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deoxynucleotide dntp solution mix  (New England Biolabs)


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    Structured Review

    New England Biolabs deoxynucleotide dntp solution mix
    Deoxynucleotide Dntp Solution Mix, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 2095 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/dntps/Deoxynucleotide+(dNTP)+Solution+Mix/pmc13010419-9-0-5
    Average 99 stars, based on 2095 article reviews
    deoxynucleotide dntp solution mix - by Bioz Stars, 2026-09
    99/100 stars

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    Related Articles

    Generated:

    Article Title: Specific elimination of m.8993T>G mitochondrial haplotype in NARP cybrid cells by CRISPR-Cas9 system.
    Article Snippet: .. Amplicons were generated in a reaction containing 1× Q5 Reaction Buffer (NEB), 12.5 pmol of each primer, 0.2 mM of dNTPs, 0.5U of Q5® High-Fidelity DNA Polymerase (NEB) in a final volume of 25 μl. ..

    Incubation:

    Article Title: The one-week automated genome-wide optical pooled screen
    Article Snippet: Padlock probe gap-fill and ligation were performed in 1X Ampligase buffer (Lucigen A3210K) containing 50 nM dNTPs (NEB N0447L), 0.1 μM each padlock probe (Integrated DNA Technologies), 200 μg/mL recombinant albumin (NEB B9200S), 0.4 U/μL RNase H (Enzymatics Y9220L), 0.02 U/μL TaqIT polymerase (Enzymatics P7620L), and 0.5 U/μL Ampligase (Lucigen A3210K). .. Samples were incubated in gap-fill and ligation solution at 37 °C for 5 minutes followed by 45 °C for 90 minutes, then washed twice with PBS-T. Rolling circle amplification (RCA) was performed in 1X Phi29 buffer (Thermo Fisher Scientific EP0091) containing 250 μM dNTPs (NEB N0447L), 5% glycerol (MilliporeSigma G5516), 200 μg/mL recombinant albumin (NEB B9200S), and 1 U/μL Phi29 DNA polymerase (Thermo Fisher Scientific EP0091) for 12 hours at 30 °C. .. Samples were washed twice with PBS-T, then 1 μM sequencing primers (Integrated DNA Technologies) were hybridized in 2X SSC (Ambion AM9763) with 10% (v/v) formamide (Thermo Fisher Scientific 4650) for 30 minutes at room temperature and washed twice with PBS-T prior to in situ sequencing.

    Article Title: Systematic assessment of diverse RNA modifications using nanopore direct RNA sequencing
    Article Snippet: .. Reverse transcription was performed by adding a master mix of nuclease-free water, dNTPs (NEB, N0447), and Induro ® RT Reaction Buffer (NEB, B0681AVIAL), followed by Induro ® Reverse Transcriptase (NEB, M0681), and incubated at 60°C for 30 min, then 70°C for 10 min. .. The reverse transcription product was purified with Agencourt RNAClean XP beads (Beckman CoulterTM, A63987) using 70% ethanol washes and eluted in 23 μl nuclease-free water.

    Ligation:

    Article Title: The one-week automated genome-wide optical pooled screen
    Article Snippet: Padlock probe gap-fill and ligation were performed in 1X Ampligase buffer (Lucigen A3210K) containing 50 nM dNTPs (NEB N0447L), 0.1 μM each padlock probe (Integrated DNA Technologies), 200 μg/mL recombinant albumin (NEB B9200S), 0.4 U/μL RNase H (Enzymatics Y9220L), 0.02 U/μL TaqIT polymerase (Enzymatics P7620L), and 0.5 U/μL Ampligase (Lucigen A3210K). .. Samples were incubated in gap-fill and ligation solution at 37 °C for 5 minutes followed by 45 °C for 90 minutes, then washed twice with PBS-T. Rolling circle amplification (RCA) was performed in 1X Phi29 buffer (Thermo Fisher Scientific EP0091) containing 250 μM dNTPs (NEB N0447L), 5% glycerol (MilliporeSigma G5516), 200 μg/mL recombinant albumin (NEB B9200S), and 1 U/μL Phi29 DNA polymerase (Thermo Fisher Scientific EP0091) for 12 hours at 30 °C. .. Samples were washed twice with PBS-T, then 1 μM sequencing primers (Integrated DNA Technologies) were hybridized in 2X SSC (Ambion AM9763) with 10% (v/v) formamide (Thermo Fisher Scientific 4650) for 30 minutes at room temperature and washed twice with PBS-T prior to in situ sequencing.

    Amplification:

    Article Title: The one-week automated genome-wide optical pooled screen
    Article Snippet: Padlock probe gap-fill and ligation were performed in 1X Ampligase buffer (Lucigen A3210K) containing 50 nM dNTPs (NEB N0447L), 0.1 μM each padlock probe (Integrated DNA Technologies), 200 μg/mL recombinant albumin (NEB B9200S), 0.4 U/μL RNase H (Enzymatics Y9220L), 0.02 U/μL TaqIT polymerase (Enzymatics P7620L), and 0.5 U/μL Ampligase (Lucigen A3210K). .. Samples were incubated in gap-fill and ligation solution at 37 °C for 5 minutes followed by 45 °C for 90 minutes, then washed twice with PBS-T. Rolling circle amplification (RCA) was performed in 1X Phi29 buffer (Thermo Fisher Scientific EP0091) containing 250 μM dNTPs (NEB N0447L), 5% glycerol (MilliporeSigma G5516), 200 μg/mL recombinant albumin (NEB B9200S), and 1 U/μL Phi29 DNA polymerase (Thermo Fisher Scientific EP0091) for 12 hours at 30 °C. .. Samples were washed twice with PBS-T, then 1 μM sequencing primers (Integrated DNA Technologies) were hybridized in 2X SSC (Ambion AM9763) with 10% (v/v) formamide (Thermo Fisher Scientific 4650) for 30 minutes at room temperature and washed twice with PBS-T prior to in situ sequencing.

    Recombinant:

    Article Title: The one-week automated genome-wide optical pooled screen
    Article Snippet: Padlock probe gap-fill and ligation were performed in 1X Ampligase buffer (Lucigen A3210K) containing 50 nM dNTPs (NEB N0447L), 0.1 μM each padlock probe (Integrated DNA Technologies), 200 μg/mL recombinant albumin (NEB B9200S), 0.4 U/μL RNase H (Enzymatics Y9220L), 0.02 U/μL TaqIT polymerase (Enzymatics P7620L), and 0.5 U/μL Ampligase (Lucigen A3210K). .. Samples were incubated in gap-fill and ligation solution at 37 °C for 5 minutes followed by 45 °C for 90 minutes, then washed twice with PBS-T. Rolling circle amplification (RCA) was performed in 1X Phi29 buffer (Thermo Fisher Scientific EP0091) containing 250 μM dNTPs (NEB N0447L), 5% glycerol (MilliporeSigma G5516), 200 μg/mL recombinant albumin (NEB B9200S), and 1 U/μL Phi29 DNA polymerase (Thermo Fisher Scientific EP0091) for 12 hours at 30 °C. .. Samples were washed twice with PBS-T, then 1 μM sequencing primers (Integrated DNA Technologies) were hybridized in 2X SSC (Ambion AM9763) with 10% (v/v) formamide (Thermo Fisher Scientific 4650) for 30 minutes at room temperature and washed twice with PBS-T prior to in situ sequencing.

    Article Title: SCIMETAR-seq tracks immunophenotype, demethylation, mutations, and transcriptomes in single cells undergoing HMA therapy
    Article Snippet: .. Single cells were sorted into 96-well plates containing 4 μL of lysis buffer per well (Tween-20 (0.1%; Sigma-Aldrich, P9416-50ML), recombinant RNase inhibitor (0.53 U/μL; New England Biolabs, M0314L), PEG 8000 (6.25%; Sigma-Aldrich, P1458-25ML), EDTA (0.1 mM; Sigma-Aldrich, 03690-100ML), Tris-HCl (2.5 mM; pH ∼7.0, Thermo Fisher Scientific, AM9850G), oligo(dT) primer (0.625 μM; Supplementary Table 3), and dNTPs (0.625 mM each; New England Biolabs, N0446S)). ..

    Polymerase Chain Reaction:

    Article Title: RNase P/MRP subunits chaperone telomerase holoenzyme assembly in fission yeast.
    Article Snippet: MaP buffer (8 μl) was added, and samples were incubated at 42 °C for 2 min. Superscript II reverse transcriptase (1 μl; ThermoFisher, 18064014) was added, and reactions were incubated at 42 °C for 3 h, followed by inactivation at 70 °C for 15 min. cDNA was purified using G-25 microspin columns (Cytiva, 27532501). .. PCR was carried out in 50 μl reactions with 1× Q5 Reaction Buffer, 200 μM dNTPs, 0.5 μM of each primer, 1 U Q5 Hot Start High-Fidelity DNA Polymerase (NEB, M0493L), and 5 μl cDNA. ..

    Article Title: Precision Fermentation of Recombinant Myofibrillar Proteins for Future Foods
    Article Snippet: Primers were designed and PCR conditions determined using NEBuilder. .. PCR reactions were carried out using NEB Q5 High-Fidelity DNA Polymerase (NEB #M0491) and dNTPs (NEB #N0447). .. Plasmids were expanded using 5-alpha competent E. coli (NEB #C2987) in LB Broth (Sigma Aldrich, St. Luois, MO, #3522) with kanamycin 50μg/mL (Sigma Aldrich #K4000) as antibiotic, and purified using Macherey-Nagel (Düren, Germany) NucleoSpin Plamid Mini kit (#740588).

    Lysis:

    Article Title: SCIMETAR-seq tracks immunophenotype, demethylation, mutations, and transcriptomes in single cells undergoing HMA therapy
    Article Snippet: .. Single cells were sorted into 96-well plates containing 4 μL of lysis buffer per well (Tween-20 (0.1%; Sigma-Aldrich, P9416-50ML), recombinant RNase inhibitor (0.53 U/μL; New England Biolabs, M0314L), PEG 8000 (6.25%; Sigma-Aldrich, P1458-25ML), EDTA (0.1 mM; Sigma-Aldrich, 03690-100ML), Tris-HCl (2.5 mM; pH ∼7.0, Thermo Fisher Scientific, AM9850G), oligo(dT) primer (0.625 μM; Supplementary Table 3), and dNTPs (0.625 mM each; New England Biolabs, N0446S)). ..

    Reverse Transcription:

    Article Title: Systematic assessment of diverse RNA modifications using nanopore direct RNA sequencing
    Article Snippet: .. Reverse transcription was performed by adding a master mix of nuclease-free water, dNTPs (NEB, N0447), and Induro ® RT Reaction Buffer (NEB, B0681AVIAL), followed by Induro ® Reverse Transcriptase (NEB, M0681), and incubated at 60°C for 30 min, then 70°C for 10 min. .. The reverse transcription product was purified with Agencourt RNAClean XP beads (Beckman CoulterTM, A63987) using 70% ethanol washes and eluted in 23 μl nuclease-free water.

    Article Title: sc-rDSeq: a robust and cost-effective full-length total RNA sequencing method for single cells reveals multilayered heterogeneity in drug-resistant lung cancer cells
    Article Snippet: Around 100–150 μl beads were centrifuged in a 1.5-ml Eppendorf tube at 1500 rcf for 2 min to obtain packed beads. .. After aspirating residual buffer from the pelleted beads, the tube was loaded onto the corresponding inlet in the microfluidics setup. (iii) Reverse transcription/lysis mix inlet: 150 μl RT/lysis mix consisted of 30 μl 10× StellarScript buffer, 15μl StellarScript RT enzyme 200 U/μl (StellarScript HT Reverse Transcriptase Kit, Watchmaker, cat #WM-7K0070), 10 μl murine RNase inhibitor (NEB, cat #M0314), 15 μl 1 M Tris–HCl (pH 8.0), 10 μl 0.1 M Dithiothreitol (DTT), 9 μl 10% (v/v) IGEPAL CA-630 (Sigma–Aldrich, cat #I8896), 6 μl 25 mM dNTPs (NEB, cat #N0446S) and 55 μl nuclease-free water. (iv) Carrier oil inlet: The carrier oil was 3 ml of HFE-7500 with 2% (w/w) fluorosurfactant. ..



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    Mutagenesis analysis of BtTdT variants. (a) L397 (green) or L397M (magenta) in BtTdT. (b) Activity test for M1. (c) R336/K338 in BtTdT (green) or R335/K337 in ZaTdT (orange). (d) Activity comparison of three BtTdT mutants. (e) Elongation by M3 with different iDNAs terminated with 16 dinucleotides and 4 types of 3′–ONH 2 –dNTPs. Reaction conditions: 1 mg/mL TdT, 1 μM iDNA, 42 °C, 10 min. “A∼, T∼, C∼, and G∼” stand for 3′–ONH 2 –dATP, 3′–ONH 2 –dTTP, 3′–ONH 2 –dCTP, and 3′–ONH 2 –dGTP, respectively. Note : Product bands at the same concentration may display different intensities due to sequence-specific effects.
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    Image Search Results


    Mutagenesis analysis of BtTdT variants. (a) L397 (green) or L397M (magenta) in BtTdT. (b) Activity test for M1. (c) R336/K338 in BtTdT (green) or R335/K337 in ZaTdT (orange). (d) Activity comparison of three BtTdT mutants. (e) Elongation by M3 with different iDNAs terminated with 16 dinucleotides and 4 types of 3′–ONH 2 –dNTPs. Reaction conditions: 1 mg/mL TdT, 1 μM iDNA, 42 °C, 10 min. “A∼, T∼, C∼, and G∼” stand for 3′–ONH 2 –dATP, 3′–ONH 2 –dTTP, 3′–ONH 2 –dCTP, and 3′–ONH 2 –dGTP, respectively. Note : Product bands at the same concentration may display different intensities due to sequence-specific effects.

    Journal: Synthetic and Systems Biotechnology

    Article Title: Semi-rational engineering of terminal deoxynucleotidyl transferase for high-efficiency enzymatic de novo DNA synthesis

    doi: 10.1016/j.synbio.2026.03.009

    Figure Lengend Snippet: Mutagenesis analysis of BtTdT variants. (a) L397 (green) or L397M (magenta) in BtTdT. (b) Activity test for M1. (c) R336/K338 in BtTdT (green) or R335/K337 in ZaTdT (orange). (d) Activity comparison of three BtTdT mutants. (e) Elongation by M3 with different iDNAs terminated with 16 dinucleotides and 4 types of 3′–ONH 2 –dNTPs. Reaction conditions: 1 mg/mL TdT, 1 μM iDNA, 42 °C, 10 min. “A∼, T∼, C∼, and G∼” stand for 3′–ONH 2 –dATP, 3′–ONH 2 –dTTP, 3′–ONH 2 –dCTP, and 3′–ONH 2 –dGTP, respectively. Note : Product bands at the same concentration may display different intensities due to sequence-specific effects.

    Article Snippet: 3′–ONH 2 –dNTPs were bought from Firebird Biomolecular Sciences (Florida, USA), and 3′- O –CH 2 N 3 –dNTP and 3′–OCHCHCN–dNTP were purchased from Huana Biomedical Technology Co. Ltd. (Hefei, China).

    Techniques: Mutagenesis, Activity Assay, Comparison, Concentration Assay, Sequencing

    Further mutational work based on M3. (a) Key amino acids at the catalytic center in BtTdT (green) and ZaTdT (cyan). (b) Activity evaluation for M3-based mutants. (c) Extension of 3′–ONH 2 –dATP by Bt15AA R336L/K338G/L397M/E456G . Reaction conditions: 1 mg/mL TdT, 1 μM iDNA, 42 °C, 10 min. Note : Product bands at the same concentration may display different intensities due to sequence-specific effects.

    Journal: Synthetic and Systems Biotechnology

    Article Title: Semi-rational engineering of terminal deoxynucleotidyl transferase for high-efficiency enzymatic de novo DNA synthesis

    doi: 10.1016/j.synbio.2026.03.009

    Figure Lengend Snippet: Further mutational work based on M3. (a) Key amino acids at the catalytic center in BtTdT (green) and ZaTdT (cyan). (b) Activity evaluation for M3-based mutants. (c) Extension of 3′–ONH 2 –dATP by Bt15AA R336L/K338G/L397M/E456G . Reaction conditions: 1 mg/mL TdT, 1 μM iDNA, 42 °C, 10 min. Note : Product bands at the same concentration may display different intensities due to sequence-specific effects.

    Article Snippet: 3′–ONH 2 –dNTPs were bought from Firebird Biomolecular Sciences (Florida, USA), and 3′- O –CH 2 N 3 –dNTP and 3′–OCHCHCN–dNTP were purchased from Huana Biomedical Technology Co. Ltd. (Hefei, China).

    Techniques: Activity Assay, Concentration Assay, Sequencing

    Mutagenesis based on AF3-based structural analysis. (a) Position of surrogate substrate ATP in M3 variants with an amino acid substitution at E456. Enzyme-ligand complexes were predicted using AF3. E456S (yellow), E456G (aquamarine), E456 (green), and E456A (magenta). (b) Activity test of M4 mutant after adding 3′–ONH 2 –dATP for different time. (c) Position of surrogate substrate ATP in M4 variants with an amino acid substitution at D395. The distances in angstrom from the substrate's 3′-end to the reference residues E456 or D395 (wild-type) are shown in different color for each mutant. Enzyme-ligand complexes were predicted using AF3. D395 (M4, yellow), D395G (white), and D395M (red). (d) Extension of 3′–ONH 2 –dNTP by M4 in 5 min. Reaction conditions: 1 mg/mL TdT and 1 μM iDNA. (e) Low-energy binding conformations of 3′–ONH 2 –dNTP in the WT and three E456 variants, along with their structural overlays. The distances between the 3′-O atom in the WT conformation and those in the mutant conformations are indicated. (f) The average distance between the substrate's O–NH 2 moiety and the geometric center of the WT and three E456 mutant backbones. (g) Time course assays of M4 mutations at D395. (h) Extension of 3′–ONH 2 –dNTP by M5 in 30 s. Reaction conditions: 1 mg/mL BtTdT and 1 μM iDNA. (i) PAGE analysis of the 10 steps of extension by M5. Extension conditions: 1 mg/mL M5, 1 μM iDNA P2, 1 min. “A∼, T∼, C∼, and G∼” stand for 3′–ONH 2 –dATP, 3′–ONH 2 –dTTP, 3′–ONH 2 –dCTP, and 3′–ONH 2 –dGTP, respectively. In panels (e) and (f), blue, purple, pink, and orange denote wild type, E456A, E456G, and E456S, respectively. Note : Product bands at the same concentration may display different intensities due to sequence-specific effects.

    Journal: Synthetic and Systems Biotechnology

    Article Title: Semi-rational engineering of terminal deoxynucleotidyl transferase for high-efficiency enzymatic de novo DNA synthesis

    doi: 10.1016/j.synbio.2026.03.009

    Figure Lengend Snippet: Mutagenesis based on AF3-based structural analysis. (a) Position of surrogate substrate ATP in M3 variants with an amino acid substitution at E456. Enzyme-ligand complexes were predicted using AF3. E456S (yellow), E456G (aquamarine), E456 (green), and E456A (magenta). (b) Activity test of M4 mutant after adding 3′–ONH 2 –dATP for different time. (c) Position of surrogate substrate ATP in M4 variants with an amino acid substitution at D395. The distances in angstrom from the substrate's 3′-end to the reference residues E456 or D395 (wild-type) are shown in different color for each mutant. Enzyme-ligand complexes were predicted using AF3. D395 (M4, yellow), D395G (white), and D395M (red). (d) Extension of 3′–ONH 2 –dNTP by M4 in 5 min. Reaction conditions: 1 mg/mL TdT and 1 μM iDNA. (e) Low-energy binding conformations of 3′–ONH 2 –dNTP in the WT and three E456 variants, along with their structural overlays. The distances between the 3′-O atom in the WT conformation and those in the mutant conformations are indicated. (f) The average distance between the substrate's O–NH 2 moiety and the geometric center of the WT and three E456 mutant backbones. (g) Time course assays of M4 mutations at D395. (h) Extension of 3′–ONH 2 –dNTP by M5 in 30 s. Reaction conditions: 1 mg/mL BtTdT and 1 μM iDNA. (i) PAGE analysis of the 10 steps of extension by M5. Extension conditions: 1 mg/mL M5, 1 μM iDNA P2, 1 min. “A∼, T∼, C∼, and G∼” stand for 3′–ONH 2 –dATP, 3′–ONH 2 –dTTP, 3′–ONH 2 –dCTP, and 3′–ONH 2 –dGTP, respectively. In panels (e) and (f), blue, purple, pink, and orange denote wild type, E456A, E456G, and E456S, respectively. Note : Product bands at the same concentration may display different intensities due to sequence-specific effects.

    Article Snippet: 3′–ONH 2 –dNTPs were bought from Firebird Biomolecular Sciences (Florida, USA), and 3′- O –CH 2 N 3 –dNTP and 3′–OCHCHCN–dNTP were purchased from Huana Biomedical Technology Co. Ltd. (Hefei, China).

    Techniques: Mutagenesis, Activity Assay, Binding Assay, Concentration Assay, Sequencing