Structured Review

Enzymatics dntps
Dntps, supplied by Enzymatics, used in various techniques. Bioz Stars score: 93/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 93 stars, based on 5 article reviews
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dntps - by Bioz Stars, 2020-04
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Amplification:

Article Title: CCR7 Receptor Expression in Mono-MAC-1 Cells: Modulation by Liver X Receptor α Activation and Prostaglandin E2
Article Snippet: RNA (2 μ g) was reverse-transcribed into cDNA in the presence of 0.5 μ g of oligonucleotide d(T)15 , 200 units of M-MLV RT (Promega, Madison, WI, USA), and 250 μ M deoxyribonucleotide triphosphates (dNTPs) at 42°C for 1 h. Amplification of human NR1H3 (LXRα ), CCR7 , and ABCG1 was performed using the SYBR Green I nucleic acid gel stain (Invitrogen, Burlington, ON, Canada) on a CFX Connect Real Time System (BIO-RAD, Mississauga, ON, Canada). .. Results were analyzed using the software BIO-RAD CFX Manager. qPCR reactions contained 0.25 μ M forward and reverse primers , 0.1 mM dNTPs, 2 mM or 3.5 mM MgCl2 , and 1.25 units of Omni Klentaq (Enzymatics, Beverly, MA, USA).

Article Title: Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Article Snippet: .. Briefly, a round of random amplification was performed by tagging the P5-N6-oligo1 (5′-CTACACGACGCTCTTCCGATCTN6 -3′) in the presence of 1 × Blue buffer (Enzymatics), 600 nM of dNTPs, 400 nM of P5-N6-oligo1 and 50 units of Klenow exo− (Enzymatics) and incubated at 37 °C for 30 min. Then, the remained oligos and dNTPs were deactivated by Exo-SAP IT reagent (Applied Biosystems) following the manufacture’s protocol. .. Next, dC tailing was conducted in the presence of 1 × Blue buffer (Enzymatics), 2.5 mM of dCTPs and 1U/μL of TdT enzyme.

Article Title: Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Article Snippet: Briefly, a round of random amplification was performed by tagging the P5-N6-oligo1 (5′-CTACACGACGCTCTTCCGATCTN6 -3′) in the presence of 1 × Blue buffer (Enzymatics), 600 nM of dNTPs, 400 nM of P5-N6-oligo1 and 50 units of Klenow exo− (Enzymatics) and incubated at 37 °C for 30 min. Then, the remained oligos and dNTPs were deactivated by Exo-SAP IT reagent (Applied Biosystems) following the manufacture’s protocol. .. After that, the second strand synthesis was performed by tagging the P7-G6-oligo2 (5′-AGACGTGTGCTCTTCCGATCTG6 HN-3′) in the presence of 1 × Blue buffer (Enzymatics), 600 nM of dNTPs, 400 nM of P7-G6-oligo2 and 100 units of Klenow exo− (Enzymatics) and incubated at 37 °C for 1 h, followed by Agencourt AMPure XP beads (Beckman) purification.

Article Title: The type of ploidy of chrysanthemum is not black or white: a comparison of a molecular approach to published cytological methods
Article Snippet: The PCR conditions were as follows: 0.2 μM of each unlabeled primer, 0.07 μM of each labeled primer and 0.07 μM of a M13 primer end-labeled with either the IRD 700 dye or the IRD 800 dye (Eurofins MWG, Ebersberg, D) in a final 25 μL reaction volume [2x Williams Buffer, 0.16 mM dNTPs, 0.7 U DCS-Taq polymerase (Enzymatics, Beverly, MA, USA) and 30 ng template DNA]. .. The conditions of the PCR amplification were as follows: 95°C (3 min), then 25 cycles at 94°C (30 s)/58°C (30 s)/72°C (45 s), followed by eight cycles at 94°C (30 s)/52°C (45 s)/72°C (60 s), and a final extension at 72°C for 10 min. All other PCR products, which were visualized by silver staining according to the protocol of , were amplified by a standard PCR reaction in a final reaction volume of 20 μl containing 1x Williams Buffer, 0.2 mM dNTPs, 0.5 μM primers, 0.5 U DCS Taq polymerase and 30 ng template DNA.

Article Title: 3′ Branch ligation: a novel method to ligate non-complementary DNA to recessed or internal 3′OH ends in DNA or RNA
Article Snippet: .. PCR amplification of tagmented and gap-ligated DNA was performed in 50 ‐µl reactions containing 2 µl of the tagmented or gap-ligated DNA, TAB buffer, 1 µl TruePrep Amplify Enzyme (Vazyme), 200 mM dNTPs (Enzymatics, Inc.), and 400 mM each of primers Pr-A and Pr-B. .. Tagmented reactions were incubated as follows: 72°C for 3 min; 98°C for 30 s; 8 cycles of 98°C for 10 s, 58°C for 30 s, and 72°C for 2 min; and 72°C for a 10-min extension.

Construct:

Article Title: Single-Molecule Enzymology Based On The Principle Of The Millikan Oil Drop Experiment
Article Snippet: This created a primed piece of single stranded DNA 425 bases long, where the primer contained the active sulfhydryl and tether attachment areas, enabling the assembly of a nanoparticle-tether-BSA construct. .. Polymerization buffer (NEB2 at 0.5x, New England Biosciences, Ipswich, MA), 22 μM dNTPs, and Mako polymerase (Enzymatics Inc., Beverly, MA) were added to a small aliquot of the primed template and incubated at room temperature for 20 minutes.

Real-time Polymerase Chain Reaction:

Article Title: CCR7 Receptor Expression in Mono-MAC-1 Cells: Modulation by Liver X Receptor α Activation and Prostaglandin E2
Article Snippet: .. Results were analyzed using the software BIO-RAD CFX Manager. qPCR reactions contained 0.25 μ M forward and reverse primers , 0.1 mM dNTPs, 2 mM or 3.5 mM MgCl2 , and 1.25 units of Omni Klentaq (Enzymatics, Beverly, MA, USA). .. In each reaction, we used 8 μ L of a 1 : 2 dilution of each cDNA (dilutions were performed using molecular grade sterile water (Wisent)).

Incubation:

Article Title: CCR7 Receptor Expression in Mono-MAC-1 Cells: Modulation by Liver X Receptor α Activation and Prostaglandin E2
Article Snippet: Real-Time Quantitative Polymerase Chain Reaction (qPCR) Analyses MM-1 cells were incubated with stimulants for the indicated times, and total RNA was extracted using Nucleospin RNA columns (Macherey-Nagel, BioLynx, Brockville, ON, Canada) according to the manufacturer's instructions. .. Results were analyzed using the software BIO-RAD CFX Manager. qPCR reactions contained 0.25 μ M forward and reverse primers , 0.1 mM dNTPs, 2 mM or 3.5 mM MgCl2 , and 1.25 units of Omni Klentaq (Enzymatics, Beverly, MA, USA).

Article Title: Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Article Snippet: .. Briefly, a round of random amplification was performed by tagging the P5-N6-oligo1 (5′-CTACACGACGCTCTTCCGATCTN6 -3′) in the presence of 1 × Blue buffer (Enzymatics), 600 nM of dNTPs, 400 nM of P5-N6-oligo1 and 50 units of Klenow exo− (Enzymatics) and incubated at 37 °C for 30 min. Then, the remained oligos and dNTPs were deactivated by Exo-SAP IT reagent (Applied Biosystems) following the manufacture’s protocol. .. Next, dC tailing was conducted in the presence of 1 × Blue buffer (Enzymatics), 2.5 mM of dCTPs and 1U/μL of TdT enzyme.

Article Title: Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Article Snippet: .. After that, the second strand synthesis was performed by tagging the P7-G6-oligo2 (5′-AGACGTGTGCTCTTCCGATCTG6 HN-3′) in the presence of 1 × Blue buffer (Enzymatics), 600 nM of dNTPs, 400 nM of P7-G6-oligo2 and 100 units of Klenow exo− (Enzymatics) and incubated at 37 °C for 1 h, followed by Agencourt AMPure XP beads (Beckman) purification. .. Final libraries were generated by eighteen cycles of PCR to incorporate universal primers and index primers (New England Biolabs), and purified by Agencourt AMPure XP beads.

Article Title: Single-Molecule Enzymology Based On The Principle Of The Millikan Oil Drop Experiment
Article Snippet: .. Polymerization buffer (NEB2 at 0.5x, New England Biosciences, Ipswich, MA), 22 μM dNTPs, and Mako polymerase (Enzymatics Inc., Beverly, MA) were added to a small aliquot of the primed template and incubated at room temperature for 20 minutes. ..

Article Title: Titration-free massively parallel pyrosequencing using trace amounts of starting material
Article Snippet: .. AB library End polishing was conducted in 50 µl reaction volume with 1 ng of DNA, 1× End repair buffer, 5 µl end repair mix containing T4 DNA Polymerase and T4 PNK, 1 µl of 1 µM dNTPs (Enzymatics, MA, USA), and was incubated at 22°C for 30 min. After purification by AMPure beads (88 µl, 175% volume), DNA was eluted in 20 µl TE. .. Adapter ligation was conducted in a 25 µl reaction with 1× slow ligation buffer, 0.4 pmol of each of the A4 and B adapter (Invitrogen, USA) and T4 DNA Ligase 180 U (Enzymatics, MA, USA).

Article Title: Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments
Article Snippet: To recover damaged fragments we added 5 μL of 10 mM (5′-CAA GCA GAA GAC GGC ATA CGA GAT TGG TCA GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T-3′), 200 μM dNTPs, 10 μL VeraSeq Buffer II (Enzymatics) and 1U VeraSeq Ultra (Enzymatics). .. The reaction mixture was incubated with 60 μg of streptavidin coated magnetic beads (Magnasphere Paramagnetic Particles, Promega) in 2x binding buffer (10 mM Tris-HCl pH 7.4, 1 mM EDTA, 2 M NaCl, 0.1% Tween 20) for 20 minutes at room temperature.

Article Title: Terminator-free template-independent enzymatic DNA synthesis for digital information storage
Article Snippet: Once the dNTPs were loaded, 100 µg of initiator-conjugated magnetic beads were suspended in the enzymatic reaction mix, comprised of 1 × Custom Synthesis Buffer (14 mm Tris-Acetate, 35 mm Potassium Acetate pH 7.9, 7 mm Magnesium Acetate, 0.1% Triton X-100, 10% (w/v) PEG 8000) with 1U/µL TdT (Enzymatics), and 0.25mU/µL apyrase (NEB). .. At every cycle, each reaction was pulse vortexed and incubated for 30 sec at room temperature.

Article Title: 3′ Branch ligation: a novel method to ligate non-complementary DNA to recessed or internal 3′OH ends in DNA or RNA
Article Snippet: The reaction was incubated at 55°C for 10 min; 40 µl of 6 M guanidine hydrochloride (Sigma) was then added to remove the transposon complex from tagmented DNA, and DNA was purified using Agencourt AMPure XP beads (Beckman Coulter). .. PCR amplification of tagmented and gap-ligated DNA was performed in 50 ‐µl reactions containing 2 µl of the tagmented or gap-ligated DNA, TAB buffer, 1 µl TruePrep Amplify Enzyme (Vazyme), 200 mM dNTPs (Enzymatics, Inc.), and 400 mM each of primers Pr-A and Pr-B.

Ligation:

Article Title: Titration-free massively parallel pyrosequencing using trace amounts of starting material
Article Snippet: AB library End polishing was conducted in 50 µl reaction volume with 1 ng of DNA, 1× End repair buffer, 5 µl end repair mix containing T4 DNA Polymerase and T4 PNK, 1 µl of 1 µM dNTPs (Enzymatics, MA, USA), and was incubated at 22°C for 30 min. After purification by AMPure beads (88 µl, 175% volume), DNA was eluted in 20 µl TE. .. Adapter ligation was conducted in a 25 µl reaction with 1× slow ligation buffer, 0.4 pmol of each of the A4 and B adapter (Invitrogen, USA) and T4 DNA Ligase 180 U (Enzymatics, MA, USA).

Article Title: Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments
Article Snippet: In brief, 50 ng of sonicated genomic DNA was blunt ended, phosphorylated and dA-tailed, before ligation of custom adapter pair 1 (NEBNext). .. To recover damaged fragments we added 5 μL of 10 mM (5′-CAA GCA GAA GAC GGC ATA CGA GAT TGG TCA GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T-3′), 200 μM dNTPs, 10 μL VeraSeq Buffer II (Enzymatics) and 1U VeraSeq Ultra (Enzymatics).

Article Title: 3′ Branch ligation: a novel method to ligate non-complementary DNA to recessed or internal 3′OH ends in DNA or RNA
Article Snippet: The gap ligation of AdB (ON28 and ON29) to the tagmented DNA was performed at 25°C for 1 h in reactions containing 100 pmol of the adapter, 600 U of T4 DNA ligase (Enzymatics, Inc.), and 3 ′ BL buffer. .. PCR amplification of tagmented and gap-ligated DNA was performed in 50 ‐µl reactions containing 2 µl of the tagmented or gap-ligated DNA, TAB buffer, 1 µl TruePrep Amplify Enzyme (Vazyme), 200 mM dNTPs (Enzymatics, Inc.), and 400 mM each of primers Pr-A and Pr-B.

Methylation:

Article Title: Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Article Snippet: Improved single-cell COOL-seq (iscCOOL-seq) library construction First, individual oocytes were methylated in vitro by GpC methylase (New England Biolabs), digested by protease and bisulfite converted as previously described , . .. Briefly, a round of random amplification was performed by tagging the P5-N6-oligo1 (5′-CTACACGACGCTCTTCCGATCTN6 -3′) in the presence of 1 × Blue buffer (Enzymatics), 600 nM of dNTPs, 400 nM of P5-N6-oligo1 and 50 units of Klenow exo− (Enzymatics) and incubated at 37 °C for 30 min. Then, the remained oligos and dNTPs were deactivated by Exo-SAP IT reagent (Applied Biosystems) following the manufacture’s protocol.

Article Title: Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Article Snippet: First, individual oocytes were methylated in vitro by GpC methylase (New England Biolabs), digested by protease and bisulfite converted as previously described , . .. After that, the second strand synthesis was performed by tagging the P7-G6-oligo2 (5′-AGACGTGTGCTCTTCCGATCTG6 HN-3′) in the presence of 1 × Blue buffer (Enzymatics), 600 nM of dNTPs, 400 nM of P7-G6-oligo2 and 100 units of Klenow exo− (Enzymatics) and incubated at 37 °C for 1 h, followed by Agencourt AMPure XP beads (Beckman) purification.

Article Title: Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments
Article Snippet: Bisulfite conversion was achieved with the Zymo EZ DNA Methylation-Gold kit, following the manufacturer’s instructions. .. To recover damaged fragments we added 5 μL of 10 mM (5′-CAA GCA GAA GAC GGC ATA CGA GAT TGG TCA GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T-3′), 200 μM dNTPs, 10 μL VeraSeq Buffer II (Enzymatics) and 1U VeraSeq Ultra (Enzymatics).

Generated:

Article Title: Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Article Snippet: Briefly, a round of random amplification was performed by tagging the P5-N6-oligo1 (5′-CTACACGACGCTCTTCCGATCTN6 -3′) in the presence of 1 × Blue buffer (Enzymatics), 600 nM of dNTPs, 400 nM of P5-N6-oligo1 and 50 units of Klenow exo− (Enzymatics) and incubated at 37 °C for 30 min. Then, the remained oligos and dNTPs were deactivated by Exo-SAP IT reagent (Applied Biosystems) following the manufacture’s protocol. .. Final libraries were generated by eighteen cycles of PCR to incorporate universal primers and index primers (New England Biolabs), and purified by Agencourt AMPure XP beads.

Article Title: Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Article Snippet: After that, the second strand synthesis was performed by tagging the P7-G6-oligo2 (5′-AGACGTGTGCTCTTCCGATCTG6 HN-3′) in the presence of 1 × Blue buffer (Enzymatics), 600 nM of dNTPs, 400 nM of P7-G6-oligo2 and 100 units of Klenow exo− (Enzymatics) and incubated at 37 °C for 1 h, followed by Agencourt AMPure XP beads (Beckman) purification. .. Final libraries were generated by eighteen cycles of PCR to incorporate universal primers and index primers (New England Biolabs), and purified by Agencourt AMPure XP beads.

Polymerase Chain Reaction:

Article Title: CCR7 Receptor Expression in Mono-MAC-1 Cells: Modulation by Liver X Receptor α Activation and Prostaglandin E2
Article Snippet: Results were analyzed using the software BIO-RAD CFX Manager. qPCR reactions contained 0.25 μ M forward and reverse primers , 0.1 mM dNTPs, 2 mM or 3.5 mM MgCl2 , and 1.25 units of Omni Klentaq (Enzymatics, Beverly, MA, USA). .. PCR cycling conditions consisted of an initial denaturation at 95°C for 3 minutes and 40 cycles of 95°C for 10 sec, 60°C for 40 sec, 72°C for 40 sec, and a melting curve at 95°C for 10 sec, 65°C for 5 sec, and 95°C for 5 sec.

Article Title: Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Article Snippet: Briefly, a round of random amplification was performed by tagging the P5-N6-oligo1 (5′-CTACACGACGCTCTTCCGATCTN6 -3′) in the presence of 1 × Blue buffer (Enzymatics), 600 nM of dNTPs, 400 nM of P5-N6-oligo1 and 50 units of Klenow exo− (Enzymatics) and incubated at 37 °C for 30 min. Then, the remained oligos and dNTPs were deactivated by Exo-SAP IT reagent (Applied Biosystems) following the manufacture’s protocol. .. Final libraries were generated by eighteen cycles of PCR to incorporate universal primers and index primers (New England Biolabs), and purified by Agencourt AMPure XP beads.

Article Title: Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Article Snippet: After that, the second strand synthesis was performed by tagging the P7-G6-oligo2 (5′-AGACGTGTGCTCTTCCGATCTG6 HN-3′) in the presence of 1 × Blue buffer (Enzymatics), 600 nM of dNTPs, 400 nM of P7-G6-oligo2 and 100 units of Klenow exo− (Enzymatics) and incubated at 37 °C for 1 h, followed by Agencourt AMPure XP beads (Beckman) purification. .. Final libraries were generated by eighteen cycles of PCR to incorporate universal primers and index primers (New England Biolabs), and purified by Agencourt AMPure XP beads.

Article Title: The type of ploidy of chrysanthemum is not black or white: a comparison of a molecular approach to published cytological methods
Article Snippet: .. The PCR conditions were as follows: 0.2 μM of each unlabeled primer, 0.07 μM of each labeled primer and 0.07 μM of a M13 primer end-labeled with either the IRD 700 dye or the IRD 800 dye (Eurofins MWG, Ebersberg, D) in a final 25 μL reaction volume [2x Williams Buffer, 0.16 mM dNTPs, 0.7 U DCS-Taq polymerase (Enzymatics, Beverly, MA, USA) and 30 ng template DNA]. .. The conditions of the PCR amplification were as follows: 95°C (3 min), then 25 cycles at 94°C (30 s)/58°C (30 s)/72°C (45 s), followed by eight cycles at 94°C (30 s)/52°C (45 s)/72°C (60 s), and a final extension at 72°C for 10 min. All other PCR products, which were visualized by silver staining according to the protocol of , were amplified by a standard PCR reaction in a final reaction volume of 20 μl containing 1x Williams Buffer, 0.2 mM dNTPs, 0.5 μM primers, 0.5 U DCS Taq polymerase and 30 ng template DNA.

Article Title: Single-Molecule Enzymology Based On The Principle Of The Millikan Oil Drop Experiment
Article Snippet: The primed template was purified with a Qiagen PCR cleanup kit to remove unhybridized capture oligonucleotides. .. Polymerization buffer (NEB2 at 0.5x, New England Biosciences, Ipswich, MA), 22 μM dNTPs, and Mako polymerase (Enzymatics Inc., Beverly, MA) were added to a small aliquot of the primed template and incubated at room temperature for 20 minutes.

Article Title: Terminator-free template-independent enzymatic DNA synthesis for digital information storage
Article Snippet: As above, a series of dNTPs were dispensed for each nucleotide of the template sequence in a 96-well PCR plate. .. Once the dNTPs were loaded, 100 µg of initiator-conjugated magnetic beads were suspended in the enzymatic reaction mix, comprised of 1 × Custom Synthesis Buffer (14 mm Tris-Acetate, 35 mm Potassium Acetate pH 7.9, 7 mm Magnesium Acetate, 0.1% Triton X-100, 10% (w/v) PEG 8000) with 1U/µL TdT (Enzymatics), and 0.25mU/µL apyrase (NEB).

Article Title: 3′ Branch ligation: a novel method to ligate non-complementary DNA to recessed or internal 3′OH ends in DNA or RNA
Article Snippet: .. PCR amplification of tagmented and gap-ligated DNA was performed in 50 ‐µl reactions containing 2 µl of the tagmented or gap-ligated DNA, TAB buffer, 1 µl TruePrep Amplify Enzyme (Vazyme), 200 mM dNTPs (Enzymatics, Inc.), and 400 mM each of primers Pr-A and Pr-B. .. Tagmented reactions were incubated as follows: 72°C for 3 min; 98°C for 30 s; 8 cycles of 98°C for 10 s, 58°C for 30 s, and 72°C for 2 min; and 72°C for a 10-min extension.

Sonication:

Article Title: Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments
Article Snippet: In brief, 50 ng of sonicated genomic DNA was blunt ended, phosphorylated and dA-tailed, before ligation of custom adapter pair 1 (NEBNext). .. To recover damaged fragments we added 5 μL of 10 mM (5′-CAA GCA GAA GAC GGC ATA CGA GAT TGG TCA GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T-3′), 200 μM dNTPs, 10 μL VeraSeq Buffer II (Enzymatics) and 1U VeraSeq Ultra (Enzymatics).

Binding Assay:

Article Title: Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments
Article Snippet: To recover damaged fragments we added 5 μL of 10 mM (5′-CAA GCA GAA GAC GGC ATA CGA GAT TGG TCA GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T-3′), 200 μM dNTPs, 10 μL VeraSeq Buffer II (Enzymatics) and 1U VeraSeq Ultra (Enzymatics). .. The reaction mixture was incubated with 60 μg of streptavidin coated magnetic beads (Magnasphere Paramagnetic Particles, Promega) in 2x binding buffer (10 mM Tris-HCl pH 7.4, 1 mM EDTA, 2 M NaCl, 0.1% Tween 20) for 20 minutes at room temperature.

Magnetic Beads:

Article Title: Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments
Article Snippet: To recover damaged fragments we added 5 μL of 10 mM (5′-CAA GCA GAA GAC GGC ATA CGA GAT TGG TCA GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T-3′), 200 μM dNTPs, 10 μL VeraSeq Buffer II (Enzymatics) and 1U VeraSeq Ultra (Enzymatics). .. The reaction mixture was incubated with 60 μg of streptavidin coated magnetic beads (Magnasphere Paramagnetic Particles, Promega) in 2x binding buffer (10 mM Tris-HCl pH 7.4, 1 mM EDTA, 2 M NaCl, 0.1% Tween 20) for 20 minutes at room temperature.

Article Title: Terminator-free template-independent enzymatic DNA synthesis for digital information storage
Article Snippet: .. Once the dNTPs were loaded, 100 µg of initiator-conjugated magnetic beads were suspended in the enzymatic reaction mix, comprised of 1 × Custom Synthesis Buffer (14 mm Tris-Acetate, 35 mm Potassium Acetate pH 7.9, 7 mm Magnesium Acetate, 0.1% Triton X-100, 10% (w/v) PEG 8000) with 1U/µL TdT (Enzymatics), and 0.25mU/µL apyrase (NEB). ..

Mutagenesis:

Article Title: The type of ploidy of chrysanthemum is not black or white: a comparison of a molecular approach to published cytological methods
Article Snippet: SSCP markers for candidate genes Mutant screens in Arabidopsis and other plants identified several genes that control shoot branching and are involved in strigolactone biosynthesis and perception. .. The PCR conditions were as follows: 0.2 μM of each unlabeled primer, 0.07 μM of each labeled primer and 0.07 μM of a M13 primer end-labeled with either the IRD 700 dye or the IRD 800 dye (Eurofins MWG, Ebersberg, D) in a final 25 μL reaction volume [2x Williams Buffer, 0.16 mM dNTPs, 0.7 U DCS-Taq polymerase (Enzymatics, Beverly, MA, USA) and 30 ng template DNA].

Isolation:

Article Title: The type of ploidy of chrysanthemum is not black or white: a comparison of a molecular approach to published cytological methods
Article Snippet: In addition, we isolated a CCD 7 homolog from chrysanthemum (unpublished) and screened this sequence and those of the other genes containing polymorphisms using SSCP analysis. .. The PCR conditions were as follows: 0.2 μM of each unlabeled primer, 0.07 μM of each labeled primer and 0.07 μM of a M13 primer end-labeled with either the IRD 700 dye or the IRD 800 dye (Eurofins MWG, Ebersberg, D) in a final 25 μL reaction volume [2x Williams Buffer, 0.16 mM dNTPs, 0.7 U DCS-Taq polymerase (Enzymatics, Beverly, MA, USA) and 30 ng template DNA].

Size-exclusion Chromatography:

Article Title: CCR7 Receptor Expression in Mono-MAC-1 Cells: Modulation by Liver X Receptor α Activation and Prostaglandin E2
Article Snippet: Results were analyzed using the software BIO-RAD CFX Manager. qPCR reactions contained 0.25 μ M forward and reverse primers , 0.1 mM dNTPs, 2 mM or 3.5 mM MgCl2 , and 1.25 units of Omni Klentaq (Enzymatics, Beverly, MA, USA). .. PCR cycling conditions consisted of an initial denaturation at 95°C for 3 minutes and 40 cycles of 95°C for 10 sec, 60°C for 40 sec, 72°C for 40 sec, and a melting curve at 95°C for 10 sec, 65°C for 5 sec, and 95°C for 5 sec.

Article Title: Terminator-free template-independent enzymatic DNA synthesis for digital information storage
Article Snippet: Once the dNTPs were loaded, 100 µg of initiator-conjugated magnetic beads were suspended in the enzymatic reaction mix, comprised of 1 × Custom Synthesis Buffer (14 mm Tris-Acetate, 35 mm Potassium Acetate pH 7.9, 7 mm Magnesium Acetate, 0.1% Triton X-100, 10% (w/v) PEG 8000) with 1U/µL TdT (Enzymatics), and 0.25mU/µL apyrase (NEB). .. At every cycle, each reaction was pulse vortexed and incubated for 30 sec at room temperature.

Labeling:

Article Title: The type of ploidy of chrysanthemum is not black or white: a comparison of a molecular approach to published cytological methods
Article Snippet: .. The PCR conditions were as follows: 0.2 μM of each unlabeled primer, 0.07 μM of each labeled primer and 0.07 μM of a M13 primer end-labeled with either the IRD 700 dye or the IRD 800 dye (Eurofins MWG, Ebersberg, D) in a final 25 μL reaction volume [2x Williams Buffer, 0.16 mM dNTPs, 0.7 U DCS-Taq polymerase (Enzymatics, Beverly, MA, USA) and 30 ng template DNA]. .. The conditions of the PCR amplification were as follows: 95°C (3 min), then 25 cycles at 94°C (30 s)/58°C (30 s)/72°C (45 s), followed by eight cycles at 94°C (30 s)/52°C (45 s)/72°C (60 s), and a final extension at 72°C for 10 min. All other PCR products, which were visualized by silver staining according to the protocol of , were amplified by a standard PCR reaction in a final reaction volume of 20 μl containing 1x Williams Buffer, 0.2 mM dNTPs, 0.5 μM primers, 0.5 U DCS Taq polymerase and 30 ng template DNA.

Purification:

Article Title: Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Article Snippet: Then, the single-cell genomic DNA was purified and subjected to iscCOOL-seq library construction by TAILS method. .. Briefly, a round of random amplification was performed by tagging the P5-N6-oligo1 (5′-CTACACGACGCTCTTCCGATCTN6 -3′) in the presence of 1 × Blue buffer (Enzymatics), 600 nM of dNTPs, 400 nM of P5-N6-oligo1 and 50 units of Klenow exo− (Enzymatics) and incubated at 37 °C for 30 min. Then, the remained oligos and dNTPs were deactivated by Exo-SAP IT reagent (Applied Biosystems) following the manufacture’s protocol.

Article Title: Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Article Snippet: .. After that, the second strand synthesis was performed by tagging the P7-G6-oligo2 (5′-AGACGTGTGCTCTTCCGATCTG6 HN-3′) in the presence of 1 × Blue buffer (Enzymatics), 600 nM of dNTPs, 400 nM of P7-G6-oligo2 and 100 units of Klenow exo− (Enzymatics) and incubated at 37 °C for 1 h, followed by Agencourt AMPure XP beads (Beckman) purification. .. Final libraries were generated by eighteen cycles of PCR to incorporate universal primers and index primers (New England Biolabs), and purified by Agencourt AMPure XP beads.

Article Title: Single-Molecule Enzymology Based On The Principle Of The Millikan Oil Drop Experiment
Article Snippet: The primed template was purified with a Qiagen PCR cleanup kit to remove unhybridized capture oligonucleotides. .. Polymerization buffer (NEB2 at 0.5x, New England Biosciences, Ipswich, MA), 22 μM dNTPs, and Mako polymerase (Enzymatics Inc., Beverly, MA) were added to a small aliquot of the primed template and incubated at room temperature for 20 minutes.

Article Title: Titration-free massively parallel pyrosequencing using trace amounts of starting material
Article Snippet: .. AB library End polishing was conducted in 50 µl reaction volume with 1 ng of DNA, 1× End repair buffer, 5 µl end repair mix containing T4 DNA Polymerase and T4 PNK, 1 µl of 1 µM dNTPs (Enzymatics, MA, USA), and was incubated at 22°C for 30 min. After purification by AMPure beads (88 µl, 175% volume), DNA was eluted in 20 µl TE. .. Adapter ligation was conducted in a 25 µl reaction with 1× slow ligation buffer, 0.4 pmol of each of the A4 and B adapter (Invitrogen, USA) and T4 DNA Ligase 180 U (Enzymatics, MA, USA).

Article Title: 3′ Branch ligation: a novel method to ligate non-complementary DNA to recessed or internal 3′OH ends in DNA or RNA
Article Snippet: Reactions were purified using AMPure XP beads. .. PCR amplification of tagmented and gap-ligated DNA was performed in 50 ‐µl reactions containing 2 µl of the tagmented or gap-ligated DNA, TAB buffer, 1 µl TruePrep Amplify Enzyme (Vazyme), 200 mM dNTPs (Enzymatics, Inc.), and 400 mM each of primers Pr-A and Pr-B.

Sequencing:

Article Title: The type of ploidy of chrysanthemum is not black or white: a comparison of a molecular approach to published cytological methods
Article Snippet: In addition, we isolated a CCD 7 homolog from chrysanthemum (unpublished) and screened this sequence and those of the other genes containing polymorphisms using SSCP analysis. .. The PCR conditions were as follows: 0.2 μM of each unlabeled primer, 0.07 μM of each labeled primer and 0.07 μM of a M13 primer end-labeled with either the IRD 700 dye or the IRD 800 dye (Eurofins MWG, Ebersberg, D) in a final 25 μL reaction volume [2x Williams Buffer, 0.16 mM dNTPs, 0.7 U DCS-Taq polymerase (Enzymatics, Beverly, MA, USA) and 30 ng template DNA].

Article Title: Single-Molecule Enzymology Based On The Principle Of The Millikan Oil Drop Experiment
Article Snippet: Next, 0.45 uL of 10 uM oligonucleotide A (the suflhydryl-containing capture oligonucleotide, which has the same sequence as the biotinylated primer, A’) was added to the single stranded solution. .. Polymerization buffer (NEB2 at 0.5x, New England Biosciences, Ipswich, MA), 22 μM dNTPs, and Mako polymerase (Enzymatics Inc., Beverly, MA) were added to a small aliquot of the primed template and incubated at room temperature for 20 minutes.

Article Title: Terminator-free template-independent enzymatic DNA synthesis for digital information storage
Article Snippet: As above, a series of dNTPs were dispensed for each nucleotide of the template sequence in a 96-well PCR plate. .. Once the dNTPs were loaded, 100 µg of initiator-conjugated magnetic beads were suspended in the enzymatic reaction mix, comprised of 1 × Custom Synthesis Buffer (14 mm Tris-Acetate, 35 mm Potassium Acetate pH 7.9, 7 mm Magnesium Acetate, 0.1% Triton X-100, 10% (w/v) PEG 8000) with 1U/µL TdT (Enzymatics), and 0.25mU/µL apyrase (NEB).

Activated Clotting Time Assay:

Article Title: Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments
Article Snippet: .. To recover damaged fragments we added 5 μL of 10 mM (5′-CAA GCA GAA GAC GGC ATA CGA GAT TGG TCA GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T-3′), 200 μM dNTPs, 10 μL VeraSeq Buffer II (Enzymatics) and 1U VeraSeq Ultra (Enzymatics). .. The reaction mixture was incubated with 60 μg of streptavidin coated magnetic beads (Magnasphere Paramagnetic Particles, Promega) in 2x binding buffer (10 mM Tris-HCl pH 7.4, 1 mM EDTA, 2 M NaCl, 0.1% Tween 20) for 20 minutes at room temperature.

Silver Staining:

Article Title: The type of ploidy of chrysanthemum is not black or white: a comparison of a molecular approach to published cytological methods
Article Snippet: The PCR conditions were as follows: 0.2 μM of each unlabeled primer, 0.07 μM of each labeled primer and 0.07 μM of a M13 primer end-labeled with either the IRD 700 dye or the IRD 800 dye (Eurofins MWG, Ebersberg, D) in a final 25 μL reaction volume [2x Williams Buffer, 0.16 mM dNTPs, 0.7 U DCS-Taq polymerase (Enzymatics, Beverly, MA, USA) and 30 ng template DNA]. .. The conditions of the PCR amplification were as follows: 95°C (3 min), then 25 cycles at 94°C (30 s)/58°C (30 s)/72°C (45 s), followed by eight cycles at 94°C (30 s)/52°C (45 s)/72°C (60 s), and a final extension at 72°C for 10 min. All other PCR products, which were visualized by silver staining according to the protocol of , were amplified by a standard PCR reaction in a final reaction volume of 20 μl containing 1x Williams Buffer, 0.2 mM dNTPs, 0.5 μM primers, 0.5 U DCS Taq polymerase and 30 ng template DNA.

Software:

Article Title: CCR7 Receptor Expression in Mono-MAC-1 Cells: Modulation by Liver X Receptor α Activation and Prostaglandin E2
Article Snippet: .. Results were analyzed using the software BIO-RAD CFX Manager. qPCR reactions contained 0.25 μ M forward and reverse primers , 0.1 mM dNTPs, 2 mM or 3.5 mM MgCl2 , and 1.25 units of Omni Klentaq (Enzymatics, Beverly, MA, USA). .. In each reaction, we used 8 μ L of a 1 : 2 dilution of each cDNA (dilutions were performed using molecular grade sterile water (Wisent)).

SYBR Green Assay:

Article Title: CCR7 Receptor Expression in Mono-MAC-1 Cells: Modulation by Liver X Receptor α Activation and Prostaglandin E2
Article Snippet: RNA (2 μ g) was reverse-transcribed into cDNA in the presence of 0.5 μ g of oligonucleotide d(T)15 , 200 units of M-MLV RT (Promega, Madison, WI, USA), and 250 μ M deoxyribonucleotide triphosphates (dNTPs) at 42°C for 1 h. Amplification of human NR1H3 (LXRα ), CCR7 , and ABCG1 was performed using the SYBR Green I nucleic acid gel stain (Invitrogen, Burlington, ON, Canada) on a CFX Connect Real Time System (BIO-RAD, Mississauga, ON, Canada). .. Results were analyzed using the software BIO-RAD CFX Manager. qPCR reactions contained 0.25 μ M forward and reverse primers , 0.1 mM dNTPs, 2 mM or 3.5 mM MgCl2 , and 1.25 units of Omni Klentaq (Enzymatics, Beverly, MA, USA).

Multiplex Assay:

Article Title: Titration-free massively parallel pyrosequencing using trace amounts of starting material
Article Snippet: AB library End polishing was conducted in 50 µl reaction volume with 1 ng of DNA, 1× End repair buffer, 5 µl end repair mix containing T4 DNA Polymerase and T4 PNK, 1 µl of 1 µM dNTPs (Enzymatics, MA, USA), and was incubated at 22°C for 30 min. After purification by AMPure beads (88 µl, 175% volume), DNA was eluted in 20 µl TE. .. We used the FLX Titanium adapter A4 (GS multiplex identifier number 4) because this adapter had performed well in previous experiments in our lab.

In Vitro:

Article Title: Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Article Snippet: Improved single-cell COOL-seq (iscCOOL-seq) library construction First, individual oocytes were methylated in vitro by GpC methylase (New England Biolabs), digested by protease and bisulfite converted as previously described , . .. Briefly, a round of random amplification was performed by tagging the P5-N6-oligo1 (5′-CTACACGACGCTCTTCCGATCTN6 -3′) in the presence of 1 × Blue buffer (Enzymatics), 600 nM of dNTPs, 400 nM of P5-N6-oligo1 and 50 units of Klenow exo− (Enzymatics) and incubated at 37 °C for 30 min. Then, the remained oligos and dNTPs were deactivated by Exo-SAP IT reagent (Applied Biosystems) following the manufacture’s protocol.

Article Title: Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Article Snippet: First, individual oocytes were methylated in vitro by GpC methylase (New England Biolabs), digested by protease and bisulfite converted as previously described , . .. After that, the second strand synthesis was performed by tagging the P7-G6-oligo2 (5′-AGACGTGTGCTCTTCCGATCTG6 HN-3′) in the presence of 1 × Blue buffer (Enzymatics), 600 nM of dNTPs, 400 nM of P7-G6-oligo2 and 100 units of Klenow exo− (Enzymatics) and incubated at 37 °C for 1 h, followed by Agencourt AMPure XP beads (Beckman) purification.

Gel Permeation Chromatography:

Article Title: Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Article Snippet: Improved single-cell COOL-seq (iscCOOL-seq) library construction First, individual oocytes were methylated in vitro by GpC methylase (New England Biolabs), digested by protease and bisulfite converted as previously described , . .. Briefly, a round of random amplification was performed by tagging the P5-N6-oligo1 (5′-CTACACGACGCTCTTCCGATCTN6 -3′) in the presence of 1 × Blue buffer (Enzymatics), 600 nM of dNTPs, 400 nM of P5-N6-oligo1 and 50 units of Klenow exo− (Enzymatics) and incubated at 37 °C for 30 min. Then, the remained oligos and dNTPs were deactivated by Exo-SAP IT reagent (Applied Biosystems) following the manufacture’s protocol.

Article Title: Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Article Snippet: First, individual oocytes were methylated in vitro by GpC methylase (New England Biolabs), digested by protease and bisulfite converted as previously described , . .. After that, the second strand synthesis was performed by tagging the P7-G6-oligo2 (5′-AGACGTGTGCTCTTCCGATCTG6 HN-3′) in the presence of 1 × Blue buffer (Enzymatics), 600 nM of dNTPs, 400 nM of P7-G6-oligo2 and 100 units of Klenow exo− (Enzymatics) and incubated at 37 °C for 1 h, followed by Agencourt AMPure XP beads (Beckman) purification.

Concentration Assay:

Article Title: Terminator-free template-independent enzymatic DNA synthesis for digital information storage
Article Snippet: The final concentration of dNTPs for each cycle were as follows: 10 µm dATP, 15 µm Bromo-dCTP, 5 µm dGTP, and 15 µm dTTP. .. Once the dNTPs were loaded, 100 µg of initiator-conjugated magnetic beads were suspended in the enzymatic reaction mix, comprised of 1 × Custom Synthesis Buffer (14 mm Tris-Acetate, 35 mm Potassium Acetate pH 7.9, 7 mm Magnesium Acetate, 0.1% Triton X-100, 10% (w/v) PEG 8000) with 1U/µL TdT (Enzymatics), and 0.25mU/µL apyrase (NEB).

Staining:

Article Title: CCR7 Receptor Expression in Mono-MAC-1 Cells: Modulation by Liver X Receptor α Activation and Prostaglandin E2
Article Snippet: RNA (2 μ g) was reverse-transcribed into cDNA in the presence of 0.5 μ g of oligonucleotide d(T)15 , 200 units of M-MLV RT (Promega, Madison, WI, USA), and 250 μ M deoxyribonucleotide triphosphates (dNTPs) at 42°C for 1 h. Amplification of human NR1H3 (LXRα ), CCR7 , and ABCG1 was performed using the SYBR Green I nucleic acid gel stain (Invitrogen, Burlington, ON, Canada) on a CFX Connect Real Time System (BIO-RAD, Mississauga, ON, Canada). .. Results were analyzed using the software BIO-RAD CFX Manager. qPCR reactions contained 0.25 μ M forward and reverse primers , 0.1 mM dNTPs, 2 mM or 3.5 mM MgCl2 , and 1.25 units of Omni Klentaq (Enzymatics, Beverly, MA, USA).

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