BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 17885

Title: Solution NMR structure of a DNA dodecamer containing the 7-aminomethyl-7-deaza-2'-deoxyguanosine adduct   PubMed: 24131376

Authors: Szulik, Marta; Ganguly, Manjori; Wang, Ruo-Wen; Gold, Barry; Stone, Michael

Citation: Szulik, Marta; Voehler, Markus; Ganguly, Manjori; Gold, Barry; Stone, Michael. "Site-specific stabilization of DNA by a tethered major groove amine, 7-aminomethyl-7-deaza-2'-deoxyguanosine."  Biochemistry 52, 7659-7668 (2013).

Assembly members:
DNA_dodecamer, polymer, 12 residues, 3005.005 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
DNA_dodecamer: GAGAXCGCTCTC

Data sets:
Data typeCount
1H chemical shifts73

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(P*AP*GP*AP*CP*GP*CP*TP*CP*TP*C)-3')1

Entities:

Entity 1, DNA (5'-D(P*AP*GP*AP*CP*GP*CP*TP*CP*TP*C)-3') 12 residues - 3005.005 Da.

selfcomplementary

1   DGDADGDA2LADCDGDCDTDC
2   DTDC

Samples:

7amG_sample: DNA dodecamer, [U-2H], 0.25 mM; sodium phosphate 10 mM; sodium chloride 200 mM; sodium azide 0.011 M; sodium EDTA 0.05 mM

7amG_sample_conditions: ionic strength: 0.21 M; pH: 7; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESY7amG_sampleisotropic7amG_sample_conditions
2D 1H-1H COSY7amG_sampleisotropic7amG_sample_conditions

Software:

TOPSPIN v2.0.b.6, Bruker Biospin - processing

SPARKY, Goddard - chemical shift assignment

AMBER v10, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

NMR spectrometers:

  • Bruker Avance 800 MHz

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