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 17746

Title: Oligonucleotide duplex contaning (5'S)-8,5'-cyclo-2'-deoxyguansine   PubMed: 22103478

Authors: Huang, Hai; Das, Rajat; Basu, Ashis; Stone, Michael

Citation: Huang, Hai; Das, Rajat; Basu, Ashis; Stone, Michael. "Structure of (5'S)-8,5'-cyclo-2'-deoxyguanosine in DNA."  J. Am. Chem. Soc. 133, 20357-20368 (2011).

Assembly members:
DNA_(5'-D(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3'), polymer, 12 residues, 3386.234 Da.
DNA_(5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'), polymer, 12 residues, 3609.425 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

Entity Sequences (FASTA):
DNA_(5'-D(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3'): GTGCXTGTTTGTA
DNA_(5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'): ACAAACACGCAC

Data sets:
Data typeCount
1H chemical shifts160

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1DNA_(5'-D(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3')1
2DNA_(5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3')2

Entities:

Entity 1, DNA_(5'-D(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3') 12 residues - 3386.234 Da.

1   DGDTDGDC2LFDTDGDTDTDT
2   DGDTDA

Entity 2, DNA_(5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3') 12 residues - 3609.425 Da.

1   DADCDADADADCDADCDGDC
2   DADC

Samples:

sample_1: DNA_(5'-D(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3') 1.0 mM; DNA_(5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3') 1.0 mM; D2O 100%; NaCl 100 mM; phosphate buffer 10 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1

Software:

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

NMR spectrometers:

  • Bruker Avance 800 MHz

Related Database Links: