. The E. coli strain BL21 (DE3) and the pET-21b (+) plasmid (Novagen, Madison, WI, USA) was used for protein expression.

Article Title: Enzymatic improvement of mitochondrial thiol oxidase Erv1 for oxidized glutathione fermentation by Saccharomyces cerevisiae
Article Snippet: The PCR product was cloned between Sph I and Bam HI sites of pUC19 (Takara Bio). .. The plasmids for preparation of Erv1 variant proteins were constructed by inverse PCR using corresponding primer pairs and templates (Additional file : Table S1).

Article Title: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues
Article Snippet: The periplasmic form of PmDAP IV comprised 723 amino acids, with a theoretical molecular weight of 79981.58 and a theoretical isoelectric point of 5.80. .. An E . coli JM109 (Takara Bio) transformant harbouring the full-length PmDAP IV M12I mutant sequence inserted into the pUC19 (Takara Bio) expression plasmid was used to produce the periplasmic form of PmDAP IV. .. Cells were grown in 2 x YT media at 310 K. Overproduction of PmDAP IV was performed by IPTG induction (final concentration, 0.1 mM) at an OD600 of approximately 0.6.

Size-exclusion Chromatography:

Article Title: Establishment of a novel hepatic steatosis cell model by Cas9/sgRNA-mediated DGKθ gene knockout
Article Snippet: According to a previously described method , the human U6 promoter and sgRNA backbone were sequentially cloned into pUC19 (Clontech Laboratories, Inc., Mountain view, CA, USA), the obtained plasmid was called the pUC19/U6-BsaI-sgRNA backbone vector. .. To construct the donor vector, an up homologous arm, 909 bp in length and located upstream of the targeting sites, was amplified through nest polymerase chain reaction (PCR) using two pairs of primers ( ) based on a template of human genomic DNA.

Labeling:

Article Title: Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein
Article Snippet: The membrane was incubated for 2 h at 68°C in 20 ml of prehybridization solution in a hybridization chamber. .. The radiolabeled probes were prepared with [γ-32 P]dCTP (6000 Ci/mmol, Amersham Pharmacia Biotech, Buckinghamshire, UK), a kit (BcaBEST™ Labeling kit, Takara Bio) and pUC19 or a human gene site (3121 bp). .. Following addition of the radiolabeled probes, the membrane was incubated at 68°C for a further 12 h. After hybridization, the membrane was washed with 200 ml 0.5× SSC (7.5 mM sodium citrate pH 7.0 and 75 mM NaCl), 0.1% SDS at 68°C.

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: 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). .. 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).

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: However, non-specific amplification products emerge as fragments with other sizes, or are migrated at over 20 kbp , . .. 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: 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 . .. By contrast, non-specific amplification products were found in all NTCs and positive controls using the commercially available Phi29 DNA polymerases (Epicentre Lot.No.

Article Title: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues
Article Snippet: Paragraph title: Overexpression and purification of PmDAPIV ... An E . coli JM109 (Takara Bio) transformant harbouring the full-length PmDAP IV M12I mutant sequence inserted into the pUC19 (Takara Bio) expression plasmid was used to produce the periplasmic form of PmDAP IV.

Reverse Transcription Polymerase Chain Reaction:

Article Title: Enzymatic improvement of mitochondrial thiol oxidase Erv1 for oxidized glutathione fermentation by Saccharomyces cerevisiae
Article Snippet: The cDNA was prepared by reverse transcription PCR using a PrimeScrip RT-PCR Kit (Takara Bio, Otsu, Japan) from total RNA extracted from S. cerevisiae YPH499 cells using NucleoSpin RNA (Takara Bio). .. The PCR product was cloned between Sph I and Bam HI sites of pUC19 (Takara Bio).

Protein Extraction:

Article Title: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues
Article Snippet: An E . coli JM109 (Takara Bio) transformant harbouring the full-length PmDAP IV M12I mutant sequence inserted into the pUC19 (Takara Bio) expression plasmid was used to produce the periplasmic form of PmDAP IV. .. Cells were grown in 2 x YT media at 310 K. Overproduction of PmDAP IV was performed by IPTG induction (final concentration, 0.1 mM) at an OD600 of approximately 0.6.

Selection:

Article Title: Precisely controlling endogenous protein dosage in hPSCs and derivatives to model FOXG1 syndrome
Article Snippet: U6-sgRNA sequence was also obtained from PX458. pMini-sgRNA was built based on puc19 (Takara, 3219) using Gibson Assembly (NEB, E2611L). .. MIT CRISPR design tool ( http://crispr.mit.edu ) or DESKGEN Cloud ( https://www.deskgen.com ) was used to design the sgRNAs (Supplementary Data ) and predict off-target sites.

CRISPR:

Article Title: Establishment of a novel hepatic steatosis cell model by Cas9/sgRNA-mediated DGKθ gene knockout
Article Snippet: The targeting regions for four pairs of single-guide RNA (sgRNA) located in exon 6, exon 7 or exon 8 of human DGKθ were selected using the CRISPR Design website ( http://crispr.mit.edu ). .. According to a previously described method , the human U6 promoter and sgRNA backbone were sequentially cloned into pUC19 (Clontech Laboratories, Inc., Mountain view, CA, USA), the obtained plasmid was called the pUC19/U6-BsaI-sgRNA backbone vector.

Article Title: Precisely controlling endogenous protein dosage in hPSCs and derivatives to model FOXG1 syndrome
Article Snippet: U6-sgRNA sequence was also obtained from PX458. pMini-sgRNA was built based on puc19 (Takara, 3219) using Gibson Assembly (NEB, E2611L). .. The pmini-sgRNA vector includes two BbsI restriction sites for rapid cloning of sgRNA.

Plasmid Preparation:

Article Title: Vpu Augments the Initial Burst Phase of HIV-1 Propagation and Downregulates BST2 and CD4 in Humanized Mice
Article Snippet: The activated human CD4+ T cells were maintained in RPMI 1640 medium containing 10% fetal calf serum, 100 U/ml interleukin-2, 100 U/ml penicillin, and 100 μg/ml streptomycin. .. For in vitro transfection experiments shown in , 1 μg of pAD8+ (a molecular clone of HIV-1 strain AD8 [HIV-1AD8 ]) , pAD8-UDEL2 , which is a derivative of AD8 carrying an 81-bp deletion and an 8-bp irrelevant insertion in the vpu region ( , ), or pUC19 (for mock control [TaKaRa]; shown as “vector” on the figures) was transfected into 293T and HeLa cells by using Lipofectamine 2000 (Life Technologies) according to the manufacturer's protocol. .. At 48 h posttransfection, the culture supernatant was harvested, centrifuged, and then filtered through a 0.45-μm-pore-size filter (Millipore) to produce virus solutions.

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). .. 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: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression
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 ( ). .. Second, three kinds of branched DNA structures, the immobile Holliday junction, and the D-loop and loop structures, were incubated with ttMutS2.

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression
Article Snippet: Such junction-specific protection was not detected when a mismatch-recognition protein, ttMutS1, was used ( ). ttMutS2 Preferably Digested Branched DNA Structures —Because competition experiments and DNase I footprinting assays revealed that ttMutS2 preferably binds to branched DNA structures, nuclease activity assays of ttMutS2 were carried out using branched DNA structures as substrates. .. 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: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression
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. .. Crystal Structure of the ttMutS2 Endonuclease Domain —We prepared ttSmr663 for x-ray crystallographic analysis.

Article Title: Establishment of a novel hepatic steatosis cell model by Cas9/sgRNA-mediated DGKθ gene knockout
Article Snippet: The sgRNAs were synthesized at the Beijing Genomics Institute (Beijing, China). .. According to a previously described method , the human U6 promoter and sgRNA backbone were sequentially cloned into pUC19 (Clontech Laboratories, Inc., Mountain view, CA, USA), the obtained plasmid was called the pUC19/U6-BsaI-sgRNA backbone vector. .. The synthesized oligos were annealed, and ligated into the BsaI sites of the pUC19/U6-BsaI-sgRNA backbone vector under the control of the U6 promoter.

Article Title: Precisely controlling endogenous protein dosage in hPSCs and derivatives to model FOXG1 syndrome
Article Snippet: Mammal codon-optimized Streptococcus pyogenes wild-type Cas9 expressing plasmid was built base on pmaxGFP (LONZA). .. U6-sgRNA sequence was also obtained from PX458. pMini-sgRNA was built based on puc19 (Takara, 3219) using Gibson Assembly (NEB, E2611L).

Article Title: Improved sugar-free succinate production by Synechocystis sp. PCC 6803 following identification of the limiting steps in glycogen catabolism
Article Snippet: The Nde I site (CATATG) of pUC19 (Takara Bio) was replaced with CACATG by digesting Aat II and Eco RI and inserting the synthetic DNA. .. Following the digestion of pBluescript-slr0168-Kmr -PrbcL-TrbcL-slr0168 with Kpn I and Hind III, the fragment containing slr0168 was integrated into the Kpn I/Hind III site of the modified pUC19 vector to yield pSKrbcL-slr0168.

Article Title: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues
Article Snippet: The periplasmic form of PmDAP IV comprised 723 amino acids, with a theoretical molecular weight of 79981.58 and a theoretical isoelectric point of 5.80. .. An E . coli JM109 (Takara Bio) transformant harbouring the full-length PmDAP IV M12I mutant sequence inserted into the pUC19 (Takara Bio) expression plasmid was used to produce the periplasmic form of PmDAP IV. .. Cells were grown in 2 x YT media at 310 K. Overproduction of PmDAP IV was performed by IPTG induction (final concentration, 0.1 mM) at an OD600 of approximately 0.6.

Article Title: Generation of Circularly Permuted Fluorescent-Protein-Based Indicators for In Vitro and In Vivo Detection of Citrate
Article Snippet: To generate the cpFPs, two fragments of the enhanced green fluorescent protein (EGFP) coding sequence were amplified from the plasmid pBEGFP-F , by PCR with the specific primers shown in : Pr3 and Pr4 for the fragment of residues 145–238 of EGFP; Pr5 and Pr6 for the fragment of residues 2–144 of EGFP (amino acid residue numbers correspond to those of the standard GFP). .. The resulting fragment encoding a circularly permuted cpFP was amplified by PCR with Pr3 and Pr6, digested with Pst I and Kpn I, and the restriction fragment covering the coding region for cpFP was inserted into pUC19 (Takara Bio).

Irradiation:

Article Title: Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein
Article Snippet: The DNA was then fixed to the membrane by ultraviolet irradiation. .. The radiolabeled probes were prepared with [γ-32 P]dCTP (6000 Ci/mmol, Amersham Pharmacia Biotech, Buckinghamshire, UK), a kit (BcaBEST™ Labeling kit, Takara Bio) and pUC19 or a human gene site (3121 bp).

Negative Control:

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression
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 ( ). .. Second, three kinds of branched DNA structures, the immobile Holliday junction, and the D-loop and loop structures, were incubated with ttMutS2.

Positron Emission Tomography:

Article Title: Enzymatic improvement of mitochondrial thiol oxidase Erv1 for oxidized glutathione fermentation by Saccharomyces cerevisiae
Article Snippet: The PCR product was cloned between Sph I and Bam HI sites of pUC19 (Takara Bio). .. The plasmids for preparation of Erv1 variant proteins were constructed by inverse PCR using corresponding primer pairs and templates (Additional file : Table S1).

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: In addition, since MPRCA and MDA use the same DNA amplification machinery, RNA-primed MPRCA can also amplify DNA fragments, (e.g., from the E. coli genome) contaminating in the polymerase. .. 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 , .

In Vitro:

Article Title: Vpu Augments the Initial Burst Phase of HIV-1 Propagation and Downregulates BST2 and CD4 in Humanized Mice
Article Snippet: The activated human CD4+ T cells were maintained in RPMI 1640 medium containing 10% fetal calf serum, 100 U/ml interleukin-2, 100 U/ml penicillin, and 100 μg/ml streptomycin. .. For in vitro transfection experiments shown in , 1 μg of pAD8+ (a molecular clone of HIV-1 strain AD8 [HIV-1AD8 ]) , pAD8-UDEL2 , which is a derivative of AD8 carrying an 81-bp deletion and an 8-bp irrelevant insertion in the vpu region ( , ), or pUC19 (for mock control [TaKaRa]; shown as “vector” on the figures) was transfected into 293T and HeLa cells by using Lipofectamine 2000 (Life Technologies) according to the manufacturer's protocol. .. At 48 h posttransfection, the culture supernatant was harvested, centrifuged, and then filtered through a 0.45-μm-pore-size filter (Millipore) to produce virus solutions.

Column Chromatography:

Article Title: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues
Article Snippet: An E . coli JM109 (Takara Bio) transformant harbouring the full-length PmDAP IV M12I mutant sequence inserted into the pUC19 (Takara Bio) expression plasmid was used to produce the periplasmic form of PmDAP IV. .. Cells were grown in 2 x YT media at 310 K. Overproduction of PmDAP IV was performed by IPTG induction (final concentration, 0.1 mM) at an OD600 of approximately 0.6.

Produced:

Article Title: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues
Article Snippet: The PmDAP IV M12I mutant produced only the 82-kDa periplasmic form (residues 23–745) due to translation from Met1 and removal of the signal sequence (residues 1–22) . .. An E . coli JM109 (Takara Bio) transformant harbouring the full-length PmDAP IV M12I mutant sequence inserted into the pUC19 (Takara Bio) expression plasmid was used to produce the periplasmic form of PmDAP IV.

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: 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). .. 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).

Variant Assay:

Article Title: Enzymatic improvement of mitochondrial thiol oxidase Erv1 for oxidized glutathione fermentation by Saccharomyces cerevisiae
Article Snippet: The PCR product was cloned between Sph I and Bam HI sites of pUC19 (Takara Bio). .. After the sequence was checked, the ERV1 gene was subcloned between Nde I and Xho I sites of pET-22b (Novagen) to give pET-ERV1 . pET-ERV1 was used for Erv1 protein preparation.

Homologous Recombination:

Article Title: Precisely controlling endogenous protein dosage in hPSCs and derivatives to model FOXG1 syndrome
Article Snippet: U6-sgRNA sequence was also obtained from PX458. pMini-sgRNA was built based on puc19 (Takara, 3219) using Gibson Assembly (NEB, E2611L). .. MIT CRISPR design tool ( http://crispr.mit.edu ) or DESKGEN Cloud ( https://www.deskgen.com ) was used to design the sgRNAs (Supplementary Data ) and predict off-target sites.

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  • 97
    TaKaRa puc19 vector
    Construction strategy of pIC-2DuCV. a Two full-length genomes of DuCV strain GH01, denoted IC1 and IC2, were amplified. b IC1 and IC2 were ligated into the <t>pUC19</t> vector to yield pIC-1 and pIC-2, respectively. c IC-2 was ligated head-to-tail to pIC-1 to produce a tandem-dimerized DuCV DNA clone, which was denoted pIC-2DuCV. d pIC-2DuCV
    Puc19 Vector, supplied by TaKaRa, used in various techniques. Bioz Stars score: 97/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/puc19 vector/product/TaKaRa
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    Price from $9.99 to $1999.99
    puc19 vector - by Bioz Stars, 2019-10
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    78
    TaKaRa 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.
    Plasmid Puc19 Dna, supplied by TaKaRa, used in various techniques. Bioz Stars score: 78/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/plasmid puc19 dna/product/TaKaRa
    Average 78 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    plasmid puc19 dna - by Bioz Stars, 2019-10
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      Buy from Supplier

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    Construction strategy of pIC-2DuCV. a Two full-length genomes of DuCV strain GH01, denoted IC1 and IC2, were amplified. b IC1 and IC2 were ligated into the pUC19 vector to yield pIC-1 and pIC-2, respectively. c IC-2 was ligated head-to-tail to pIC-1 to produce a tandem-dimerized DuCV DNA clone, which was denoted pIC-2DuCV. d pIC-2DuCV

    Journal: Virology Journal

    Article Title: Rescue of a duck circovirus from an infectious DNA clone in ducklings

    doi: 10.1186/s12985-015-0312-6

    Figure Lengend Snippet: Construction strategy of pIC-2DuCV. a Two full-length genomes of DuCV strain GH01, denoted IC1 and IC2, were amplified. b IC1 and IC2 were ligated into the pUC19 vector to yield pIC-1 and pIC-2, respectively. c IC-2 was ligated head-to-tail to pIC-1 to produce a tandem-dimerized DuCV DNA clone, which was denoted pIC-2DuCV. d pIC-2DuCV

    Article Snippet: The products were subsequently inserted into a pUC19 vector (TaKaRa, Dalian, China) that had been previously digested with Hind III/BamH I or BamH I/EcoR I, respectively.

    Techniques: Amplification, Plasmid Preparation

    Construction strategy of pIC-Mu2DuCV. a Two full-length genomes of DuCV strain GH01, denoted IC-Mu1 and IC-Mu2, were amplified by overlapping PCR. b IC-Mu1 and IC-Mu2 were ligated into the pUC19 vector to yield pIC-Mu1 and pIC-Mu2, respectively. c IC-Mu2 was ligated head-to-tail to pIC-Mu1 to produce a tandem-dimerized DuCV DNA clone, which was denoted pIC-Mu2DuCV. d pIC-Mu2DuCV

    Journal: Virology Journal

    Article Title: Rescue of a duck circovirus from an infectious DNA clone in ducklings

    doi: 10.1186/s12985-015-0312-6

    Figure Lengend Snippet: Construction strategy of pIC-Mu2DuCV. a Two full-length genomes of DuCV strain GH01, denoted IC-Mu1 and IC-Mu2, were amplified by overlapping PCR. b IC-Mu1 and IC-Mu2 were ligated into the pUC19 vector to yield pIC-Mu1 and pIC-Mu2, respectively. c IC-Mu2 was ligated head-to-tail to pIC-Mu1 to produce a tandem-dimerized DuCV DNA clone, which was denoted pIC-Mu2DuCV. d pIC-Mu2DuCV

    Article Snippet: The products were subsequently inserted into a pUC19 vector (TaKaRa, Dalian, China) that had been previously digested with Hind III/BamH I or BamH I/EcoR I, respectively.

    Techniques: Amplification, Polymerase Chain Reaction, Plasmid Preparation

    Identification of recombinant pIC-Mu2DuCV plasmid by restriction enzyme digestion. M, wide-range DNA marker (500 ~ 12,000); 1, digested with Hind III; 2, digested with Hind III and BamH I; 3, digested with BamH I and EcoR I; 4, digested with Hind III and EcoR I; 5, digested with Xho I; 6, pUC19 digested with Hind III; 7, pUC19

    Journal: Virology Journal

    Article Title: Rescue of a duck circovirus from an infectious DNA clone in ducklings

    doi: 10.1186/s12985-015-0312-6

    Figure Lengend Snippet: Identification of recombinant pIC-Mu2DuCV plasmid by restriction enzyme digestion. M, wide-range DNA marker (500 ~ 12,000); 1, digested with Hind III; 2, digested with Hind III and BamH I; 3, digested with BamH I and EcoR I; 4, digested with Hind III and EcoR I; 5, digested with Xho I; 6, pUC19 digested with Hind III; 7, pUC19

    Article Snippet: The products were subsequently inserted into a pUC19 vector (TaKaRa, Dalian, China) that had been previously digested with Hind III/BamH I or BamH I/EcoR I, respectively.

    Techniques: Recombinant, Plasmid Preparation, Marker

    Identification of the recombinant plasmid pIC-2DuCV by restriction enzyme digestion. M, wide-range DNA marker (500 ~ 12,000); 1, digested with Hind III; 2, digested with Hind III and BamH I; 3, digested with BamH I and EcoR I; 4, digested with Hind III and EcoR I; 5, pUC19 digested with Hind III

    Journal: Virology Journal

    Article Title: Rescue of a duck circovirus from an infectious DNA clone in ducklings

    doi: 10.1186/s12985-015-0312-6

    Figure Lengend Snippet: Identification of the recombinant plasmid pIC-2DuCV by restriction enzyme digestion. M, wide-range DNA marker (500 ~ 12,000); 1, digested with Hind III; 2, digested with Hind III and BamH I; 3, digested with BamH I and EcoR I; 4, digested with Hind III and EcoR I; 5, pUC19 digested with Hind III

    Article Snippet: The products were subsequently inserted into a pUC19 vector (TaKaRa, Dalian, China) that had been previously digested with Hind III/BamH I or BamH I/EcoR I, respectively.

    Techniques: Recombinant, Plasmid Preparation, Marker

    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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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