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 17791

Title: Structure of the duplex containing HNE derived (6S,8R,11S) gamma-HO-PdG when placed opposite dT

Authors: Huang, Hai; Wang, Hao; Kozekova, Albena; LLoyd, R.; Rizzo, Carmelo; Stone, Michael

Citation: Huang, Hai; Wang, Hao; Kozekova, Albena; LLoyd, R.; Rizzo, Carmelo; Stone, Michael. "Ring-chain tautomerization of trans-4-hydroxynonenal derived (6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct when placed opposite 2'-deoxythymidine in duplex"  Not known ., .-..

Assembly members:
DNA_(5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'), polymer, 12 residues, 3663.422 Da.
DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3'), polymer, 12 residues, 3678.433 Da.
HNE, non-polymer, 156.222 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*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'): GCTAGCGAGTCC
DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3'): GGACTTGCTAGC

Data sets:
Data typeCount
1H chemical shifts141

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1DNA_(5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3')1
2DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3')2
3HNE3

Entities:

Entity 1, DNA_(5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3') 12 residues - 3663.422 Da.

1   DGDCDTDADGDCDGDADGDT
2   DCDC

Entity 2, DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3') 12 residues - 3678.433 Da.

1   DGDGDADCDTDTDGDCDTDA
2   DGDC

Entity 3, HNE - C9 H16 O2 - 156.222 Da.

1   HNE

Samples:

sample_1: DNA_(5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3') 1 mM; DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3') 1 mM; HNE 1 mM; D2O 100%

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

Software:

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

NMR spectrometers:

  • Bruker Avance 800 MHz

Related Database Links: