BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 17887

Title: DNA sequence context conceals alpha anomeric lesion   PubMed: 22227386

Authors: Johnson, Christopher; Spring, Alexander; Cunningham, Richard; Germann, Markus

Citation: Johnson, Christopher; Spring, Alexander; Desai, Sunil; Cunningham, Richard; Germann, Markus. "DNA Sequence Context Conceals -Anomeric Lesions."  J. Mol. Biol. 416, 425-437 (2012).

Assembly members:
DNA_(5'-D(*GP*TP*CP*CP*ADA*GP*GP*AP*CP*G)-3')_, polymer, 10 residues, 2756.833 Da.
DNA_(5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3')_, polymer, 10 residues, 3021.004 Da.

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: chemical synthesis   Host organism: n/a

Entity Sequences (FASTA):
DNA_(5'-D(*GP*TP*CP*CP*ADA*GP*GP*AP*CP*G)-3')_: GTCCXGGACG
DNA_(5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3')_: CGTCCTGGAC

Data sets:
Data typeCount
13C chemical shifts56
1H chemical shifts171
31P chemical shifts18

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1DNA_chain_11
2DNA_chain_22

Entities:

Entity 1, DNA_chain_1 10 residues - 2756.833 Da.

1   DGDTDCDCA3ADGDGDADCDG

Entity 2, DNA_chain_2 10 residues - 3021.004 Da.

1   DCDGDTDCDCDTDGDGDADC

Samples:

water_sample: DNA_chain_1 0.75 mM; DNA_chain_2 0.75 mM; sodium phosphate 10 mM; sodium chloride 50 mM; D2O 10%; DSS 0.2 uM; EDTA 2 mM; H2O 90%

D2O_sample: DNA_chain_1 0.75 mM; DNA_chain_2 0.75 mM; sodium phosphate 10 mM; sodium chloride 50 mM; D2O 100%; DSS 0.2 uM; EDTA 2 mM

sample_conditions_1: ionic strength: 50 mM; pH: 6.65; pressure: 1 atm; temperature: 276 K

sample_conditions_2: ionic strength: 50 mM; pH*: 7.05; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
1-1 jump returnwater_sampleisotropicsample_conditions_1
1D NOEwater_sampleisotropicsample_conditions_1
1-1 NOESY 2D 150 mswater_sampleisotropicsample_conditions_1
Low Flip COSYD2O_sampleisotropicsample_conditions_2
TOCYSD2O_sampleisotropicsample_conditions_2
2D 1H 1H NOESY 75 msD2O_sampleisotropicsample_conditions_2
2D 1H 1H NOESY 125 msD2O_sampleisotropicsample_conditions_2
2D 1H-1H NOESY 250 msD2O_sampleisotropicsample_conditions_2
Constant Time COSYD2O_sampleisotropicsample_conditions_2
2D 1H-13C HSQCD2O_sampleisotropicsample_conditions_2
2D 1H-31P CORRD2O_sampleisotropicsample_conditions_2
1D 31PD2O_sampleisotropicsample_conditions_2

Software:

AMBER v9.0, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - structure solution

SPARKY v3.3, Goddard - chemical shift assignment

TOPSPIN, Bruker Biospin - data analysis

CORMA, Thomas James - structure solution

MARDGIRAS, Thomas James - structure solution

CURVES v5.1, Heinz Sklenar, Richard Lavery - analysis

NMR spectrometers:

  • Bruker Avance 600 MHz

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