Structured Review

Millipore dntp
Characterization of DNA analogs. ( A ) PCR assays analyzed by 5% native polyacrylamide gel electrophoresis. Total PCR volume 100 µl: 20 ng 418-bp DNA template (pJ1506), 0.4 mM each LJM-3222 (5'-G TA CGC AG T ) and LJM-3223 (5'-TGTGAGT AGCTCACTCAT AG ), 0.2 mM each <t>dNTP</t> with indicated analog triphosphate ( 1–9 ) completely replacing appropriate dNTP, and 5 U DNA polymerase (indicated with plus symbol) with associated buffer and cycle conditions. Taq DNA polymerase ( Taq ) conditions: Taq DNA polymerase buffer with 100 mg/ml BSA and 2 mM MgCl ; 98°C (3 min), 30 cycles of [94°C (30 s), 60°C (30 s), and 72°C (45 s)], 72°C (5 min). PrimeSTAR HS DNA polymerase (PS) conditions: PrimeSTAR GC buffer with 2 M betaine; 98°C (3 min), 30 cycles of [98°C (15 s), 60°C (5 s), and 72°C (45 s)], 72°C (5 min). <t>Pwo</t> SuperYield DNA Polymerase ( Pwo ) conditions: Pwo PCR buffer with GC-rich solution and 2 M betaine; 98°C (3 min), 30 cycles of [98°C (1 min), 60°C (2 min), and 72°C (8 min)], 72°C (5 min). Lane 1 is marker (M) DNA (100 bp DNA ladder, Invitrogen) with 400 - and 500-bp bands indicated. ( B ) Anion exchange chromatography of 98-bp DNA-like polymers (pJ1923). Following equilibration in 20 mM Tris–HCl, pH 8 (buffer A), samples were eluted over 25 min at a 1 ml/min flow rate in a linear gradient from 50 to 100% buffer B (buffer A plus 1 M NaCl). Eluent absorbance at 260 nm (milli-absorbance units) was monitored with elution time (min).
Dntp, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 415 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/dntp/product/Millipore
Average 99 stars, based on 415 article reviews
Price from $9.99 to $1999.99
dntp - by Bioz Stars, 2020-03
99/100 stars

Images

1) Product Images from "Mechanical properties of DNA-like polymers"

Article Title: Mechanical properties of DNA-like polymers

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkt808

Characterization of DNA analogs. ( A ) PCR assays analyzed by 5% native polyacrylamide gel electrophoresis. Total PCR volume 100 µl: 20 ng 418-bp DNA template (pJ1506), 0.4 mM each LJM-3222 (5'-G TA CGC AG T ) and LJM-3223 (5'-TGTGAGT AGCTCACTCAT AG ), 0.2 mM each dNTP with indicated analog triphosphate ( 1–9 ) completely replacing appropriate dNTP, and 5 U DNA polymerase (indicated with plus symbol) with associated buffer and cycle conditions. Taq DNA polymerase ( Taq ) conditions: Taq DNA polymerase buffer with 100 mg/ml BSA and 2 mM MgCl ; 98°C (3 min), 30 cycles of [94°C (30 s), 60°C (30 s), and 72°C (45 s)], 72°C (5 min). PrimeSTAR HS DNA polymerase (PS) conditions: PrimeSTAR GC buffer with 2 M betaine; 98°C (3 min), 30 cycles of [98°C (15 s), 60°C (5 s), and 72°C (45 s)], 72°C (5 min). Pwo SuperYield DNA Polymerase ( Pwo ) conditions: Pwo PCR buffer with GC-rich solution and 2 M betaine; 98°C (3 min), 30 cycles of [98°C (1 min), 60°C (2 min), and 72°C (8 min)], 72°C (5 min). Lane 1 is marker (M) DNA (100 bp DNA ladder, Invitrogen) with 400 - and 500-bp bands indicated. ( B ) Anion exchange chromatography of 98-bp DNA-like polymers (pJ1923). Following equilibration in 20 mM Tris–HCl, pH 8 (buffer A), samples were eluted over 25 min at a 1 ml/min flow rate in a linear gradient from 50 to 100% buffer B (buffer A plus 1 M NaCl). Eluent absorbance at 260 nm (milli-absorbance units) was monitored with elution time (min).
Figure Legend Snippet: Characterization of DNA analogs. ( A ) PCR assays analyzed by 5% native polyacrylamide gel electrophoresis. Total PCR volume 100 µl: 20 ng 418-bp DNA template (pJ1506), 0.4 mM each LJM-3222 (5'-G TA CGC AG T ) and LJM-3223 (5'-TGTGAGT AGCTCACTCAT AG ), 0.2 mM each dNTP with indicated analog triphosphate ( 1–9 ) completely replacing appropriate dNTP, and 5 U DNA polymerase (indicated with plus symbol) with associated buffer and cycle conditions. Taq DNA polymerase ( Taq ) conditions: Taq DNA polymerase buffer with 100 mg/ml BSA and 2 mM MgCl ; 98°C (3 min), 30 cycles of [94°C (30 s), 60°C (30 s), and 72°C (45 s)], 72°C (5 min). PrimeSTAR HS DNA polymerase (PS) conditions: PrimeSTAR GC buffer with 2 M betaine; 98°C (3 min), 30 cycles of [98°C (15 s), 60°C (5 s), and 72°C (45 s)], 72°C (5 min). Pwo SuperYield DNA Polymerase ( Pwo ) conditions: Pwo PCR buffer with GC-rich solution and 2 M betaine; 98°C (3 min), 30 cycles of [98°C (1 min), 60°C (2 min), and 72°C (8 min)], 72°C (5 min). Lane 1 is marker (M) DNA (100 bp DNA ladder, Invitrogen) with 400 - and 500-bp bands indicated. ( B ) Anion exchange chromatography of 98-bp DNA-like polymers (pJ1923). Following equilibration in 20 mM Tris–HCl, pH 8 (buffer A), samples were eluted over 25 min at a 1 ml/min flow rate in a linear gradient from 50 to 100% buffer B (buffer A plus 1 M NaCl). Eluent absorbance at 260 nm (milli-absorbance units) was monitored with elution time (min).

Techniques Used: Polymerase Chain Reaction, Polyacrylamide Gel Electrophoresis, Marker, Chromatography, Flow Cytometry

2) Product Images from "Direct Cell Lysis for Single-Cell Gene Expression Profiling"

Article Title: Direct Cell Lysis for Single-Cell Gene Expression Profiling

Journal: Frontiers in Oncology

doi: 10.3389/fonc.2013.00274

Evaluation of direct cell lysis protocols on RT-qPCR . (A) The RT-qPCR yields of Gapdh , Vim , Dll1 , Jag1 , DNA, and RNA spike using 17 lysis conditions. Five nanograms of purified RNA was used in all RT reactions. Relative RT yields are presented as Cq-values on the left y -axis and relative transcript numbers on the right y -axis. The relative transcript number is expressed in percentage relative to the water control for each gene, assuming 100% RT efficiency and 100% PCR efficiency. Lysis conditions with Cq-values below that of the water control are RT enhancing agents, while conditions with higher Cq-values are inhibitory. Data are shown as mean ± SD ( n = 4). Missing data were excluded and are shown in Table S4 in Supplementary Material. (B) Mean RT yield for Gapdh , Vim , Dll , and Jag1 . The relative transcript yield of each transcript was averaged and compared to the optimal RT-qPCR condition (RT mix). Data are shown as mean ± SD ( n = 4). 7-deaz GTP, 7-deaza-2′ deoxyguanosine 5′ triphosphate lithium salt; GTC, guanidine thiocyanate; LPA, linear polyacrylamide; polyI, polyinosinic acid potassium salt; 2× RT buffer, 2× reverse transcription buffer; RT mix, 2× RT buffer, 5 μM random hexamers, 5 μM oligo-dT, and 1 mM dNTP.
Figure Legend Snippet: Evaluation of direct cell lysis protocols on RT-qPCR . (A) The RT-qPCR yields of Gapdh , Vim , Dll1 , Jag1 , DNA, and RNA spike using 17 lysis conditions. Five nanograms of purified RNA was used in all RT reactions. Relative RT yields are presented as Cq-values on the left y -axis and relative transcript numbers on the right y -axis. The relative transcript number is expressed in percentage relative to the water control for each gene, assuming 100% RT efficiency and 100% PCR efficiency. Lysis conditions with Cq-values below that of the water control are RT enhancing agents, while conditions with higher Cq-values are inhibitory. Data are shown as mean ± SD ( n = 4). Missing data were excluded and are shown in Table S4 in Supplementary Material. (B) Mean RT yield for Gapdh , Vim , Dll , and Jag1 . The relative transcript yield of each transcript was averaged and compared to the optimal RT-qPCR condition (RT mix). Data are shown as mean ± SD ( n = 4). 7-deaz GTP, 7-deaza-2′ deoxyguanosine 5′ triphosphate lithium salt; GTC, guanidine thiocyanate; LPA, linear polyacrylamide; polyI, polyinosinic acid potassium salt; 2× RT buffer, 2× reverse transcription buffer; RT mix, 2× RT buffer, 5 μM random hexamers, 5 μM oligo-dT, and 1 mM dNTP.

Techniques Used: Lysis, Quantitative RT-PCR, Purification, Polymerase Chain Reaction

Evaluation of direct cell lysis protocols . (A) The lysis yields of Gapdh , Vim , Dll1 , Jag1 , DNA, and RNA spike compared at 17 lysis conditions. Thirty-two astrocytes were sorted for each condition. Relative cDNA yields are presented as Cq-values on the left y -axis and relative transcript numbers on the right y -axis. The relative transcript number is expressed in percentage compared to the optimal lysis condition for each gene, assuming 100% RT efficiency and 100% PCR efficiency. Data are shown as mean ± SD ( n = 4). Missing data were excluded and are listed in Table S3 in Supplementary Material. (B) Mean cDNA yield of the transcripts. Expressions of Gapdh , Vim , Dll , and Jag1 were averaged and are compared to the overall optimal lysis condition (1 mg/ml BSA). Data are shown as mean ± SD ( n = 4). 7-deaz GTP, 7-deaza-2′ deoxyguanosine 5′ triphosphate lithium salt; GTC, guanidine thiocyanate; LPA, linear polyacrylamide; polyI, polyinosinic acid potassium salt; 2× RT buffer, 2× reverse transcription buffer; RT mix, 2× RT buffer, 5 μM random hexamers, 5 μM oligo-dT, and 1 mM dNTP.
Figure Legend Snippet: Evaluation of direct cell lysis protocols . (A) The lysis yields of Gapdh , Vim , Dll1 , Jag1 , DNA, and RNA spike compared at 17 lysis conditions. Thirty-two astrocytes were sorted for each condition. Relative cDNA yields are presented as Cq-values on the left y -axis and relative transcript numbers on the right y -axis. The relative transcript number is expressed in percentage compared to the optimal lysis condition for each gene, assuming 100% RT efficiency and 100% PCR efficiency. Data are shown as mean ± SD ( n = 4). Missing data were excluded and are listed in Table S3 in Supplementary Material. (B) Mean cDNA yield of the transcripts. Expressions of Gapdh , Vim , Dll , and Jag1 were averaged and are compared to the overall optimal lysis condition (1 mg/ml BSA). Data are shown as mean ± SD ( n = 4). 7-deaz GTP, 7-deaza-2′ deoxyguanosine 5′ triphosphate lithium salt; GTC, guanidine thiocyanate; LPA, linear polyacrylamide; polyI, polyinosinic acid potassium salt; 2× RT buffer, 2× reverse transcription buffer; RT mix, 2× RT buffer, 5 μM random hexamers, 5 μM oligo-dT, and 1 mM dNTP.

Techniques Used: Lysis, Polymerase Chain Reaction

3) Product Images from "Interactions between HIV-1 Reverse Transcriptase and the Downstream Template Strand in Stable Complexes with Primer-Template"

Article Title: Interactions between HIV-1 Reverse Transcriptase and the Downstream Template Strand in Stable Complexes with Primer-Template

Journal: PLoS ONE

doi: 10.1371/journal.pone.0003561

Stalling of primer extension by HIV-1 RT due to a biotin residue placed at a specific position in the template in the absence or presence of SA. (Left panel) Five nM 5′-[ 32 P]-L20 primer annealed to WL50-Bio39 template was extended with 200 nM RT and various concentrations of dNTP (indicated above the lanes) and 6 µM biotin for 45 min at 37°C. (Right panel) 5′-[ 32 P]-L20/WL50-Bio39 P/T was first incubated for 2-3 min with 100 nM SA at 37°C and then RT, dNTPs and biotin were added and primer extension was carried out as above. Labeled products were fractionated on 20% polyacrylamide under denaturing conditions. Arrows indicate 50 nt (full length of template), 39 nt (primer extended to the position of the biotin residue), and 37 nt (primary stop site for primer extension in the presence of SA.). Diagrams at the bottom of the figure show the direction of primer extension (arrows) and the likely position of RT (box) after stalling on a template containing the biotin residue (triangle) in the absence (left) or presence (right) of SA (shown as a tetramer of circles).
Figure Legend Snippet: Stalling of primer extension by HIV-1 RT due to a biotin residue placed at a specific position in the template in the absence or presence of SA. (Left panel) Five nM 5′-[ 32 P]-L20 primer annealed to WL50-Bio39 template was extended with 200 nM RT and various concentrations of dNTP (indicated above the lanes) and 6 µM biotin for 45 min at 37°C. (Right panel) 5′-[ 32 P]-L20/WL50-Bio39 P/T was first incubated for 2-3 min with 100 nM SA at 37°C and then RT, dNTPs and biotin were added and primer extension was carried out as above. Labeled products were fractionated on 20% polyacrylamide under denaturing conditions. Arrows indicate 50 nt (full length of template), 39 nt (primer extended to the position of the biotin residue), and 37 nt (primary stop site for primer extension in the presence of SA.). Diagrams at the bottom of the figure show the direction of primer extension (arrows) and the likely position of RT (box) after stalling on a template containing the biotin residue (triangle) in the absence (left) or presence (right) of SA (shown as a tetramer of circles).

Techniques Used: Incubation, Labeling

Photo-cross-linking of HIV-1 RT to template containing two adjacent BrdU residues. (A) Stable complexes were formed by incubating 40 nM HIV-1 RT, 9 nM P/T (the indicated primer annealed to CBB template ( Figure 1 )), and 100 µM of the +1 dNTP (+1 complex); or 200 nM HIV-1 RT, 9 nM P/T, and 3.2 mM foscarnet (PFA complex) for 10 min at 37°C followed by cooling in ice. Heparin was added and the mixture was kept in ice and exposed to UV light as described in the text. Samples were analyzed by SDS-PAGE. Positions of MW markers are indicated at the left of each panel. (B) Complexes were prepared and analyzed as in (A) except that 5 nM of each P/T was mixed with 200 nM RT only or with RT plus 100 µM of each of the indicated dNTPs or RT plus 3.2 mM foscarnet. “+1” indicates the dNTP complementary to the first unpaired template nucleotide following the primer terminus. (C) Portions of the CBB template (T) sequence and selected primer (P) sequences are shown. “B” indicates BrdU. Subscript “ H ” denotes a dideoxynucleotide residue. The experiment in (A) was repeated with heterodimer RT obtained from Worthington Biochemical Corp. with similar results.
Figure Legend Snippet: Photo-cross-linking of HIV-1 RT to template containing two adjacent BrdU residues. (A) Stable complexes were formed by incubating 40 nM HIV-1 RT, 9 nM P/T (the indicated primer annealed to CBB template ( Figure 1 )), and 100 µM of the +1 dNTP (+1 complex); or 200 nM HIV-1 RT, 9 nM P/T, and 3.2 mM foscarnet (PFA complex) for 10 min at 37°C followed by cooling in ice. Heparin was added and the mixture was kept in ice and exposed to UV light as described in the text. Samples were analyzed by SDS-PAGE. Positions of MW markers are indicated at the left of each panel. (B) Complexes were prepared and analyzed as in (A) except that 5 nM of each P/T was mixed with 200 nM RT only or with RT plus 100 µM of each of the indicated dNTPs or RT plus 3.2 mM foscarnet. “+1” indicates the dNTP complementary to the first unpaired template nucleotide following the primer terminus. (C) Portions of the CBB template (T) sequence and selected primer (P) sequences are shown. “B” indicates BrdU. Subscript “ H ” denotes a dideoxynucleotide residue. The experiment in (A) was repeated with heterodimer RT obtained from Worthington Biochemical Corp. with similar results.

Techniques Used: SDS Page, Sequencing

Effect of preformed RT stable ternary complexes on SA binding to a template biotin residue. Five nM 5′- 32 P-labeled P/T L35-ddA/WL50-Bio39 (A,C) or L36-ddA/WL50-Bio39 (B,D) were incubated without or with 100 nM RT in the absence of ligands or with 0.8, 3.2 or 6.4 mM dNTP. In A and B, SA (50 nM) was added for 5 min at 37°C, and 0.6 µM biotin was added to bind excess SA. Then RT was dissociated with SDS and urea, and SA-biotin-DNA complexes were separated from free DNA by electrophoresis on nondenaturing gels. For C and D, complexes formed with dNTP were transferred to ice, treated with heparin to dissociate RT•P/T binary complexes and fractionated by nondenaturing gel electrophoresis. Arrows to the right of each panel indicate positions of free DNA (P/T) and SA-biotin-DNA complexes (A,B) or dNTP•RT•P/T ternary complexes (C,D). A portion of each P/T sequence is shown. “Bio” indicates the biotin-ON linkage. Subscript “ H ” denotes a dideoxyribonucleotide residue.
Figure Legend Snippet: Effect of preformed RT stable ternary complexes on SA binding to a template biotin residue. Five nM 5′- 32 P-labeled P/T L35-ddA/WL50-Bio39 (A,C) or L36-ddA/WL50-Bio39 (B,D) were incubated without or with 100 nM RT in the absence of ligands or with 0.8, 3.2 or 6.4 mM dNTP. In A and B, SA (50 nM) was added for 5 min at 37°C, and 0.6 µM biotin was added to bind excess SA. Then RT was dissociated with SDS and urea, and SA-biotin-DNA complexes were separated from free DNA by electrophoresis on nondenaturing gels. For C and D, complexes formed with dNTP were transferred to ice, treated with heparin to dissociate RT•P/T binary complexes and fractionated by nondenaturing gel electrophoresis. Arrows to the right of each panel indicate positions of free DNA (P/T) and SA-biotin-DNA complexes (A,B) or dNTP•RT•P/T ternary complexes (C,D). A portion of each P/T sequence is shown. “Bio” indicates the biotin-ON linkage. Subscript “ H ” denotes a dideoxyribonucleotide residue.

Techniques Used: Binding Assay, Labeling, Incubation, Nucleic Acid Electrophoresis, Sequencing

4) Product Images from "Mechanical properties of DNA-like polymers"

Article Title: Mechanical properties of DNA-like polymers

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkt808

Characterization of DNA analogs. ( A ) PCR assays analyzed by 5% native polyacrylamide gel electrophoresis. Total PCR volume 100 µl: 20 ng 418-bp DNA template (pJ1506), 0.4 mM each LJM-3222 (5'-G TA CGC AG T ) and LJM-3223 (5'-TGTGAGT AGCTCACTCAT AG ), 0.2 mM each dNTP with indicated analog triphosphate ( 1–9 ) completely replacing appropriate dNTP, and 5 U DNA polymerase (indicated with plus symbol) with associated buffer and cycle conditions. Taq DNA polymerase ( Taq ) conditions: Taq DNA polymerase buffer with 100 mg/ml BSA and 2 mM MgCl ; 98°C (3 min), 30 cycles of [94°C (30 s), 60°C (30 s), and 72°C (45 s)], 72°C (5 min). PrimeSTAR HS DNA polymerase (PS) conditions: PrimeSTAR GC buffer with 2 M betaine; 98°C (3 min), 30 cycles of [98°C (15 s), 60°C (5 s), and 72°C (45 s)], 72°C (5 min). Pwo SuperYield DNA Polymerase ( Pwo ) conditions: Pwo PCR buffer with GC-rich solution and 2 M betaine; 98°C (3 min), 30 cycles of [98°C (1 min), 60°C (2 min), and 72°C (8 min)], 72°C (5 min). Lane 1 is marker (M) DNA (100 bp DNA ladder, Invitrogen) with 400 - and 500-bp bands indicated. ( B ) Anion exchange chromatography of 98-bp DNA-like polymers (pJ1923). Following equilibration in 20 mM Tris–HCl, pH 8 (buffer A), samples were eluted over 25 min at a 1 ml/min flow rate in a linear gradient from 50 to 100% buffer B (buffer A plus 1 M NaCl). Eluent absorbance at 260 nm (milli-absorbance units) was monitored with elution time (min).
Figure Legend Snippet: Characterization of DNA analogs. ( A ) PCR assays analyzed by 5% native polyacrylamide gel electrophoresis. Total PCR volume 100 µl: 20 ng 418-bp DNA template (pJ1506), 0.4 mM each LJM-3222 (5'-G TA CGC AG T ) and LJM-3223 (5'-TGTGAGT AGCTCACTCAT AG ), 0.2 mM each dNTP with indicated analog triphosphate ( 1–9 ) completely replacing appropriate dNTP, and 5 U DNA polymerase (indicated with plus symbol) with associated buffer and cycle conditions. Taq DNA polymerase ( Taq ) conditions: Taq DNA polymerase buffer with 100 mg/ml BSA and 2 mM MgCl ; 98°C (3 min), 30 cycles of [94°C (30 s), 60°C (30 s), and 72°C (45 s)], 72°C (5 min). PrimeSTAR HS DNA polymerase (PS) conditions: PrimeSTAR GC buffer with 2 M betaine; 98°C (3 min), 30 cycles of [98°C (15 s), 60°C (5 s), and 72°C (45 s)], 72°C (5 min). Pwo SuperYield DNA Polymerase ( Pwo ) conditions: Pwo PCR buffer with GC-rich solution and 2 M betaine; 98°C (3 min), 30 cycles of [98°C (1 min), 60°C (2 min), and 72°C (8 min)], 72°C (5 min). Lane 1 is marker (M) DNA (100 bp DNA ladder, Invitrogen) with 400 - and 500-bp bands indicated. ( B ) Anion exchange chromatography of 98-bp DNA-like polymers (pJ1923). Following equilibration in 20 mM Tris–HCl, pH 8 (buffer A), samples were eluted over 25 min at a 1 ml/min flow rate in a linear gradient from 50 to 100% buffer B (buffer A plus 1 M NaCl). Eluent absorbance at 260 nm (milli-absorbance units) was monitored with elution time (min).

Techniques Used: Polymerase Chain Reaction, Polyacrylamide Gel Electrophoresis, Marker, Chromatography, Flow Cytometry

5) Product Images from "Nucleotide modification at the ?-phosphate leads to the improved fidelity of HIV-1 reverse transcriptase"

Article Title: Nucleotide modification at the ?-phosphate leads to the improved fidelity of HIV-1 reverse transcriptase

Journal: Nucleic Acids Research

doi: 10.1093/nar/gki779

The modeled structures of dTTP and ANS-dTTP within the HIV-RT ternary complex. The backbone structures of p66 and p51 are rendered in brown and green ribbons, respectively, and the DNA template and primer backbone structures are rendered in red and blue ribbons. ( A ) The final conformation of the modeled structure containing dTTP displayed at the same viewing angle as in Figure 4A . ( B ) The final conformation of the modeled structure containing ANS-dTTP displayed at the same viewing angle as in Figure 4B . ( C ) Comparison of the dTTP structure with the modeled, non-complementary structures. ( D ) Comparison of the ANS-dTTP structure with the modeled, non-complementary structures. For clarity, panels C and D do not show the p66 and p51 domains or the two Mg 2+ ions. In panels C and D the dNTP and ANS-dNTP structures for A, C, and G are colored in white, cyan, and green, respectively, while the rest of the atoms are colored as in Figure 4 .
Figure Legend Snippet: The modeled structures of dTTP and ANS-dTTP within the HIV-RT ternary complex. The backbone structures of p66 and p51 are rendered in brown and green ribbons, respectively, and the DNA template and primer backbone structures are rendered in red and blue ribbons. ( A ) The final conformation of the modeled structure containing dTTP displayed at the same viewing angle as in Figure 4A . ( B ) The final conformation of the modeled structure containing ANS-dTTP displayed at the same viewing angle as in Figure 4B . ( C ) Comparison of the dTTP structure with the modeled, non-complementary structures. ( D ) Comparison of the ANS-dTTP structure with the modeled, non-complementary structures. For clarity, panels C and D do not show the p66 and p51 domains or the two Mg 2+ ions. In panels C and D the dNTP and ANS-dNTP structures for A, C, and G are colored in white, cyan, and green, respectively, while the rest of the atoms are colored as in Figure 4 .

Techniques Used:

6) Product Images from "The GABA transaminase, ABAT, is essential for mitochondrial nucleoside metabolism"

Article Title: The GABA transaminase, ABAT, is essential for mitochondrial nucleoside metabolism

Journal: Cell metabolism

doi: 10.1016/j.cmet.2015.02.008

ABAT functions in the conversion of dNDP to dNTP in the mitochondrial nucleoside salvage pathway
Figure Legend Snippet: ABAT functions in the conversion of dNDP to dNTP in the mitochondrial nucleoside salvage pathway

Techniques Used:

Related Articles

Clone Assay:

Article Title: Frequent epigenetic inactivation of Wnt antagonist genes in breast cancer
Article Snippet: PCR was run in a 25-μ l volume containing 50 ng bisulphite-treated DNA, 1 × MSP buffer (67 mM Tris-HCl (pH 8.8), 16.6 mM (NH4 )2 SO4 , 6.7 mM MgCl2 and 10 mM 2-mercaptoethanol), 1.25 mM dNTP, 0.4 μ M each primer and 0.5 U of JumpStart REDTaq DNA Polymerase (Sigma). .. Amplified bisulphite-sequencing PCR products were cloned into pCR2.1-TOPO vector (Invitrogen), and 10 clones from each sample were sequenced.

Amplification:

Article Title: Mechanical properties of DNA-like polymers
Article Snippet: Paragraph title: Polymerase chain reaction amplification of modified DNAs ... For analogs 7 and 8 , PCR reactions (100 µl) included 20 ng template, 0.4 mM forward and reverse primers, Pwo PCR buffer (Roche), GC-rich solution (Roche), 0.2 mM each dNTP (dTTP completely replaced with analog), 2 M betaine (Sigma-Aldrich) and 5 U Pwo SuperYield DNA Polymerase (Roche).

Article Title: Frequent epigenetic inactivation of Wnt antagonist genes in breast cancer
Article Snippet: PCR was run in a 25-μ l volume containing 50 ng bisulphite-treated DNA, 1 × MSP buffer (67 mM Tris-HCl (pH 8.8), 16.6 mM (NH4 )2 SO4 , 6.7 mM MgCl2 and 10 mM 2-mercaptoethanol), 1.25 mM dNTP, 0.4 μ M each primer and 0.5 U of JumpStart REDTaq DNA Polymerase (Sigma). .. Amplified bisulphite-sequencing PCR products were cloned into pCR2.1-TOPO vector (Invitrogen), and 10 clones from each sample were sequenced.

Article Title: Taxonomic hypotheses regarding the genus Gerbillus ( Rodentia, Muridae, Gerbillinae) based on molecular analyses of museum specimens
Article Snippet: Due to the degradation of DNA in museum samples, we amplified a short fragment of cytb by designing two new primers named GERBCYTB-F2 (5’- GCA AAC GGA GCC TCA ATA TT - 3’) and GERBCYTB-R3 (5’-CAT TCT ACR ATT GTT GGG CCA - 3’). .. The 25μl reaction solution was prepared by mixing 14.5μl of DNase-RNase free water (Qiagen), 2.5μl of buffer (1X concentration), 2μl MgCl2 (2mM), 2.5μl dNTP (250μM; Sigma), 0.5μl of each primer (0.5μM), 0.5μl of AmpliTaq Gold (2.5 units; Applied biosystems).

Article Title: Staphylococcus aureus and MRSA Growth and Biofilm Formation after Treatment with Antibiotics and SeNPs
Article Snippet: Paragraph title: 3.5.2. Reverse Transcription and Amplification of cDNA for mecA Gene ... The final volume of the PCR reaction mixture was 25 μL containing 17.3 μL of sterile water, 2.5 μL of 1× Taq reaction buffer, 0.5 μL of 100 mM dNTP, 1 μL of forward primer, 1 μL of reverse primer and 0.2 μL of Taq DNA polymerase (Sigma-Aldrich, St. Louis, MO, USA) and 2.5 µL of cDNA.

Article Title: Screening of Viral Pathogens from Pediatric Ileal Tissue Samples after Vaccination
Article Snippet: .. Samples were amplified by combining 5 μ L of the double-stranded cDNA product with 5 μ L 10x Sigma Taq buffer, 1 μ L dNTP (12.5 mM), 1 μ L primer 5′-GATGAGGGAAGATGGGG-3′ (100 pmole/μ L), 1 μ L Sigma KlenTaq LA polymerase, and 37 μ L water. .. Reactions were placed in a thermocycler (Tetrad Thermal Cycler, MJ Research, Quebec, Canada) with the following conditions: 94°C for 2 min; 40 cycles of 94°C for 30 sec, 50°C for 1 min, and 68°C for 1 min; and 72°C for 10 min. Amplified samples were purified using the Qiaquick PCR Purification Columns (Qiagen) according to manufacturer's instructions.

Article Title: Analysis of transcribed human endogenous retrovirus W env loci clarifies the origin of multiple sclerosis-associated retrovirus env sequences
Article Snippet: PCR primer sequences for amplification of HERV-W env were as follows: forward primer 5'-TTCACTGCCCACACCCAT-3'; reverse primer 5'-GAGGTACCACAGACAAAAAATATTCCT-3'. .. Conventional PCR was performed in a 50-μl reaction containing 1 μl of cDNA, 0.5 μM of each primer, 200 μM of each dNTP, reaction buffer (10 mM Tris-HCl, 50 mM KCl, 1.5 mM MgCl2 ), and 0.05 units/μl of Taq DNA Polymerase (D1806, Sigma).

Article Title: Genetic Structure, Diversity and Long Term Viability of a Medicinal Plant, Nothapodytes nimmoniana Graham. (Icacinaceae), in Protected and Non-Protected Areas in the Western Ghats Biodiversity Hotspot
Article Snippet: .. The PCR amplification was carried out in a 25-µl-volume reaction mixture containing 25 ng template DNA, 2.5 µl 10× reaction buffer containing 15 µM MgCl2 , 3 µM of each dNTP, 0.25 µM each forward and reverse primer and 0.5 unit Taq DNA polymerase (Sigma). ..

Article Title: Discovery of EST-derived microsatellite primers in the legume Lens culinaris (Fabaceae) 1
Article Snippet: PCR mixtures of 20 μL consisted of 2.0 μL 10× buffer (100 mM Tris-HCl, 500 mM KCl, 15 mM MgCl2 , 0.01% gelatin), 200 μM each dNTP, 0.5 μM each of forward and reverse primers, 1 U Taq DNA polymerase (PCR reagents and primers procured from Sigma-Aldrich, St. Louis, Missouri, USA), and ∼40 ng DNA and were performed in a Veriti Thermal Cycler (Applied Biosystems, Life Technologies, Singapore). .. The amplification fragments were separated on 3% MetaPhor Agarose gels (Lonza, Rockland, Maine, USA) and visualized by ethidium bromide staining.

Article Title: Clostridium leptum group bacteria abundance and diversity in the fecal microbiota of patients with inflammatory bowel disease: a case-control study in India
Article Snippet: Paragraph title: DNA extraction and polymerase chain reaction amplification ... Polymerase chain reaction (PCR) was performed in a reaction volume of 20 μl containing 1X PCR buffer, 2.5 mM MgCl2 , 200 mM each dNTP, 250 nmol of both forward and reverse primers, 2.5 U of Jumpstart Taq polymerase (Sigma Aldrich Co, St. Louis, MO, USA), and approximately 10 ng of DNA template.

Article Title: Lab to Field Assessment of the Ecotoxicological Impact of Chlorpyrifos, Isoproturon, or Tebuconazole on the Diversity and Composition of the Soil Bacterial Community
Article Snippet: Paragraph title: Amplicon sequencing samples preparation and data analysis ... Concerning the samples from the field study, first-step PCR amplifications were carried out in 50 μL reaction volumes containing 2.5 U of Accuzyme polymerase (Bioline), 0.2 μM of each primer, 1x AccuBuffer with 2 mM Mg2+ , 0.5 mM of each dNTP, 0.4 μg/μL of bovine serum albumin (BSA, Sigma) (Kreader, ) and 2 ng of soil DNA.

Whole Genome Amplification:

Article Title: Screening of Viral Pathogens from Pediatric Ileal Tissue Samples after Vaccination
Article Snippet: Paragraph title: 2.4.1. Whole Genome Amplification and Purification ... Samples were amplified by combining 5 μ L of the double-stranded cDNA product with 5 μ L 10x Sigma Taq buffer, 1 μ L dNTP (12.5 mM), 1 μ L primer 5′-GATGAGGGAAGATGGGG-3′ (100 pmole/μ L), 1 μ L Sigma KlenTaq LA polymerase, and 37 μ L water.

Synthesized:

Article Title: Nucleotide modification at the ?-phosphate leads to the improved fidelity of HIV-1 reverse transcriptase
Article Snippet: Synthesis of (5-sulfonate)-naphthalenyl-amino-γ-phosphoramidate-β,α-diphosphate-deoxynucleotides (γ-ANS-dATP) The four γ-P-aminonaphalene-5-sulfonate dNTP compounds, A, C, G and T, were synthesized using a modified procedure for the synthesis of the ANS-ATP ( ). .. 1-Aminonaphthalene-5-sulphonic acid (ANS) and 1-(3-dimethylaminopropyl)-3-ethyl-carbodiimide hydrochloride (DEC) (Lancaster); dNTP (Sigma), and DEAE-Sephadex ion exchange resin (A-25-120) (Aldrich).

Electrophoresis:

Article Title: Clostridium leptum group bacteria abundance and diversity in the fecal microbiota of patients with inflammatory bowel disease: a case-control study in India
Article Snippet: The concentration and integrity of the nucleic acids were determined by electrophoresis on 1% agarose gel containing ethidium bromide. .. Polymerase chain reaction (PCR) was performed in a reaction volume of 20 μl containing 1X PCR buffer, 2.5 mM MgCl2 , 200 mM each dNTP, 250 nmol of both forward and reverse primers, 2.5 U of Jumpstart Taq polymerase (Sigma Aldrich Co, St. Louis, MO, USA), and approximately 10 ng of DNA template.

Article Title: Interactions between HIV-1 Reverse Transcriptase and the Downstream Template Strand in Stable Complexes with Primer-Template
Article Snippet: After 10 min incubation at 37°C with dNTP, the reaction mixtures were cooled on ice for 5 min and SA was added to a final concentration of 50 to 250 nM and incubated at 37°C for 2–5 min. Then free biotin (Sigma Aldrich) was added to a final concentration of 0.6 to 6.0 µM as indicated and the incubation was continued at 37°C for 5 min to trap excess SA. .. RT was dissociated by addition of an equal volume of loading dye-urea-TTE (16 M urea, 180 mM Tris-HCl, pH 9.0, 60 mM taurine, 0.5 mM EDTA, 0.25% (w/v) bromphenol blue, 0.25% (w/v) xylene cyanol) with 0.5% SDS prior to electrophoresis.

Incubation:

Article Title: Direct Cell Lysis for Single-Cell Gene Expression Profiling
Article Snippet: .. Directly lysed cells were incubated in 0.5 mM dNTP (Sigma-Aldrich), 2.5 μM oligo-dT (Metabion), and 2.5 μM random hexamers (Metabion) at 65°C for 5 min and then chilled on ice. .. 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2 , 5 mM dithiothreitol, 10 U RNaseOut, and 50 U SuperScript III were added to a final volume of 10 μl (all Invitrogen).

Article Title: Screening of Viral Pathogens from Pediatric Ileal Tissue Samples after Vaccination
Article Snippet: Next, the samples were incubated for 2 min at 85°C and immediately placed on ice for 2 min. Lastly, 1 μ L Klenow buffer was added to the samples and allowed to incubate at 37°C for 60 min followed by 70°C for 20 min. .. Samples were amplified by combining 5 μ L of the double-stranded cDNA product with 5 μ L 10x Sigma Taq buffer, 1 μ L dNTP (12.5 mM), 1 μ L primer 5′-GATGAGGGAAGATGGGG-3′ (100 pmole/μ L), 1 μ L Sigma KlenTaq LA polymerase, and 37 μ L water.

Article Title: Analysis of transcribed human endogenous retrovirus W env loci clarifies the origin of multiple sclerosis-associated retrovirus env sequences
Article Snippet: Another 2 units of TURBO DNase were added and the incubation was continued for 30 minutes at 37°C. .. Conventional PCR was performed in a 50-μl reaction containing 1 μl of cDNA, 0.5 μM of each primer, 200 μM of each dNTP, reaction buffer (10 mM Tris-HCl, 50 mM KCl, 1.5 mM MgCl2 ), and 0.05 units/μl of Taq DNA Polymerase (D1806, Sigma).

Article Title: Interactions between HIV-1 Reverse Transcriptase and the Downstream Template Strand in Stable Complexes with Primer-Template
Article Snippet: .. After 10 min incubation at 37°C with dNTP, the reaction mixtures were cooled on ice for 5 min and SA was added to a final concentration of 50 to 250 nM and incubated at 37°C for 2–5 min. Then free biotin (Sigma Aldrich) was added to a final concentration of 0.6 to 6.0 µM as indicated and the incubation was continued at 37°C for 5 min to trap excess SA. .. RT was dissociated by addition of an equal volume of loading dye-urea-TTE (16 M urea, 180 mM Tris-HCl, pH 9.0, 60 mM taurine, 0.5 mM EDTA, 0.25% (w/v) bromphenol blue, 0.25% (w/v) xylene cyanol) with 0.5% SDS prior to electrophoresis.

Modification:

Article Title: Mechanical properties of DNA-like polymers
Article Snippet: Paragraph title: Polymerase chain reaction amplification of modified DNAs ... For analogs 7 and 8 , PCR reactions (100 µl) included 20 ng template, 0.4 mM forward and reverse primers, Pwo PCR buffer (Roche), GC-rich solution (Roche), 0.2 mM each dNTP (dTTP completely replaced with analog), 2 M betaine (Sigma-Aldrich) and 5 U Pwo SuperYield DNA Polymerase (Roche).

Article Title: Genetic Structure, Diversity and Long Term Viability of a Medicinal Plant, Nothapodytes nimmoniana Graham. (Icacinaceae), in Protected and Non-Protected Areas in the Western Ghats Biodiversity Hotspot
Article Snippet: Leaf samples were air-dried and preserved in silica gel until the extraction of total genomic DNA using a modified CTAB (cetryl trimethyl ammonium bromide) protocol at the Conservation Genetics Laboratory at ATREE. .. The PCR amplification was carried out in a 25-µl-volume reaction mixture containing 25 ng template DNA, 2.5 µl 10× reaction buffer containing 15 µM MgCl2 , 3 µM of each dNTP, 0.25 µM each forward and reverse primer and 0.5 unit Taq DNA polymerase (Sigma).

Article Title: Nucleotide modification at the ?-phosphate leads to the improved fidelity of HIV-1 reverse transcriptase
Article Snippet: Synthesis of (5-sulfonate)-naphthalenyl-amino-γ-phosphoramidate-β,α-diphosphate-deoxynucleotides (γ-ANS-dATP) The four γ-P-aminonaphalene-5-sulfonate dNTP compounds, A, C, G and T, were synthesized using a modified procedure for the synthesis of the ANS-ATP ( ). .. 1-Aminonaphthalene-5-sulphonic acid (ANS) and 1-(3-dimethylaminopropyl)-3-ethyl-carbodiimide hydrochloride (DEC) (Lancaster); dNTP (Sigma), and DEAE-Sephadex ion exchange resin (A-25-120) (Aldrich).

Bisulfite Sequencing:

Article Title: Frequent epigenetic inactivation of Wnt antagonist genes in breast cancer
Article Snippet: Methylation was then analysed using methylation-specific PCR (MSP) and bisulphite sequencing. .. PCR was run in a 25-μ l volume containing 50 ng bisulphite-treated DNA, 1 × MSP buffer (67 mM Tris-HCl (pH 8.8), 16.6 mM (NH4 )2 SO4 , 6.7 mM MgCl2 and 10 mM 2-mercaptoethanol), 1.25 mM dNTP, 0.4 μ M each primer and 0.5 U of JumpStart REDTaq DNA Polymerase (Sigma).

Activation Assay:

Article Title: Taxonomic hypotheses regarding the genus Gerbillus ( Rodentia, Muridae, Gerbillinae) based on molecular analyses of museum specimens
Article Snippet: The 25μl reaction solution was prepared by mixing 14.5μl of DNase-RNase free water (Qiagen), 2.5μl of buffer (1X concentration), 2μl MgCl2 (2mM), 2.5μl dNTP (250μM; Sigma), 0.5μl of each primer (0.5μM), 0.5μl of AmpliTaq Gold (2.5 units; Applied biosystems). .. The cytb amplification was done at the CBGP molecular biology platform (Montferrier-sur-Lez, France) using PCR programs on a Master Cycle rep Gradient (eppendorf), including an activation step of 95 °C for 10 min followed by 55 cycles comprising a first denaturation at 94 °C for 30 s, hybridization at 50 °C for 30 s and elongation at 72 °C for 45s.

Cell Culture:

Article Title: The GABA transaminase, ABAT, is essential for mitochondrial nucleoside metabolism
Article Snippet: Low serum medium (LSM) (DMEM, 0.5% FBS) was added and the cells cultured for 24 hours. .. Subsequently, LSM was replaced with fresh LSM containing either dNMP, dNDP or dNTP (Sigma-Aldrich) each at a final concentration of 50uM.

Generated:

Article Title: Analysis of transcribed human endogenous retrovirus W env loci clarifies the origin of multiple sclerosis-associated retrovirus env sequences
Article Snippet: Negative controls were generated in parallel for each sample by omission of Superscript II from the reaction. .. Conventional PCR was performed in a 50-μl reaction containing 1 μl of cDNA, 0.5 μM of each primer, 200 μM of each dNTP, reaction buffer (10 mM Tris-HCl, 50 mM KCl, 1.5 mM MgCl2 ), and 0.05 units/μl of Taq DNA Polymerase (D1806, Sigma).

Polymerase Chain Reaction:

Article Title: Mechanical properties of DNA-like polymers
Article Snippet: .. For analogs 7 and 8 , PCR reactions (100 µl) included 20 ng template, 0.4 mM forward and reverse primers, Pwo PCR buffer (Roche), GC-rich solution (Roche), 0.2 mM each dNTP (dTTP completely replaced with analog), 2 M betaine (Sigma-Aldrich) and 5 U Pwo SuperYield DNA Polymerase (Roche). .. To generate DNA where only one strand contained analog 8 , the previous conditions were modified so that the template was replaced with the desired amount of unmodified PCR product and the number of cycles was reduced from 30 to a single extension cycle.

Article Title: Frequent epigenetic inactivation of Wnt antagonist genes in breast cancer
Article Snippet: .. PCR was run in a 25-μ l volume containing 50 ng bisulphite-treated DNA, 1 × MSP buffer (67 mM Tris-HCl (pH 8.8), 16.6 mM (NH4 )2 SO4 , 6.7 mM MgCl2 and 10 mM 2-mercaptoethanol), 1.25 mM dNTP, 0.4 μ M each primer and 0.5 U of JumpStart REDTaq DNA Polymerase (Sigma). .. The PCR protocol for MSP entailed 5 min at 95°C; 35 cycles of 30 s at 95°C, 30 s at 60°C and 30 s at 72°C; and a 7-min final extension at 72°C.

Article Title: Taxonomic hypotheses regarding the genus Gerbillus ( Rodentia, Muridae, Gerbillinae) based on molecular analyses of museum specimens
Article Snippet: The 25μl reaction solution was prepared by mixing 14.5μl of DNase-RNase free water (Qiagen), 2.5μl of buffer (1X concentration), 2μl MgCl2 (2mM), 2.5μl dNTP (250μM; Sigma), 0.5μl of each primer (0.5μM), 0.5μl of AmpliTaq Gold (2.5 units; Applied biosystems). .. The cytb amplification was done at the CBGP molecular biology platform (Montferrier-sur-Lez, France) using PCR programs on a Master Cycle rep Gradient (eppendorf), including an activation step of 95 °C for 10 min followed by 55 cycles comprising a first denaturation at 94 °C for 30 s, hybridization at 50 °C for 30 s and elongation at 72 °C for 45s.

Article Title: Staphylococcus aureus and MRSA Growth and Biofilm Formation after Treatment with Antibiotics and SeNPs
Article Snippet: .. The final volume of the PCR reaction mixture was 25 μL containing 17.3 μL of sterile water, 2.5 μL of 1× Taq reaction buffer, 0.5 μL of 100 mM dNTP, 1 μL of forward primer, 1 μL of reverse primer and 0.2 μL of Taq DNA polymerase (Sigma-Aldrich, St. Louis, MO, USA) and 2.5 µL of cDNA. ..

Article Title: Mechanical properties of DNA-like polymers
Article Snippet: .. For analogs 3 , 4 , 5 , 6 and 9 , PCR reactions (100 µl) included 20 ng template, 0.4 mM forward and reverse primers, PrimeSTAR GC buffer (Takara), 0.2 mM each dNTP (again with dTTP completely replaced with analog, except for variant 9 , which completely replaced dATP), 2 M betaine (Sigma-Aldrich) and 5 U PrimeSTAR HS DNA polymerase (Takara). .. For analogs 7 and 8 , PCR reactions (100 µl) included 20 ng template, 0.4 mM forward and reverse primers, Pwo PCR buffer (Roche), GC-rich solution (Roche), 0.2 mM each dNTP (dTTP completely replaced with analog), 2 M betaine (Sigma-Aldrich) and 5 U Pwo SuperYield DNA Polymerase (Roche).

Article Title: Screening of Viral Pathogens from Pediatric Ileal Tissue Samples after Vaccination
Article Snippet: Samples were amplified by combining 5 μ L of the double-stranded cDNA product with 5 μ L 10x Sigma Taq buffer, 1 μ L dNTP (12.5 mM), 1 μ L primer 5′-GATGAGGGAAGATGGGG-3′ (100 pmole/μ L), 1 μ L Sigma KlenTaq LA polymerase, and 37 μ L water. .. Reactions were placed in a thermocycler (Tetrad Thermal Cycler, MJ Research, Quebec, Canada) with the following conditions: 94°C for 2 min; 40 cycles of 94°C for 30 sec, 50°C for 1 min, and 68°C for 1 min; and 72°C for 10 min. Amplified samples were purified using the Qiaquick PCR Purification Columns (Qiagen) according to manufacturer's instructions.

Article Title: Analysis of transcribed human endogenous retrovirus W env loci clarifies the origin of multiple sclerosis-associated retrovirus env sequences
Article Snippet: .. Conventional PCR was performed in a 50-μl reaction containing 1 μl of cDNA, 0.5 μM of each primer, 200 μM of each dNTP, reaction buffer (10 mM Tris-HCl, 50 mM KCl, 1.5 mM MgCl2 ), and 0.05 units/μl of Taq DNA Polymerase (D1806, Sigma). .. Cycling parameters were as follows: 3 minutes at 95°C; 40 cycles of 50 sec at 95°C, 50 sec at 58°C, and 1 minute at 72°C; and 10 minutes at 72°C.

Article Title: Genetic Structure, Diversity and Long Term Viability of a Medicinal Plant, Nothapodytes nimmoniana Graham. (Icacinaceae), in Protected and Non-Protected Areas in the Western Ghats Biodiversity Hotspot
Article Snippet: .. The PCR amplification was carried out in a 25-µl-volume reaction mixture containing 25 ng template DNA, 2.5 µl 10× reaction buffer containing 15 µM MgCl2 , 3 µM of each dNTP, 0.25 µM each forward and reverse primer and 0.5 unit Taq DNA polymerase (Sigma). ..

Article Title: Discovery of EST-derived microsatellite primers in the legume Lens culinaris (Fabaceae) 1
Article Snippet: .. PCR mixtures of 20 μL consisted of 2.0 μL 10× buffer (100 mM Tris-HCl, 500 mM KCl, 15 mM MgCl2 , 0.01% gelatin), 200 μM each dNTP, 0.5 μM each of forward and reverse primers, 1 U Taq DNA polymerase (PCR reagents and primers procured from Sigma-Aldrich, St. Louis, Missouri, USA), and ∼40 ng DNA and were performed in a Veriti Thermal Cycler (Applied Biosystems, Life Technologies, Singapore). .. The PCR protocol consisted of one denaturation cycle at 94°C for 4 min followed by 30 cycles of 94°C for 1 min, annealing at 59–62°C (depending upon the primer) for 30 s, extension at 72°C for 1 min, and a final extension at 72°C for 8 min.

Article Title: Clostridium leptum group bacteria abundance and diversity in the fecal microbiota of patients with inflammatory bowel disease: a case-control study in India
Article Snippet: .. Polymerase chain reaction (PCR) was performed in a reaction volume of 20 μl containing 1X PCR buffer, 2.5 mM MgCl2 , 200 mM each dNTP, 250 nmol of both forward and reverse primers, 2.5 U of Jumpstart Taq polymerase (Sigma Aldrich Co, St. Louis, MO, USA), and approximately 10 ng of DNA template. .. Samples were amplified in a MJ Mini thermal cycler (Bio-Rad, Hercules, CA, USA) using the following program: 95°C for 1 minutes, 30 cycles of 95°C for 30 seconds, 56°C for 30 seconds, 72°C for 30 seconds, and finally 72°C for 10 minutes.

Article Title: Lab to Field Assessment of the Ecotoxicological Impact of Chlorpyrifos, Isoproturon, or Tebuconazole on the Diversity and Composition of the Soil Bacterial Community
Article Snippet: .. Concerning the samples from the field study, first-step PCR amplifications were carried out in 50 μL reaction volumes containing 2.5 U of Accuzyme polymerase (Bioline), 0.2 μM of each primer, 1x AccuBuffer with 2 mM Mg2+ , 0.5 mM of each dNTP, 0.4 μg/μL of bovine serum albumin (BSA, Sigma) (Kreader, ) and 2 ng of soil DNA. .. The PCR products were visualized on a 1.5% agarose gel to verify the correct size of amplicons.

Reverse Transcription Polymerase Chain Reaction:

Article Title: Analysis of transcribed human endogenous retrovirus W env loci clarifies the origin of multiple sclerosis-associated retrovirus env sequences
Article Snippet: Paragraph title: RT-PCR ... Conventional PCR was performed in a 50-μl reaction containing 1 μl of cDNA, 0.5 μM of each primer, 200 μM of each dNTP, reaction buffer (10 mM Tris-HCl, 50 mM KCl, 1.5 mM MgCl2 ), and 0.05 units/μl of Taq DNA Polymerase (D1806, Sigma).

Hybridization:

Article Title: Taxonomic hypotheses regarding the genus Gerbillus ( Rodentia, Muridae, Gerbillinae) based on molecular analyses of museum specimens
Article Snippet: The 25μl reaction solution was prepared by mixing 14.5μl of DNase-RNase free water (Qiagen), 2.5μl of buffer (1X concentration), 2μl MgCl2 (2mM), 2.5μl dNTP (250μM; Sigma), 0.5μl of each primer (0.5μM), 0.5μl of AmpliTaq Gold (2.5 units; Applied biosystems). .. The cytb amplification was done at the CBGP molecular biology platform (Montferrier-sur-Lez, France) using PCR programs on a Master Cycle rep Gradient (eppendorf), including an activation step of 95 °C for 10 min followed by 55 cycles comprising a first denaturation at 94 °C for 30 s, hybridization at 50 °C for 30 s and elongation at 72 °C for 45s.

DNA Extraction:

Article Title: Taxonomic hypotheses regarding the genus Gerbillus ( Rodentia, Muridae, Gerbillinae) based on molecular analyses of museum specimens
Article Snippet: The 25μl reaction solution was prepared by mixing 14.5μl of DNase-RNase free water (Qiagen), 2.5μl of buffer (1X concentration), 2μl MgCl2 (2mM), 2.5μl dNTP (250μM; Sigma), 0.5μl of each primer (0.5μM), 0.5μl of AmpliTaq Gold (2.5 units; Applied biosystems). .. Three negative controls were used to check for contamination during DNA extraction, preparation of the mix and DNA distribution.

Article Title: Genetic Structure, Diversity and Long Term Viability of a Medicinal Plant, Nothapodytes nimmoniana Graham. (Icacinaceae), in Protected and Non-Protected Areas in the Western Ghats Biodiversity Hotspot
Article Snippet: Paragraph title: DNA extraction and amplification protocol ... The PCR amplification was carried out in a 25-µl-volume reaction mixture containing 25 ng template DNA, 2.5 µl 10× reaction buffer containing 15 µM MgCl2 , 3 µM of each dNTP, 0.25 µM each forward and reverse primer and 0.5 unit Taq DNA polymerase (Sigma).

Article Title: Clostridium leptum group bacteria abundance and diversity in the fecal microbiota of patients with inflammatory bowel disease: a case-control study in India
Article Snippet: Paragraph title: DNA extraction and polymerase chain reaction amplification ... Polymerase chain reaction (PCR) was performed in a reaction volume of 20 μl containing 1X PCR buffer, 2.5 mM MgCl2 , 200 mM each dNTP, 250 nmol of both forward and reverse primers, 2.5 U of Jumpstart Taq polymerase (Sigma Aldrich Co, St. Louis, MO, USA), and approximately 10 ng of DNA template.

Nucleic Acid Electrophoresis:

Article Title: Interactions between HIV-1 Reverse Transcriptase and the Downstream Template Strand in Stable Complexes with Primer-Template
Article Snippet: After 10 min incubation at 37°C with dNTP, the reaction mixtures were cooled on ice for 5 min and SA was added to a final concentration of 50 to 250 nM and incubated at 37°C for 2–5 min. Then free biotin (Sigma Aldrich) was added to a final concentration of 0.6 to 6.0 µM as indicated and the incubation was continued at 37°C for 5 min to trap excess SA. .. SA-DNA complexes were separated from free DNA by electrophoresis on a 6% native polyacrylamide gel in Tris-taurine buffer (90 mM Tris, 30 mM taurine, pH 7.5).

Methylation:

Article Title: Frequent epigenetic inactivation of Wnt antagonist genes in breast cancer
Article Snippet: Paragraph title: Methylation analysis ... PCR was run in a 25-μ l volume containing 50 ng bisulphite-treated DNA, 1 × MSP buffer (67 mM Tris-HCl (pH 8.8), 16.6 mM (NH4 )2 SO4 , 6.7 mM MgCl2 and 10 mM 2-mercaptoethanol), 1.25 mM dNTP, 0.4 μ M each primer and 0.5 U of JumpStart REDTaq DNA Polymerase (Sigma).

Mutagenesis:

Article Title: Mechanical properties of DNA-like polymers
Article Snippet: Polymerase chain reaction amplification of modified DNAs pUC19-based plasmids containing intrinsically straight ∼200-bp sequences ( ) were subjected to site-directed mutagenesis to obtain suitable restriction sites ( Supplementary Data S2 ). .. For analogs 7 and 8 , PCR reactions (100 µl) included 20 ng template, 0.4 mM forward and reverse primers, Pwo PCR buffer (Roche), GC-rich solution (Roche), 0.2 mM each dNTP (dTTP completely replaced with analog), 2 M betaine (Sigma-Aldrich) and 5 U Pwo SuperYield DNA Polymerase (Roche).

Article Title: The GABA transaminase, ABAT, is essential for mitochondrial nucleoside metabolism
Article Snippet: Subsequently, LSM was replaced with fresh LSM containing either dNMP, dNDP or dNTP (Sigma-Aldrich) each at a final concentration of 50uM. .. Fibroblast cell lines used as controls in this experiment included an individual with MDS due to homozygous SUCLA2 : p.Gly424Aspfs*18 mutation and a subject who is homozygous for DGUOK p.Phe256* ( ) (OMIM #612073, OMIM #251880).

Isolation:

Article Title: Discovery of EST-derived microsatellite primers in the legume Lens culinaris (Fabaceae) 1
Article Snippet: The genomic DNA from each individual was isolated using the cetyltrimethylammonium bromide (CTAB) method as described by . .. PCR mixtures of 20 μL consisted of 2.0 μL 10× buffer (100 mM Tris-HCl, 500 mM KCl, 15 mM MgCl2 , 0.01% gelatin), 200 μM each dNTP, 0.5 μM each of forward and reverse primers, 1 U Taq DNA polymerase (PCR reagents and primers procured from Sigma-Aldrich, St. Louis, Missouri, USA), and ∼40 ng DNA and were performed in a Veriti Thermal Cycler (Applied Biosystems, Life Technologies, Singapore).

Size-exclusion Chromatography:

Article Title: Screening of Viral Pathogens from Pediatric Ileal Tissue Samples after Vaccination
Article Snippet: Samples were amplified by combining 5 μ L of the double-stranded cDNA product with 5 μ L 10x Sigma Taq buffer, 1 μ L dNTP (12.5 mM), 1 μ L primer 5′-GATGAGGGAAGATGGGG-3′ (100 pmole/μ L), 1 μ L Sigma KlenTaq LA polymerase, and 37 μ L water. .. Reactions were placed in a thermocycler (Tetrad Thermal Cycler, MJ Research, Quebec, Canada) with the following conditions: 94°C for 2 min; 40 cycles of 94°C for 30 sec, 50°C for 1 min, and 68°C for 1 min; and 72°C for 10 min. Amplified samples were purified using the Qiaquick PCR Purification Columns (Qiagen) according to manufacturer's instructions.

Article Title: Analysis of transcribed human endogenous retrovirus W env loci clarifies the origin of multiple sclerosis-associated retrovirus env sequences
Article Snippet: Conventional PCR was performed in a 50-μl reaction containing 1 μl of cDNA, 0.5 μM of each primer, 200 μM of each dNTP, reaction buffer (10 mM Tris-HCl, 50 mM KCl, 1.5 mM MgCl2 ), and 0.05 units/μl of Taq DNA Polymerase (D1806, Sigma). .. Cycling parameters were as follows: 3 minutes at 95°C; 40 cycles of 50 sec at 95°C, 50 sec at 58°C, and 1 minute at 72°C; and 10 minutes at 72°C.

Electrophoretic Mobility Shift Assay:

Article Title: Interactions between HIV-1 Reverse Transcriptase and the Downstream Template Strand in Stable Complexes with Primer-Template
Article Snippet: Paragraph title: Electrophoretic Mobility Shift Assays (EMSA) for dNTP-Induced Stable Complex Formation and for Detection of Streptavidin (SA) Bound to Biotin-Containing DNA ... After 10 min incubation at 37°C with dNTP, the reaction mixtures were cooled on ice for 5 min and SA was added to a final concentration of 50 to 250 nM and incubated at 37°C for 2–5 min. Then free biotin (Sigma Aldrich) was added to a final concentration of 0.6 to 6.0 µM as indicated and the incubation was continued at 37°C for 5 min to trap excess SA.

Purification:

Article Title: Mechanical properties of DNA-like polymers
Article Snippet: For analog 2 , PCR reactions (100 µl) included 20 ng plasmid template (or alternatively 20 ng of purified PCR product from a previous reaction), 0.4 mM forward and reverse primers, 100 mg/ml bovine serum albumin (BSA), Taq DNA polymerase buffer (Invitrogen), 2 mM MgCl , 0.2 mM each dNTP (with dTTP completely replaced by the analog triphosphate) and 5 U Taq DNA polymerase (Invitrogen). .. For analogs 7 and 8 , PCR reactions (100 µl) included 20 ng template, 0.4 mM forward and reverse primers, Pwo PCR buffer (Roche), GC-rich solution (Roche), 0.2 mM each dNTP (dTTP completely replaced with analog), 2 M betaine (Sigma-Aldrich) and 5 U Pwo SuperYield DNA Polymerase (Roche).

Article Title: Screening of Viral Pathogens from Pediatric Ileal Tissue Samples after Vaccination
Article Snippet: Paragraph title: 2.4.1. Whole Genome Amplification and Purification ... Samples were amplified by combining 5 μ L of the double-stranded cDNA product with 5 μ L 10x Sigma Taq buffer, 1 μ L dNTP (12.5 mM), 1 μ L primer 5′-GATGAGGGAAGATGGGG-3′ (100 pmole/μ L), 1 μ L Sigma KlenTaq LA polymerase, and 37 μ L water.

Sequencing:

Article Title: Lab to Field Assessment of the Ecotoxicological Impact of Chlorpyrifos, Isoproturon, or Tebuconazole on the Diversity and Composition of the Soil Bacterial Community
Article Snippet: Paragraph title: Amplicon sequencing samples preparation and data analysis ... Concerning the samples from the field study, first-step PCR amplifications were carried out in 50 μL reaction volumes containing 2.5 U of Accuzyme polymerase (Bioline), 0.2 μM of each primer, 1x AccuBuffer with 2 mM Mg2+ , 0.5 mM of each dNTP, 0.4 μg/μL of bovine serum albumin (BSA, Sigma) (Kreader, ) and 2 ng of soil DNA.

Lysis:

Article Title: Direct Cell Lysis for Single-Cell Gene Expression Profiling
Article Snippet: Directly lysed cells were incubated in 0.5 mM dNTP (Sigma-Aldrich), 2.5 μM oligo-dT (Metabion), and 2.5 μM random hexamers (Metabion) at 65°C for 5 min and then chilled on ice. .. To be able to use all RNA from the column based extraction experiments 20 μl RT reaction volumes were used in the comparison between direct lysis with 1 mg/ml BSA and columns based extraction.

Nucleic Acid Concentration:

Article Title: Screening of Viral Pathogens from Pediatric Ileal Tissue Samples after Vaccination
Article Snippet: Samples were amplified by combining 5 μ L of the double-stranded cDNA product with 5 μ L 10x Sigma Taq buffer, 1 μ L dNTP (12.5 mM), 1 μ L primer 5′-GATGAGGGAAGATGGGG-3′ (100 pmole/μ L), 1 μ L Sigma KlenTaq LA polymerase, and 37 μ L water. .. Samples were eluted in 40 μ L of Buffer EB from the Qiagen kit and nucleic acid concentration determined by Qubit fluorometer.

Chromatin Immunoprecipitation:

Article Title: Lab to Field Assessment of the Ecotoxicological Impact of Chlorpyrifos, Isoproturon, or Tebuconazole on the Diversity and Composition of the Soil Bacterial Community
Article Snippet: Concerning the samples from the field study, first-step PCR amplifications were carried out in 50 μL reaction volumes containing 2.5 U of Accuzyme polymerase (Bioline), 0.2 μM of each primer, 1x AccuBuffer with 2 mM Mg2+ , 0.5 mM of each dNTP, 0.4 μg/μL of bovine serum albumin (BSA, Sigma) (Kreader, ) and 2 ng of soil DNA. .. Amplicon sizes of randomly selected samples were further analyzed by Bioanalyzer DNA 1000 chip (Agilent Technologies).

Plasmid Preparation:

Article Title: Mechanical properties of DNA-like polymers
Article Snippet: For analog 2 , PCR reactions (100 µl) included 20 ng plasmid template (or alternatively 20 ng of purified PCR product from a previous reaction), 0.4 mM forward and reverse primers, 100 mg/ml bovine serum albumin (BSA), Taq DNA polymerase buffer (Invitrogen), 2 mM MgCl , 0.2 mM each dNTP (with dTTP completely replaced by the analog triphosphate) and 5 U Taq DNA polymerase (Invitrogen). .. For analogs 7 and 8 , PCR reactions (100 µl) included 20 ng template, 0.4 mM forward and reverse primers, Pwo PCR buffer (Roche), GC-rich solution (Roche), 0.2 mM each dNTP (dTTP completely replaced with analog), 2 M betaine (Sigma-Aldrich) and 5 U Pwo SuperYield DNA Polymerase (Roche).

Article Title: Frequent epigenetic inactivation of Wnt antagonist genes in breast cancer
Article Snippet: PCR was run in a 25-μ l volume containing 50 ng bisulphite-treated DNA, 1 × MSP buffer (67 mM Tris-HCl (pH 8.8), 16.6 mM (NH4 )2 SO4 , 6.7 mM MgCl2 and 10 mM 2-mercaptoethanol), 1.25 mM dNTP, 0.4 μ M each primer and 0.5 U of JumpStart REDTaq DNA Polymerase (Sigma). .. Amplified bisulphite-sequencing PCR products were cloned into pCR2.1-TOPO vector (Invitrogen), and 10 clones from each sample were sequenced.

Software:

Article Title: Discovery of EST-derived microsatellite primers in the legume Lens culinaris (Fabaceae) 1
Article Snippet: The fragments with inappropriate flanking sequences or with less than 500 bp were excluded and 82 SSRs were designed using Primer3 software ( ). .. PCR mixtures of 20 μL consisted of 2.0 μL 10× buffer (100 mM Tris-HCl, 500 mM KCl, 15 mM MgCl2 , 0.01% gelatin), 200 μM each dNTP, 0.5 μM each of forward and reverse primers, 1 U Taq DNA polymerase (PCR reagents and primers procured from Sigma-Aldrich, St. Louis, Missouri, USA), and ∼40 ng DNA and were performed in a Veriti Thermal Cycler (Applied Biosystems, Life Technologies, Singapore).

Binding Assay:

Article Title: Interactions between HIV-1 Reverse Transcriptase and the Downstream Template Strand in Stable Complexes with Primer-Template
Article Snippet: Additional EMSA assays were carried out to determine if prior binding of dNTP could prevent the binding of SA (Sigma Aldrich) to the template biotin residue . .. After 10 min incubation at 37°C with dNTP, the reaction mixtures were cooled on ice for 5 min and SA was added to a final concentration of 50 to 250 nM and incubated at 37°C for 2–5 min. Then free biotin (Sigma Aldrich) was added to a final concentration of 0.6 to 6.0 µM as indicated and the incubation was continued at 37°C for 5 min to trap excess SA.

Agarose Gel Electrophoresis:

Article Title: Clostridium leptum group bacteria abundance and diversity in the fecal microbiota of patients with inflammatory bowel disease: a case-control study in India
Article Snippet: The concentration and integrity of the nucleic acids were determined by electrophoresis on 1% agarose gel containing ethidium bromide. .. Polymerase chain reaction (PCR) was performed in a reaction volume of 20 μl containing 1X PCR buffer, 2.5 mM MgCl2 , 200 mM each dNTP, 250 nmol of both forward and reverse primers, 2.5 U of Jumpstart Taq polymerase (Sigma Aldrich Co, St. Louis, MO, USA), and approximately 10 ng of DNA template.

Article Title: Lab to Field Assessment of the Ecotoxicological Impact of Chlorpyrifos, Isoproturon, or Tebuconazole on the Diversity and Composition of the Soil Bacterial Community
Article Snippet: Concerning the samples from the field study, first-step PCR amplifications were carried out in 50 μL reaction volumes containing 2.5 U of Accuzyme polymerase (Bioline), 0.2 μM of each primer, 1x AccuBuffer with 2 mM Mg2+ , 0.5 mM of each dNTP, 0.4 μg/μL of bovine serum albumin (BSA, Sigma) (Kreader, ) and 2 ng of soil DNA. .. The PCR products were visualized on a 1.5% agarose gel to verify the correct size of amplicons.

Random Hexamer Labeling:

Article Title: Analysis of transcribed human endogenous retrovirus W env loci clarifies the origin of multiple sclerosis-associated retrovirus env sequences
Article Snippet: Subsequently, 0.3–0.5 μg of DNase digested cellular RNA was reverse transcribed in a 20-μl reaction using Superscript II (Invitrogen) and 25 μM random hexamer primers (MWG-Biotech AG) according to the protocol of the manufacturer. .. Conventional PCR was performed in a 50-μl reaction containing 1 μl of cDNA, 0.5 μM of each primer, 200 μM of each dNTP, reaction buffer (10 mM Tris-HCl, 50 mM KCl, 1.5 mM MgCl2 ), and 0.05 units/μl of Taq DNA Polymerase (D1806, Sigma).

Spectrophotometry:

Article Title: Genetic Structure, Diversity and Long Term Viability of a Medicinal Plant, Nothapodytes nimmoniana Graham. (Icacinaceae), in Protected and Non-Protected Areas in the Western Ghats Biodiversity Hotspot
Article Snippet: The extracted DNA was visualized on ethidium bromide stained 0.8% agarose gels and quantified by measuring the absorption at 260 nm using a spectrophotometer. .. The PCR amplification was carried out in a 25-µl-volume reaction mixture containing 25 ng template DNA, 2.5 µl 10× reaction buffer containing 15 µM MgCl2 , 3 µM of each dNTP, 0.25 µM each forward and reverse primer and 0.5 unit Taq DNA polymerase (Sigma).

Produced:

Article Title: Discovery of EST-derived microsatellite primers in the legume Lens culinaris (Fabaceae) 1
Article Snippet: The unigenes containing 951 contigs and 3092 singletons produced a total of 251 putative SSRs using the software Troll ( ). .. PCR mixtures of 20 μL consisted of 2.0 μL 10× buffer (100 mM Tris-HCl, 500 mM KCl, 15 mM MgCl2 , 0.01% gelatin), 200 μM each dNTP, 0.5 μM each of forward and reverse primers, 1 U Taq DNA polymerase (PCR reagents and primers procured from Sigma-Aldrich, St. Louis, Missouri, USA), and ∼40 ng DNA and were performed in a Veriti Thermal Cycler (Applied Biosystems, Life Technologies, Singapore).

Concentration Assay:

Article Title: The GABA transaminase, ABAT, is essential for mitochondrial nucleoside metabolism
Article Snippet: .. Subsequently, LSM was replaced with fresh LSM containing either dNMP, dNDP or dNTP (Sigma-Aldrich) each at a final concentration of 50uM. .. Fibroblast cell lines used as controls in this experiment included an individual with MDS due to homozygous SUCLA2 : p.Gly424Aspfs*18 mutation and a subject who is homozygous for DGUOK p.Phe256* ( ) (OMIM #612073, OMIM #251880).

Article Title: Taxonomic hypotheses regarding the genus Gerbillus ( Rodentia, Muridae, Gerbillinae) based on molecular analyses of museum specimens
Article Snippet: .. The 25μl reaction solution was prepared by mixing 14.5μl of DNase-RNase free water (Qiagen), 2.5μl of buffer (1X concentration), 2μl MgCl2 (2mM), 2.5μl dNTP (250μM; Sigma), 0.5μl of each primer (0.5μM), 0.5μl of AmpliTaq Gold (2.5 units; Applied biosystems). .. 1μl and 2μl of DNA aliquots of the extracted samples were amplified separately, and used for further comparisons.

Article Title: Genetic Structure, Diversity and Long Term Viability of a Medicinal Plant, Nothapodytes nimmoniana Graham. (Icacinaceae), in Protected and Non-Protected Areas in the Western Ghats Biodiversity Hotspot
Article Snippet: The DNA was diluted to a concentration of 10 ng/µl and used for PCR amplification. .. The PCR amplification was carried out in a 25-µl-volume reaction mixture containing 25 ng template DNA, 2.5 µl 10× reaction buffer containing 15 µM MgCl2 , 3 µM of each dNTP, 0.25 µM each forward and reverse primer and 0.5 unit Taq DNA polymerase (Sigma).

Article Title: Clostridium leptum group bacteria abundance and diversity in the fecal microbiota of patients with inflammatory bowel disease: a case-control study in India
Article Snippet: The concentration and integrity of the nucleic acids were determined by electrophoresis on 1% agarose gel containing ethidium bromide. .. Polymerase chain reaction (PCR) was performed in a reaction volume of 20 μl containing 1X PCR buffer, 2.5 mM MgCl2 , 200 mM each dNTP, 250 nmol of both forward and reverse primers, 2.5 U of Jumpstart Taq polymerase (Sigma Aldrich Co, St. Louis, MO, USA), and approximately 10 ng of DNA template.

Article Title: Interactions between HIV-1 Reverse Transcriptase and the Downstream Template Strand in Stable Complexes with Primer-Template
Article Snippet: .. After 10 min incubation at 37°C with dNTP, the reaction mixtures were cooled on ice for 5 min and SA was added to a final concentration of 50 to 250 nM and incubated at 37°C for 2–5 min. Then free biotin (Sigma Aldrich) was added to a final concentration of 0.6 to 6.0 µM as indicated and the incubation was continued at 37°C for 5 min to trap excess SA. .. RT was dissociated by addition of an equal volume of loading dye-urea-TTE (16 M urea, 180 mM Tris-HCl, pH 9.0, 60 mM taurine, 0.5 mM EDTA, 0.25% (w/v) bromphenol blue, 0.25% (w/v) xylene cyanol) with 0.5% SDS prior to electrophoresis.

Staining:

Article Title: Genetic Structure, Diversity and Long Term Viability of a Medicinal Plant, Nothapodytes nimmoniana Graham. (Icacinaceae), in Protected and Non-Protected Areas in the Western Ghats Biodiversity Hotspot
Article Snippet: The extracted DNA was visualized on ethidium bromide stained 0.8% agarose gels and quantified by measuring the absorption at 260 nm using a spectrophotometer. .. The PCR amplification was carried out in a 25-µl-volume reaction mixture containing 25 ng template DNA, 2.5 µl 10× reaction buffer containing 15 µM MgCl2 , 3 µM of each dNTP, 0.25 µM each forward and reverse primer and 0.5 unit Taq DNA polymerase (Sigma).

Article Title: Discovery of EST-derived microsatellite primers in the legume Lens culinaris (Fabaceae) 1
Article Snippet: PCR mixtures of 20 μL consisted of 2.0 μL 10× buffer (100 mM Tris-HCl, 500 mM KCl, 15 mM MgCl2 , 0.01% gelatin), 200 μM each dNTP, 0.5 μM each of forward and reverse primers, 1 U Taq DNA polymerase (PCR reagents and primers procured from Sigma-Aldrich, St. Louis, Missouri, USA), and ∼40 ng DNA and were performed in a Veriti Thermal Cycler (Applied Biosystems, Life Technologies, Singapore). .. The amplification fragments were separated on 3% MetaPhor Agarose gels (Lonza, Rockland, Maine, USA) and visualized by ethidium bromide staining.

Variant Assay:

Article Title: Mechanical properties of DNA-like polymers
Article Snippet: For analogs 3 , 4 , 5 , 6 and 9 , PCR reactions (100 µl) included 20 ng template, 0.4 mM forward and reverse primers, PrimeSTAR GC buffer (Takara), 0.2 mM each dNTP (again with dTTP completely replaced with analog, except for variant 9 , which completely replaced dATP), 2 M betaine (Sigma-Aldrich) and 5 U PrimeSTAR HS DNA polymerase (Takara). .. For analogs 7 and 8 , PCR reactions (100 µl) included 20 ng template, 0.4 mM forward and reverse primers, Pwo PCR buffer (Roche), GC-rich solution (Roche), 0.2 mM each dNTP (dTTP completely replaced with analog), 2 M betaine (Sigma-Aldrich) and 5 U Pwo SuperYield DNA Polymerase (Roche).

Article Title: Mechanical properties of DNA-like polymers
Article Snippet: .. For analogs 3 , 4 , 5 , 6 and 9 , PCR reactions (100 µl) included 20 ng template, 0.4 mM forward and reverse primers, PrimeSTAR GC buffer (Takara), 0.2 mM each dNTP (again with dTTP completely replaced with analog, except for variant 9 , which completely replaced dATP), 2 M betaine (Sigma-Aldrich) and 5 U PrimeSTAR HS DNA polymerase (Takara). .. For analogs 7 and 8 , PCR reactions (100 µl) included 20 ng template, 0.4 mM forward and reverse primers, Pwo PCR buffer (Roche), GC-rich solution (Roche), 0.2 mM each dNTP (dTTP completely replaced with analog), 2 M betaine (Sigma-Aldrich) and 5 U Pwo SuperYield DNA Polymerase (Roche).

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 79
    Millipore deoxynucleotidyltransferase mediated digoxigenin dntp nick end labeling
    Blockade of CERT function induces apoptosis. CHK were treated with vehicle, 10 μ m HPA-12 active, 10 μ m HPA-12 inactive, or UVB as above. Apoptotic cells were assessed by terminal <t>deoxynucleotidyltransferase-mediated</t> <t>digoxigenin-dNTP</t> nick
    Deoxynucleotidyltransferase Mediated Digoxigenin Dntp Nick End Labeling, supplied by Millipore, used in various techniques. Bioz Stars score: 79/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/deoxynucleotidyltransferase mediated digoxigenin dntp nick end labeling/product/Millipore
    Average 79 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    deoxynucleotidyltransferase mediated digoxigenin dntp nick end labeling - by Bioz Stars, 2020-03
    79/100 stars
      Buy from Supplier

    80
    Millipore ternary dpo4 dna dntp complexes dpo4 polymerase
    Structure of the ternary <t>Dpo4·DNA·dATP</t> complex 2 . (A) Active site of Dpo4 (cartoon form, cyan) containing a primer/template junction (yellow) with the ring-opened N 2 -(3-oxopropyl)-dG or N 2 -(3,3-dihydroxypropyl)-dG adduct (red) opposite the 3′-terminal dC, incoming dATP (yellow), and Ca 2+ ions (green dot). (B) Electron density at the active site. (C) Top view of the Watson–Crick base pair between the adduct and the 3′-terminal dC. All electron densities are from (2 F o – F c ) maps at the 1σ level.
    Ternary Dpo4 Dna Dntp Complexes Dpo4 Polymerase, supplied by Millipore, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ternary dpo4 dna dntp complexes dpo4 polymerase/product/Millipore
    Average 80 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ternary dpo4 dna dntp complexes dpo4 polymerase - by Bioz Stars, 2020-03
    80/100 stars
      Buy from Supplier

    86
    Millipore dntps mixture
    Structure of the ternary <t>Dpo4·DNA·dATP</t> complex 2 . (A) Active site of Dpo4 (cartoon form, cyan) containing a primer/template junction (yellow) with the ring-opened N 2 -(3-oxopropyl)-dG or N 2 -(3,3-dihydroxypropyl)-dG adduct (red) opposite the 3′-terminal dC, incoming dATP (yellow), and Ca 2+ ions (green dot). (B) Electron density at the active site. (C) Top view of the Watson–Crick base pair between the adduct and the 3′-terminal dC. All electron densities are from (2 F o – F c ) maps at the 1σ level.
    Dntps Mixture, supplied by Millipore, used in various techniques. Bioz Stars score: 86/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dntps mixture/product/Millipore
    Average 86 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    dntps mixture - by Bioz Stars, 2020-03
    86/100 stars
      Buy from Supplier

    99
    Millipore dntps
    Structure of the ternary <t>Dpo4·DNA·dATP</t> complex 2 . (A) Active site of Dpo4 (cartoon form, cyan) containing a primer/template junction (yellow) with the ring-opened N 2 -(3-oxopropyl)-dG or N 2 -(3,3-dihydroxypropyl)-dG adduct (red) opposite the 3′-terminal dC, incoming dATP (yellow), and Ca 2+ ions (green dot). (B) Electron density at the active site. (C) Top view of the Watson–Crick base pair between the adduct and the 3′-terminal dC. All electron densities are from (2 F o – F c ) maps at the 1σ level.
    Dntps, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 456 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dntps/product/Millipore
    Average 99 stars, based on 456 article reviews
    Price from $9.99 to $1999.99
    dntps - by Bioz Stars, 2020-03
    99/100 stars
      Buy from Supplier

    Image Search Results


    Blockade of CERT function induces apoptosis. CHK were treated with vehicle, 10 μ m HPA-12 active, 10 μ m HPA-12 inactive, or UVB as above. Apoptotic cells were assessed by terminal deoxynucleotidyltransferase-mediated digoxigenin-dNTP nick

    Journal:

    Article Title: Decreased Ceramide Transport Protein (CERT) Function Alters Sphingomyelin Production following UVB Irradiation *

    doi: 10.1074/jbc.M800799200

    Figure Lengend Snippet: Blockade of CERT function induces apoptosis. CHK were treated with vehicle, 10 μ m HPA-12 active, 10 μ m HPA-12 inactive, or UVB as above. Apoptotic cells were assessed by terminal deoxynucleotidyltransferase-mediated digoxigenin-dNTP nick

    Article Snippet: Apoptosis Assay —Apoptosis was assessed by determining changes in cellular nuclear chromatin as described previously ( ) using 2-(4-amidinophenyl)-1 H -indole-6-carboxamidine and by terminal deoxynucleotidyltransferase-mediated digoxigenin-dNTP nick end labeling using the DNA Fragmentation Detection kit following the manufacturer's protocol (EMD Chemicals, Inc., Gibbstown, NJ).

    Techniques:

    Structure of the ternary Dpo4·DNA·dATP complex 2 . (A) Active site of Dpo4 (cartoon form, cyan) containing a primer/template junction (yellow) with the ring-opened N 2 -(3-oxopropyl)-dG or N 2 -(3,3-dihydroxypropyl)-dG adduct (red) opposite the 3′-terminal dC, incoming dATP (yellow), and Ca 2+ ions (green dot). (B) Electron density at the active site. (C) Top view of the Watson–Crick base pair between the adduct and the 3′-terminal dC. All electron densities are from (2 F o – F c ) maps at the 1σ level.

    Journal: Chemical Research in Toxicology

    Article Title: Ring-Opening of the ?-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4

    doi: 10.1021/tx400200b

    Figure Lengend Snippet: Structure of the ternary Dpo4·DNA·dATP complex 2 . (A) Active site of Dpo4 (cartoon form, cyan) containing a primer/template junction (yellow) with the ring-opened N 2 -(3-oxopropyl)-dG or N 2 -(3,3-dihydroxypropyl)-dG adduct (red) opposite the 3′-terminal dC, incoming dATP (yellow), and Ca 2+ ions (green dot). (B) Electron density at the active site. (C) Top view of the Watson–Crick base pair between the adduct and the 3′-terminal dC. All electron densities are from (2 F o – F c ) maps at the 1σ level.

    Article Snippet: Crystallization of Ternary Dpo4·DNA·dNTP Complexes Dpo4 polymerase was concentrated to 50–60 mg/mL using a spin concentrator with a 104 M r Amicon cutoff filter (Millipore, Inc., Billerica, MA) in 50 mM Tris-HCl buffer (pH 7.4 at 25 °C) containing 100 mM NaCl, 5 mM β-mercaptoethanol, and 50% glycerol (v/v).

    Techniques:

    Superimposed structures of the ternary Dpo4·DNA·dNTP complexes 3 and 4 . Overall conformations (A) and modified DNA conformations and positions of Ca 2+ ions (B) at the active site. Complexes 3 and 4 are colored in black and red, respectively. (RMSD = 0.309 Å).

    Journal: Chemical Research in Toxicology

    Article Title: Ring-Opening of the ?-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4

    doi: 10.1021/tx400200b

    Figure Lengend Snippet: Superimposed structures of the ternary Dpo4·DNA·dNTP complexes 3 and 4 . Overall conformations (A) and modified DNA conformations and positions of Ca 2+ ions (B) at the active site. Complexes 3 and 4 are colored in black and red, respectively. (RMSD = 0.309 Å).

    Article Snippet: Crystallization of Ternary Dpo4·DNA·dNTP Complexes Dpo4 polymerase was concentrated to 50–60 mg/mL using a spin concentrator with a 104 M r Amicon cutoff filter (Millipore, Inc., Billerica, MA) in 50 mM Tris-HCl buffer (pH 7.4 at 25 °C) containing 100 mM NaCl, 5 mM β-mercaptoethanol, and 50% glycerol (v/v).

    Techniques: Modification

    Structure of the ternary Dpo4·DNA·dGTP complex 1 . (A) Active site of Dpo4 (cartoon form, cyan) containing a primer–template junction (yellow) with the ring-opened N 2 -(3-oxopropyl)-dG or N 2 -(3,3-dihydroxypropyl)-dG adduct (red) opposite the 3′-terminal dC, incoming dGTP (yellow), and Ca 2+ ions (green dot). (B) Electron density at the active site. (C) Top view of the Watson–Crick base pair between the adduct and the 3′-terminal dC. All electron densities are from (2 F o – F c ) maps at the 1σ level.

    Journal: Chemical Research in Toxicology

    Article Title: Ring-Opening of the ?-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4

    doi: 10.1021/tx400200b

    Figure Lengend Snippet: Structure of the ternary Dpo4·DNA·dGTP complex 1 . (A) Active site of Dpo4 (cartoon form, cyan) containing a primer–template junction (yellow) with the ring-opened N 2 -(3-oxopropyl)-dG or N 2 -(3,3-dihydroxypropyl)-dG adduct (red) opposite the 3′-terminal dC, incoming dGTP (yellow), and Ca 2+ ions (green dot). (B) Electron density at the active site. (C) Top view of the Watson–Crick base pair between the adduct and the 3′-terminal dC. All electron densities are from (2 F o – F c ) maps at the 1σ level.

    Article Snippet: Crystallization of Ternary Dpo4·DNA·dNTP Complexes Dpo4 polymerase was concentrated to 50–60 mg/mL using a spin concentrator with a 104 M r Amicon cutoff filter (Millipore, Inc., Billerica, MA) in 50 mM Tris-HCl buffer (pH 7.4 at 25 °C) containing 100 mM NaCl, 5 mM β-mercaptoethanol, and 50% glycerol (v/v).

    Techniques:

    Structure of the ternary Dpo4·DNA·dATP complex 4 . (A) Active site of Dpo4 (cartoon form, cyan) containing a primer–template junction (yellow) with the ring closed γ-OH-PdG adduct (red), incoming dATP (yellow), and Ca 2+ ions (green dot). (B) Electron density at the active site. (C) Top view of the Watson–Crick base pair between incoming dATP and the 5′-neighboring template dT. All electron densities are from (2 F o – F c ) maps at the 1σ level.

    Journal: Chemical Research in Toxicology

    Article Title: Ring-Opening of the ?-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4

    doi: 10.1021/tx400200b

    Figure Lengend Snippet: Structure of the ternary Dpo4·DNA·dATP complex 4 . (A) Active site of Dpo4 (cartoon form, cyan) containing a primer–template junction (yellow) with the ring closed γ-OH-PdG adduct (red), incoming dATP (yellow), and Ca 2+ ions (green dot). (B) Electron density at the active site. (C) Top view of the Watson–Crick base pair between incoming dATP and the 5′-neighboring template dT. All electron densities are from (2 F o – F c ) maps at the 1σ level.

    Article Snippet: Crystallization of Ternary Dpo4·DNA·dNTP Complexes Dpo4 polymerase was concentrated to 50–60 mg/mL using a spin concentrator with a 104 M r Amicon cutoff filter (Millipore, Inc., Billerica, MA) in 50 mM Tris-HCl buffer (pH 7.4 at 25 °C) containing 100 mM NaCl, 5 mM β-mercaptoethanol, and 50% glycerol (v/v).

    Techniques:

    Structure of the ternary Dpo4·DNA·dGTP complex 3 . (A) Active site of Dpo4 (cartoon form, cyan) containing a primer–template junction (yellow) with the ring-closed γ-OH-PdG adduct (red), incoming dGTP (yellow), and Ca 2+ ions (green dot). (B) Electron density at the active site. (C) Top view of the Watson–Crick base pair between incoming dGTP and the 5′-neighboring template dC. All electron densities are from (2 F o – F c ) maps at the 1σ level.

    Journal: Chemical Research in Toxicology

    Article Title: Ring-Opening of the ?-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4

    doi: 10.1021/tx400200b

    Figure Lengend Snippet: Structure of the ternary Dpo4·DNA·dGTP complex 3 . (A) Active site of Dpo4 (cartoon form, cyan) containing a primer–template junction (yellow) with the ring-closed γ-OH-PdG adduct (red), incoming dGTP (yellow), and Ca 2+ ions (green dot). (B) Electron density at the active site. (C) Top view of the Watson–Crick base pair between incoming dGTP and the 5′-neighboring template dC. All electron densities are from (2 F o – F c ) maps at the 1σ level.

    Article Snippet: Crystallization of Ternary Dpo4·DNA·dNTP Complexes Dpo4 polymerase was concentrated to 50–60 mg/mL using a spin concentrator with a 104 M r Amicon cutoff filter (Millipore, Inc., Billerica, MA) in 50 mM Tris-HCl buffer (pH 7.4 at 25 °C) containing 100 mM NaCl, 5 mM β-mercaptoethanol, and 50% glycerol (v/v).

    Techniques:

    Superimposed structures of the ternary Dpo4·DNA·dNTP complexes 1 and 2 . Overall conformations (A) and modified DNA conformations and positions of Ca 2+ ions (B) at the active site. Complexes 1 and 2 are colored in black and red, respectively. (RMSD = 0.315 Å).

    Journal: Chemical Research in Toxicology

    Article Title: Ring-Opening of the ?-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4

    doi: 10.1021/tx400200b

    Figure Lengend Snippet: Superimposed structures of the ternary Dpo4·DNA·dNTP complexes 1 and 2 . Overall conformations (A) and modified DNA conformations and positions of Ca 2+ ions (B) at the active site. Complexes 1 and 2 are colored in black and red, respectively. (RMSD = 0.315 Å).

    Article Snippet: Crystallization of Ternary Dpo4·DNA·dNTP Complexes Dpo4 polymerase was concentrated to 50–60 mg/mL using a spin concentrator with a 104 M r Amicon cutoff filter (Millipore, Inc., Billerica, MA) in 50 mM Tris-HCl buffer (pH 7.4 at 25 °C) containing 100 mM NaCl, 5 mM β-mercaptoethanol, and 50% glycerol (v/v).

    Techniques: Modification