dra i New England Biolabs Search Results


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  • 95
    New England Biolabs dra i
    Expression of the 46-bp insertion and detection of the two types of 16S rRNA by <t>RT-PCR.</t> The strains analyzed are indicated at the top. (A) Lanes +, use of consensual primer pair 27f and 590r; lanes ins, use of an insertion-specific pair of primers, ins1 and 590r. (B) Lanes +, RT-PCR products obtained with the primers 27f and 590r; lanes Dra I, RT-PCR products obtained in + lanes digested by Dra I. Lanes − (A and B), negative controls performed on the RNA of strain PR17/sat without reverse transcription and with the primers 27f and 590r (negative controls were also obtained for other strains and for the primers ins1 and 590r but are not shown); lane M, 100-bp DNA ladder (Promega) as a molecular weight marker.
    Dra I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 250 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Thermo Fisher dra i
    Expression of the 46-bp insertion and detection of the two types of 16S rRNA by <t>RT-PCR.</t> The strains analyzed are indicated at the top. (A) Lanes +, use of consensual primer pair 27f and 590r; lanes ins, use of an insertion-specific pair of primers, ins1 and 590r. (B) Lanes +, RT-PCR products obtained with the primers 27f and 590r; lanes Dra I, RT-PCR products obtained in + lanes digested by Dra I. Lanes − (A and B), negative controls performed on the RNA of strain PR17/sat without reverse transcription and with the primers 27f and 590r (negative controls were also obtained for other strains and for the primers ins1 and 590r but are not shown); lane M, 100-bp DNA ladder (Promega) as a molecular weight marker.
    Dra I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 337 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    TaKaRa dra i
    Expression of the 46-bp insertion and detection of the two types of 16S rRNA by <t>RT-PCR.</t> The strains analyzed are indicated at the top. (A) Lanes +, use of consensual primer pair 27f and 590r; lanes ins, use of an insertion-specific pair of primers, ins1 and 590r. (B) Lanes +, RT-PCR products obtained with the primers 27f and 590r; lanes Dra I, RT-PCR products obtained in + lanes digested by Dra I. Lanes − (A and B), negative controls performed on the RNA of strain PR17/sat without reverse transcription and with the primers 27f and 590r (negative controls were also obtained for other strains and for the primers ins1 and 590r but are not shown); lane M, 100-bp DNA ladder (Promega) as a molecular weight marker.
    Dra I, supplied by TaKaRa, used in various techniques. Bioz Stars score: 94/100, based on 129 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    dra i  (Roche)
    91
    Roche dra i
    Expression of the 46-bp insertion and detection of the two types of 16S rRNA by <t>RT-PCR.</t> The strains analyzed are indicated at the top. (A) Lanes +, use of consensual primer pair 27f and 590r; lanes ins, use of an insertion-specific pair of primers, ins1 and 590r. (B) Lanes +, RT-PCR products obtained with the primers 27f and 590r; lanes Dra I, RT-PCR products obtained in + lanes digested by Dra I. Lanes − (A and B), negative controls performed on the RNA of strain PR17/sat without reverse transcription and with the primers 27f and 590r (negative controls were also obtained for other strains and for the primers ins1 and 590r but are not shown); lane M, 100-bp DNA ladder (Promega) as a molecular weight marker.
    Dra I, supplied by Roche, used in various techniques. Bioz Stars score: 91/100, based on 47 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    GE Healthcare dra iii
    Expression of the 46-bp insertion and detection of the two types of 16S rRNA by <t>RT-PCR.</t> The strains analyzed are indicated at the top. (A) Lanes +, use of consensual primer pair 27f and 590r; lanes ins, use of an insertion-specific pair of primers, ins1 and 590r. (B) Lanes +, RT-PCR products obtained with the primers 27f and 590r; lanes Dra I, RT-PCR products obtained in + lanes digested by Dra I. Lanes − (A and B), negative controls performed on the RNA of strain PR17/sat without reverse transcription and with the primers 27f and 590r (negative controls were also obtained for other strains and for the primers ins1 and 590r but are not shown); lane M, 100-bp DNA ladder (Promega) as a molecular weight marker.
    Dra Iii, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 89/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    New England Biolabs dra
    Mutation analysis in patient 91 and his family. A, PCR amplification of a 1,058-bp HPS3 cDNA fragment showing heterozygous skipping of exon 14 (with an additional 950-bp band) in patient 91, his two full sisters, and his mother. B, PCR amplification of exon 6 HPS3 genomic DNA (233-bp), followed by restriction enzyme digestion with <t>Dra</t> <t>III.</t> The paternal C1329T mutation introduces a Dra III recognition site, resulting in 102-bp and 131-bp bands after digestion. Patient 91, his father, and his affected sister carry the C1329T mutation.
    Dra, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 88/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Roche dra ii
    Mutation analysis in patient 91 and his family. A, PCR amplification of a 1,058-bp HPS3 cDNA fragment showing heterozygous skipping of exon 14 (with an additional 950-bp band) in patient 91, his two full sisters, and his mother. B, PCR amplification of exon 6 HPS3 genomic DNA (233-bp), followed by restriction enzyme digestion with <t>Dra</t> <t>III.</t> The paternal C1329T mutation introduces a Dra III recognition site, resulting in 102-bp and 131-bp bands after digestion. Patient 91, his father, and his affected sister carry the C1329T mutation.
    Dra Ii, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Boehringer Mannheim dra i
    Mutation analysis in patient 91 and his family. A, PCR amplification of a 1,058-bp HPS3 cDNA fragment showing heterozygous skipping of exon 14 (with an additional 950-bp band) in patient 91, his two full sisters, and his mother. B, PCR amplification of exon 6 HPS3 genomic DNA (233-bp), followed by restriction enzyme digestion with <t>Dra</t> <t>III.</t> The paternal C1329T mutation introduces a Dra III recognition site, resulting in 102-bp and 131-bp bands after digestion. Patient 91, his father, and his affected sister carry the C1329T mutation.
    Dra I, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 91/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    New England Biolabs 10x dra
    Mutation analysis in patient 91 and his family. A, PCR amplification of a 1,058-bp HPS3 cDNA fragment showing heterozygous skipping of exon 14 (with an additional 950-bp band) in patient 91, his two full sisters, and his mother. B, PCR amplification of exon 6 HPS3 genomic DNA (233-bp), followed by restriction enzyme digestion with <t>Dra</t> <t>III.</t> The paternal C1329T mutation introduces a Dra III recognition site, resulting in 102-bp and 131-bp bands after digestion. Patient 91, his father, and his affected sister carry the C1329T mutation.
    10x Dra, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Promega dra i
    REs with increasing specificity show decreasing effects on chromosome elastic response. Force data are before, during, and after 350-sec exposures to various REs; force is normalized to units of initial applied force, which ranged between 0.2 and 0.8 nN in the five separate experiments shown. Alu I AG↓CT (black) relaxes the force in ≈30 sec; Cac 8I GCN↓NGC (red) only partially reduces the force. Hin cII GT(T/C)↓(A/G)AC (blue) and <t>Dra</t> I TTT↓AAA (green) induce an increase in force during spraying, with a return to the original force when spraying stops (≈600 sec), similar to spraying with reaction buffer and no enzyme (violet). These results indicate that chromatin–chromatin crosslinks occur roughly every 15 kb (see text). A video of Alu .
    Dra I, supplied by Promega, used in various techniques. Bioz Stars score: 91/100, based on 65 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs dra iii wt
    The <t>Dra</t> <t>III</t> overall protein structure . (A) The complete Dra III structure derived in the presence of magnesium chloride. The ion binding motifs are shown. (B) The 11-bp phosphorothioate canonical DNA duplex. (C) The secondary structure of the Dra III subunit. Elements of secondary structure are indicated by α-helix (red rectangle) and β-strand (blue arrow). Catalytic residues of the HNH endonuclease motif are indicated with blue font. Zinc-binding cysteine residues are indicated with red font. The location of N-terminal domain, C-terminal domain and ββα-metal motif is indicated by the orange, cyan and black underlines respectively
    Dra Iii Wt, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    New England Biolabs endonucleases dra i
    The <t>Dra</t> <t>III</t> overall protein structure . (A) The complete Dra III structure derived in the presence of magnesium chloride. The ion binding motifs are shown. (B) The 11-bp phosphorothioate canonical DNA duplex. (C) The secondary structure of the Dra III subunit. Elements of secondary structure are indicated by α-helix (red rectangle) and β-strand (blue arrow). Catalytic residues of the HNH endonuclease motif are indicated with blue font. Zinc-binding cysteine residues are indicated with red font. The location of N-terminal domain, C-terminal domain and ββα-metal motif is indicated by the orange, cyan and black underlines respectively
    Endonucleases Dra I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    New England Biolabs dra i enzyme
    The <t>Dra</t> <t>III</t> overall protein structure . (A) The complete Dra III structure derived in the presence of magnesium chloride. The ion binding motifs are shown. (B) The 11-bp phosphorothioate canonical DNA duplex. (C) The secondary structure of the Dra III subunit. Elements of secondary structure are indicated by α-helix (red rectangle) and β-strand (blue arrow). Catalytic residues of the HNH endonuclease motif are indicated with blue font. Zinc-binding cysteine residues are indicated with red font. The location of N-terminal domain, C-terminal domain and ββα-metal motif is indicated by the orange, cyan and black underlines respectively
    Dra I Enzyme, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 91/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    New England Biolabs cotton dra i
    The <t>Dra</t> <t>III</t> overall protein structure . (A) The complete Dra III structure derived in the presence of magnesium chloride. The ion binding motifs are shown. (B) The 11-bp phosphorothioate canonical DNA duplex. (C) The secondary structure of the Dra III subunit. Elements of secondary structure are indicated by α-helix (red rectangle) and β-strand (blue arrow). Catalytic residues of the HNH endonuclease motif are indicated with blue font. Zinc-binding cysteine residues are indicated with red font. The location of N-terminal domain, C-terminal domain and ββα-metal motif is indicated by the orange, cyan and black underlines respectively
    Cotton Dra I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    New England Biolabs complete dra i
    The <t>Dra</t> <t>III</t> overall protein structure . (A) The complete Dra III structure derived in the presence of magnesium chloride. The ion binding motifs are shown. (B) The 11-bp phosphorothioate canonical DNA duplex. (C) The secondary structure of the Dra III subunit. Elements of secondary structure are indicated by α-helix (red rectangle) and β-strand (blue arrow). Catalytic residues of the HNH endonuclease motif are indicated with blue font. Zinc-binding cysteine residues are indicated with red font. The location of N-terminal domain, C-terminal domain and ββα-metal motif is indicated by the orange, cyan and black underlines respectively
    Complete Dra I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 92/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    New England Biolabs dra i restriction digestion
    The <t>Dra</t> <t>III</t> overall protein structure . (A) The complete Dra III structure derived in the presence of magnesium chloride. The ion binding motifs are shown. (B) The 11-bp phosphorothioate canonical DNA duplex. (C) The secondary structure of the Dra III subunit. Elements of secondary structure are indicated by α-helix (red rectangle) and β-strand (blue arrow). Catalytic residues of the HNH endonuclease motif are indicated with blue font. Zinc-binding cysteine residues are indicated with red font. The location of N-terminal domain, C-terminal domain and ββα-metal motif is indicated by the orange, cyan and black underlines respectively
    Dra I Restriction Digestion, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    New England Biolabs restriction enzyme dra i
    Examples of genomic DNA macrorestriction profiles of S. maltophilia produced by PFGE after <t>Dra</t> I digestion. Lane 1, c12; lane 2, c1; lane 3, c7; lane 4, c17; lane 5, c5; lane 6, e1; lane 7, e2; lane 8, lambda ladder marker (size range, 225 to 1,900 kb); lane 9, e9; lane 10, e10; lane 11, t20; lane 12, e18; lane 13, e5.
    Restriction Enzyme Dra I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 88/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Roche dra i restriction enzyme
    <t>Dra</t> I protection assay. a Oligonucleotide sequences of TFOs and the oligonucleotide complementary to the TFO and pso-TFO used in this study. Several nucleotides within the TFO are modified to enhance the stability of the triplex. Lower case nucleotides,
    Dra I Restriction Enzyme, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    New England Biolabs bsp hi dra i
    Analysis of vanB long PCR amplicons. (Top) Representative agarose electrophoresis gel of vanB long PCR amplicons. Lanes 1 and 6, 1-kb ladder (Life Technologies, Gaithersburg, Md.); lane 2, vanB2 isolate TUH2-18; lane 3, vanB3 isolate TUH7-68; lane 4, vanB2 isolate TUH7-15 with a 789-bp insertion; lane 5, vanB1 isolate TUH4-64. (Bottom) Restriction fragment analysis of vanB long PCR amplicons. Shown are <t>Bsp</t> HI/ Dra I-digested vanB long PCR amplicons analyzed by agarose gel electrophoresis. Lanes 1 and 6, 1-kb ladder; lane 2, vanB2 isolate TUH2-18 with RFLP-2; lane 3, vanB3 isolate TUH7-68 RFLP-2; lane 4, vanB2 isolate TUH7-15 with a 789-bp enlargement of fragment 4 (RFLP-2*); lane 5, vanB1 isolate TUH4-64 with RFLP-1. Molecular sizes shown to the left of each gel (in base pairs) refer to the 1-kb ladder.
    Bsp Hi Dra I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 80/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    New England Biolabs sph i dra iii
    Analysis of vanB long PCR amplicons. (Top) Representative agarose electrophoresis gel of vanB long PCR amplicons. Lanes 1 and 6, 1-kb ladder (Life Technologies, Gaithersburg, Md.); lane 2, vanB2 isolate TUH2-18; lane 3, vanB3 isolate TUH7-68; lane 4, vanB2 isolate TUH7-15 with a 789-bp insertion; lane 5, vanB1 isolate TUH4-64. (Bottom) Restriction fragment analysis of vanB long PCR amplicons. Shown are <t>Bsp</t> HI/ Dra I-digested vanB long PCR amplicons analyzed by agarose gel electrophoresis. Lanes 1 and 6, 1-kb ladder; lane 2, vanB2 isolate TUH2-18 with RFLP-2; lane 3, vanB3 isolate TUH7-68 RFLP-2; lane 4, vanB2 isolate TUH7-15 with a 789-bp enlargement of fragment 4 (RFLP-2*); lane 5, vanB1 isolate TUH4-64 with RFLP-1. Molecular sizes shown to the left of each gel (in base pairs) refer to the 1-kb ladder.
    Sph I Dra Iii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 91/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Expression of the 46-bp insertion and detection of the two types of 16S rRNA by RT-PCR. The strains analyzed are indicated at the top. (A) Lanes +, use of consensual primer pair 27f and 590r; lanes ins, use of an insertion-specific pair of primers, ins1 and 590r. (B) Lanes +, RT-PCR products obtained with the primers 27f and 590r; lanes Dra I, RT-PCR products obtained in + lanes digested by Dra I. Lanes − (A and B), negative controls performed on the RNA of strain PR17/sat without reverse transcription and with the primers 27f and 590r (negative controls were also obtained for other strains and for the primers ins1 and 590r but are not shown); lane M, 100-bp DNA ladder (Promega) as a molecular weight marker.

    Journal: Journal of Bacteriology

    Article Title: Atypical 16S rRNA Gene Copies in Ochrobactrum intermedium Strains Reveal a Large Genomic Rearrangement by Recombination between rrn Copies

    doi: 10.1128/JB.185.9.2901-2909.2003

    Figure Lengend Snippet: Expression of the 46-bp insertion and detection of the two types of 16S rRNA by RT-PCR. The strains analyzed are indicated at the top. (A) Lanes +, use of consensual primer pair 27f and 590r; lanes ins, use of an insertion-specific pair of primers, ins1 and 590r. (B) Lanes +, RT-PCR products obtained with the primers 27f and 590r; lanes Dra I, RT-PCR products obtained in + lanes digested by Dra I. Lanes − (A and B), negative controls performed on the RNA of strain PR17/sat without reverse transcription and with the primers 27f and 590r (negative controls were also obtained for other strains and for the primers ins1 and 590r but are not shown); lane M, 100-bp DNA ladder (Promega) as a molecular weight marker.

    Article Snippet: Restriction analysis of PCR products was done with 10 U of Dra I (New England Biolabs, Hertfordshire, United Kingdom) by following the supplier's recommendations. ) and with sequences deposited in the Ribosomal Database Project, version 7.0, by using SIMILARITY RANK and SUGGEST TREE ( ).

    Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Molecular Weight, Marker

    Mutation analysis in patient 91 and his family. A, PCR amplification of a 1,058-bp HPS3 cDNA fragment showing heterozygous skipping of exon 14 (with an additional 950-bp band) in patient 91, his two full sisters, and his mother. B, PCR amplification of exon 6 HPS3 genomic DNA (233-bp), followed by restriction enzyme digestion with Dra III. The paternal C1329T mutation introduces a Dra III recognition site, resulting in 102-bp and 131-bp bands after digestion. Patient 91, his father, and his affected sister carry the C1329T mutation.

    Journal: American Journal of Human Genetics

    Article Title: Hermansky-Pudlak Syndrome Type 3 in Ashkenazi Jews and Other Non-Puerto Rican Patients with Hypopigmentation and Platelet Storage-Pool Deficiency

    doi:

    Figure Lengend Snippet: Mutation analysis in patient 91 and his family. A, PCR amplification of a 1,058-bp HPS3 cDNA fragment showing heterozygous skipping of exon 14 (with an additional 950-bp band) in patient 91, his two full sisters, and his mother. B, PCR amplification of exon 6 HPS3 genomic DNA (233-bp), followed by restriction enzyme digestion with Dra III. The paternal C1329T mutation introduces a Dra III recognition site, resulting in 102-bp and 131-bp bands after digestion. Patient 91, his father, and his affected sister carry the C1329T mutation.

    Article Snippet: Incubation of PCR-amplified exon 6 fragments of all family members with Dra III ( ) indicated that the father is heterozygous for the C1329T mutation, that both of his affected children inherited the mutant allele, and that his unaffected daughter inherited his normal allele.

    Techniques: Mutagenesis, Polymerase Chain Reaction, Amplification

    REs with increasing specificity show decreasing effects on chromosome elastic response. Force data are before, during, and after 350-sec exposures to various REs; force is normalized to units of initial applied force, which ranged between 0.2 and 0.8 nN in the five separate experiments shown. Alu I AG↓CT (black) relaxes the force in ≈30 sec; Cac 8I GCN↓NGC (red) only partially reduces the force. Hin cII GT(T/C)↓(A/G)AC (blue) and Dra I TTT↓AAA (green) induce an increase in force during spraying, with a return to the original force when spraying stops (≈600 sec), similar to spraying with reaction buffer and no enzyme (violet). These results indicate that chromatin–chromatin crosslinks occur roughly every 15 kb (see text). A video of Alu .

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Mitotic chromosomes are chromatin networks without a mechanically contiguous protein scaffold

    doi: 10.1073/pnas.232442599

    Figure Lengend Snippet: REs with increasing specificity show decreasing effects on chromosome elastic response. Force data are before, during, and after 350-sec exposures to various REs; force is normalized to units of initial applied force, which ranged between 0.2 and 0.8 nN in the five separate experiments shown. Alu I AG↓CT (black) relaxes the force in ≈30 sec; Cac 8I GCN↓NGC (red) only partially reduces the force. Hin cII GT(T/C)↓(A/G)AC (blue) and Dra I TTT↓AAA (green) induce an increase in force during spraying, with a return to the original force when spraying stops (≈600 sec), similar to spraying with reaction buffer and no enzyme (violet). These results indicate that chromatin–chromatin crosslinks occur roughly every 15 kb (see text). A video of Alu .

    Article Snippet: Experiments with Dra I (TTT↓AAA, Promega, Fig. ), Stu I (AGG↓CCT, New England Biolabs; data not shown), and Pvu II (CAG↓CTG, Promega; data not shown), which cut random DNA once every 46 = 4,096 bases, also do not produce observable force reduction.

    Techniques: Size-exclusion Chromatography

    The Dra III overall protein structure . (A) The complete Dra III structure derived in the presence of magnesium chloride. The ion binding motifs are shown. (B) The 11-bp phosphorothioate canonical DNA duplex. (C) The secondary structure of the Dra III subunit. Elements of secondary structure are indicated by α-helix (red rectangle) and β-strand (blue arrow). Catalytic residues of the HNH endonuclease motif are indicated with blue font. Zinc-binding cysteine residues are indicated with red font. The location of N-terminal domain, C-terminal domain and ββα-metal motif is indicated by the orange, cyan and black underlines respectively

    Journal: Protein & Cell

    Article Title: Elimination of inter-domain interactions increases the cleavage fidelity of the restriction endonuclease DraIII

    doi: 10.1007/s13238-014-0038-z

    Figure Lengend Snippet: The Dra III overall protein structure . (A) The complete Dra III structure derived in the presence of magnesium chloride. The ion binding motifs are shown. (B) The 11-bp phosphorothioate canonical DNA duplex. (C) The secondary structure of the Dra III subunit. Elements of secondary structure are indicated by α-helix (red rectangle) and β-strand (blue arrow). Catalytic residues of the HNH endonuclease motif are indicated with blue font. Zinc-binding cysteine residues are indicated with red font. The location of N-terminal domain, C-terminal domain and ββα-metal motif is indicated by the orange, cyan and black underlines respectively

    Article Snippet: 100 nmol/L of the canonical or star DNA was incubated with 500 nmol/L of Dra III WT in NEBuffer 4 at 37°C for 1 h. The reactions were stopped by adding EDTA to 20 mmol/L.

    Techniques: Derivative Assay, Binding Assay

    Comparison of the sequence and structures of HNH REases . (A) Sequence alignment of the Dra III, Hpy 99I, Pac I, T4 Endo VII and Kpn I HNH catalytic motif. (B–D) Dra III HNH motif (orange) aligned to Hpy 991 (B: cyan, PDB 3GOX), Pac I (C: green, PDB 3M7K) and T4 Endo VII (D: blue, PDB 2QNF), respectively. The zinc ion is shown as green sphere, magnesium ion and DNA are shown in red

    Journal: Protein & Cell

    Article Title: Elimination of inter-domain interactions increases the cleavage fidelity of the restriction endonuclease DraIII

    doi: 10.1007/s13238-014-0038-z

    Figure Lengend Snippet: Comparison of the sequence and structures of HNH REases . (A) Sequence alignment of the Dra III, Hpy 99I, Pac I, T4 Endo VII and Kpn I HNH catalytic motif. (B–D) Dra III HNH motif (orange) aligned to Hpy 991 (B: cyan, PDB 3GOX), Pac I (C: green, PDB 3M7K) and T4 Endo VII (D: blue, PDB 2QNF), respectively. The zinc ion is shown as green sphere, magnesium ion and DNA are shown in red

    Article Snippet: 100 nmol/L of the canonical or star DNA was incubated with 500 nmol/L of Dra III WT in NEBuffer 4 at 37°C for 1 h. The reactions were stopped by adding EDTA to 20 mmol/L.

    Techniques: Sequencing

    Determination of Dra III Fidelity Index (FI) and star sites . (A) Determination of Dra III Fidelity Index (FI). λ DNA (1.6 nmol/L; 16 nmol/L CACNNNGTG sites) is digested by Dra III in a series of two fold dilutions. Dra III concentration: Lane 1, 3.2 μmol/L; Lane 10, 6.25 nmol/L; Lane 11, 3.125 nmol/L; Lane 21, 3.05 pmol/L; Lane 22, 1-kb DNA Ladder (NEB). The vertical arrows indicate the two critical points: HNS —the H ighest REases concentration showing N o S tar activity and LCC —the L owest REase concentration needed for C omplete C leavage on canonical sites. FI = HNS/LCC, which is 2 in this case. Asterisk represents a star band, and the hash represents a band that resulted from partial cleavage of λ DNA. The theoretical digestion pattern of Dra III to λ DNA was predicted using NEBcutter (Vincze et al., 2003 ) and was shown on the left. (B) Dra III star site in pUC19 was predicted to be the CATGTTGTG site. Lane 1: Bam HI (cut at nt 417) and Xmn I (cut at nt 2298) double digestion on pUC19 generated the 1.9-kb and 0.8-kb bands. Lane 2: Bam HI, Xmn I and Dra III triple digestion on pUC19. Asterisk indicates the star band. According to the approximate size of star bands, the CATGTTGTG site (nt 2033) was hypothesized to be the Dra III star site. Cleavage on predicted CATGTTGTG site generated the 1.6-kb and 0.3-kb star bands. Lane 3: 1-kb DNA Ladder. (C) Dra III star activity cleaves the CATGTTGTG site in pXba. Lane 1: 1-kb DNA Ladder. Lane 2: pXba was digested by Dra III. Asterisk indicates the star bands. Dra III star activity generates the expected 6.5-kb and 4.5-kb star bands on pXba. (D) Dra III star activity shows selectivity to the central “NNN” part of CATNNNGTG site. There are 11 CATNNNGTG sites in pXba and the sequences containing these sites were tested independently on oligonucleotide duplex DNAs carrying each of the sites (Table S1). The canonical CACGGCGTG site was used as positive control. Dra III shows cleavage activity to CATATGGTG, CATTACGTG, CATGTGGTG, CATAAAGTG and CATGTTGTG sites. Dra III did not cut the pseudo-palindromic CATGTTATG site

    Journal: Protein & Cell

    Article Title: Elimination of inter-domain interactions increases the cleavage fidelity of the restriction endonuclease DraIII

    doi: 10.1007/s13238-014-0038-z

    Figure Lengend Snippet: Determination of Dra III Fidelity Index (FI) and star sites . (A) Determination of Dra III Fidelity Index (FI). λ DNA (1.6 nmol/L; 16 nmol/L CACNNNGTG sites) is digested by Dra III in a series of two fold dilutions. Dra III concentration: Lane 1, 3.2 μmol/L; Lane 10, 6.25 nmol/L; Lane 11, 3.125 nmol/L; Lane 21, 3.05 pmol/L; Lane 22, 1-kb DNA Ladder (NEB). The vertical arrows indicate the two critical points: HNS —the H ighest REases concentration showing N o S tar activity and LCC —the L owest REase concentration needed for C omplete C leavage on canonical sites. FI = HNS/LCC, which is 2 in this case. Asterisk represents a star band, and the hash represents a band that resulted from partial cleavage of λ DNA. The theoretical digestion pattern of Dra III to λ DNA was predicted using NEBcutter (Vincze et al., 2003 ) and was shown on the left. (B) Dra III star site in pUC19 was predicted to be the CATGTTGTG site. Lane 1: Bam HI (cut at nt 417) and Xmn I (cut at nt 2298) double digestion on pUC19 generated the 1.9-kb and 0.8-kb bands. Lane 2: Bam HI, Xmn I and Dra III triple digestion on pUC19. Asterisk indicates the star band. According to the approximate size of star bands, the CATGTTGTG site (nt 2033) was hypothesized to be the Dra III star site. Cleavage on predicted CATGTTGTG site generated the 1.6-kb and 0.3-kb star bands. Lane 3: 1-kb DNA Ladder. (C) Dra III star activity cleaves the CATGTTGTG site in pXba. Lane 1: 1-kb DNA Ladder. Lane 2: pXba was digested by Dra III. Asterisk indicates the star bands. Dra III star activity generates the expected 6.5-kb and 4.5-kb star bands on pXba. (D) Dra III star activity shows selectivity to the central “NNN” part of CATNNNGTG site. There are 11 CATNNNGTG sites in pXba and the sequences containing these sites were tested independently on oligonucleotide duplex DNAs carrying each of the sites (Table S1). The canonical CACGGCGTG site was used as positive control. Dra III shows cleavage activity to CATATGGTG, CATTACGTG, CATGTGGTG, CATAAAGTG and CATGTTGTG sites. Dra III did not cut the pseudo-palindromic CATGTTATG site

    Article Snippet: 100 nmol/L of the canonical or star DNA was incubated with 500 nmol/L of Dra III WT in NEBuffer 4 at 37°C for 1 h. The reactions were stopped by adding EDTA to 20 mmol/L.

    Techniques: Concentration Assay, Activity Assay, Generated, Positive Control

    The interactions between the N-terminal domain and C-terminal domain of Dra III subunit . (A) Dra III subunit structure. N-terminal domain in orange; C-terminal domain in cyan; Zinc in green; Magnesium in red. Left: Dra III subunit displayed in surface mode. Right: Dra III subunit displayed in cartoon mode. Interactions in the mouth, middle region and hydrophobic residues in the hinge region were shown in gray boxes. The locations of potential hydrogen bonds are indicated with red dotted line. (B) Determination FI of Dra III T181A. λ DNA was cleaved by diluted T181A. Lane 1: 3.2 μmol/L T181A; Lane 13: 0.78 nmol/L (LCC); Lane 21: 3.05 pmol/L; Lane 22: 1-kb DNA Ladder. FI is larger than 4000. The hash represents a partially digested band. No star band was observed. Disrupting hydrogen bond between T181 and D55 in the middle region remarkably enhanced FI

    Journal: Protein & Cell

    Article Title: Elimination of inter-domain interactions increases the cleavage fidelity of the restriction endonuclease DraIII

    doi: 10.1007/s13238-014-0038-z

    Figure Lengend Snippet: The interactions between the N-terminal domain and C-terminal domain of Dra III subunit . (A) Dra III subunit structure. N-terminal domain in orange; C-terminal domain in cyan; Zinc in green; Magnesium in red. Left: Dra III subunit displayed in surface mode. Right: Dra III subunit displayed in cartoon mode. Interactions in the mouth, middle region and hydrophobic residues in the hinge region were shown in gray boxes. The locations of potential hydrogen bonds are indicated with red dotted line. (B) Determination FI of Dra III T181A. λ DNA was cleaved by diluted T181A. Lane 1: 3.2 μmol/L T181A; Lane 13: 0.78 nmol/L (LCC); Lane 21: 3.05 pmol/L; Lane 22: 1-kb DNA Ladder. FI is larger than 4000. The hash represents a partially digested band. No star band was observed. Disrupting hydrogen bond between T181 and D55 in the middle region remarkably enhanced FI

    Article Snippet: 100 nmol/L of the canonical or star DNA was incubated with 500 nmol/L of Dra III WT in NEBuffer 4 at 37°C for 1 h. The reactions were stopped by adding EDTA to 20 mmol/L.

    Techniques:

    Dra III digests star site sequence in asymmetrical pattern . (A) Sequences of Cy5-labeled DNA substrates. (B) Star activity cleavage occurs in CAT↑GTT↓GTG. Cy5-labeled canonical or star DNA was digested by Dra III as described in Supplementary EXPERIMENTAL. The single strand product was separated by TBE urea polyacrylmide gel and compared with synthesized single-stranded markers. Star activity cleavage occurs in CAT↑GTT↓GTG (↑ indicates nicking on the bottom strand; ↓ indicates nicking on the top strand). (C and D) Dra III digests a star site sequence in an asymmetrical manner. 100 nmol/L Cy5-labeled star DNA was digested by 500 nmol/L Dra III. The samples were collected at the designated time intervals and were analyzed by electrophoresis using TBE urea polyacrylmide gel. The amount of the quantified products was plotted against time

    Journal: Protein & Cell

    Article Title: Elimination of inter-domain interactions increases the cleavage fidelity of the restriction endonuclease DraIII

    doi: 10.1007/s13238-014-0038-z

    Figure Lengend Snippet: Dra III digests star site sequence in asymmetrical pattern . (A) Sequences of Cy5-labeled DNA substrates. (B) Star activity cleavage occurs in CAT↑GTT↓GTG. Cy5-labeled canonical or star DNA was digested by Dra III as described in Supplementary EXPERIMENTAL. The single strand product was separated by TBE urea polyacrylmide gel and compared with synthesized single-stranded markers. Star activity cleavage occurs in CAT↑GTT↓GTG (↑ indicates nicking on the bottom strand; ↓ indicates nicking on the top strand). (C and D) Dra III digests a star site sequence in an asymmetrical manner. 100 nmol/L Cy5-labeled star DNA was digested by 500 nmol/L Dra III. The samples were collected at the designated time intervals and were analyzed by electrophoresis using TBE urea polyacrylmide gel. The amount of the quantified products was plotted against time

    Article Snippet: 100 nmol/L of the canonical or star DNA was incubated with 500 nmol/L of Dra III WT in NEBuffer 4 at 37°C for 1 h. The reactions were stopped by adding EDTA to 20 mmol/L.

    Techniques: Sequencing, Labeling, Activity Assay, Synthesized, Electrophoresis

    Examples of genomic DNA macrorestriction profiles of S. maltophilia produced by PFGE after Dra I digestion. Lane 1, c12; lane 2, c1; lane 3, c7; lane 4, c17; lane 5, c5; lane 6, e1; lane 7, e2; lane 8, lambda ladder marker (size range, 225 to 1,900 kb); lane 9, e9; lane 10, e10; lane 11, t20; lane 12, e18; lane 13, e5.

    Journal: Journal of Clinical Microbiology

    Article Title: Genotypic and Phenotypic Relationships between Clinical and Environmental Isolates of Stenotrophomonas maltophilia

    doi:

    Figure Lengend Snippet: Examples of genomic DNA macrorestriction profiles of S. maltophilia produced by PFGE after Dra I digestion. Lane 1, c12; lane 2, c1; lane 3, c7; lane 4, c17; lane 5, c5; lane 6, e1; lane 7, e2; lane 8, lambda ladder marker (size range, 225 to 1,900 kb); lane 9, e9; lane 10, e10; lane 11, t20; lane 12, e18; lane 13, e5.

    Article Snippet: Agarose plugs were digested with restriction enzyme Dra I (New England Biolabs, Schalbach, Germany) for 20 h at 35°C according to the manufacturer's recommendations.

    Techniques: Produced, Marker

    Dra I protection assay. a Oligonucleotide sequences of TFOs and the oligonucleotide complementary to the TFO and pso-TFO used in this study. Several nucleotides within the TFO are modified to enhance the stability of the triplex. Lower case nucleotides,

    Journal: Methods in Molecular Biology (Clifton, N.j.)

    Article Title: Homologous Recombination Assay for Interstrand Cross-Link Repair

    doi: 10.1007/978-1-61779-129-1_16

    Figure Lengend Snippet: Dra I protection assay. a Oligonucleotide sequences of TFOs and the oligonucleotide complementary to the TFO and pso-TFO used in this study. Several nucleotides within the TFO are modified to enhance the stability of the triplex. Lower case nucleotides,

    Article Snippet: Dra I restriction enzyme (40 U/μl; Roche).

    Techniques: Modification

    Analysis of vanB long PCR amplicons. (Top) Representative agarose electrophoresis gel of vanB long PCR amplicons. Lanes 1 and 6, 1-kb ladder (Life Technologies, Gaithersburg, Md.); lane 2, vanB2 isolate TUH2-18; lane 3, vanB3 isolate TUH7-68; lane 4, vanB2 isolate TUH7-15 with a 789-bp insertion; lane 5, vanB1 isolate TUH4-64. (Bottom) Restriction fragment analysis of vanB long PCR amplicons. Shown are Bsp HI/ Dra I-digested vanB long PCR amplicons analyzed by agarose gel electrophoresis. Lanes 1 and 6, 1-kb ladder; lane 2, vanB2 isolate TUH2-18 with RFLP-2; lane 3, vanB3 isolate TUH7-68 RFLP-2; lane 4, vanB2 isolate TUH7-15 with a 789-bp enlargement of fragment 4 (RFLP-2*); lane 5, vanB1 isolate TUH4-64 with RFLP-1. Molecular sizes shown to the left of each gel (in base pairs) refer to the 1-kb ladder.

    Journal: Antimicrobial Agents and Chemotherapy

    Article Title: Heterogeneity in the vanB Gene Cluster of Genomically Diverse Clinical Strains of Vancomycin-Resistant Enterococci

    doi:

    Figure Lengend Snippet: Analysis of vanB long PCR amplicons. (Top) Representative agarose electrophoresis gel of vanB long PCR amplicons. Lanes 1 and 6, 1-kb ladder (Life Technologies, Gaithersburg, Md.); lane 2, vanB2 isolate TUH2-18; lane 3, vanB3 isolate TUH7-68; lane 4, vanB2 isolate TUH7-15 with a 789-bp insertion; lane 5, vanB1 isolate TUH4-64. (Bottom) Restriction fragment analysis of vanB long PCR amplicons. Shown are Bsp HI/ Dra I-digested vanB long PCR amplicons analyzed by agarose gel electrophoresis. Lanes 1 and 6, 1-kb ladder; lane 2, vanB2 isolate TUH2-18 with RFLP-2; lane 3, vanB3 isolate TUH7-68 RFLP-2; lane 4, vanB2 isolate TUH7-15 with a 789-bp enlargement of fragment 4 (RFLP-2*); lane 5, vanB1 isolate TUH4-64 with RFLP-1. Molecular sizes shown to the left of each gel (in base pairs) refer to the 1-kb ladder.

    Article Snippet: Bsp HI/ Dra I (New England Biolabs)-digested vanB long PCR products were analyzed on ethidium bromide-stained agarose gels.

    Techniques: Polymerase Chain Reaction, Electrophoresis, Agarose Gel Electrophoresis