BMRB Entry 17562

Title:
N2-dG:N2-dG interstrand cross-link induced by trans-4-hydroxynonenal
Deposition date:
2011-03-31
Original release date:
2012-04-02
Authors:
Huang, Hai; Kozekov, Ivan; Wang, Hao; Kozekova, Albena; Rizzo, Carmelo; Stone, Michael
Citation:

Citation: Huang, Hai; Wang, Hao; Kozekova, Albena; Rizzo, Carmelo; Stone, Michael. "Formation of a N2-dG:N2-dG carbinolamine DNA cross-link by the trans-4-hydroxynonenal-derived (6S,8R,11S) 1,N2-dG adduct"  J. Am. Chem. Soc. 133, 16101-16110 (2011).
PubMed: 21916419

Assembly members:

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*CP*GP*CP*TP*AP*GP*C)-3'), polymer, 12 residues, 3663.422 Da.
HNE, non-polymer, 156.224 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

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*CP*GP*CP*TP*AP*GP*C)-3'): GGACTCGCTAGC

Data sets:
Data typeCount
1H chemical shifts150

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

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*CP*GP*CP*TP*AP*GP*C)-3')2
3(2E,4R)-4-HYDROXYNON-2-ENAL3

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*CP*GP*CP*TP*AP*GP*C)-3') 12 residues - 3663.422 Da.

1   DGDGDADCDTDCDGDCDTDA
2   DGDC

Entity 3, (2E,4R)-4-HYDROXYNON-2-ENAL - C9 H16 O2 - 156.224 Da.

1   HNE

Samples:

sample_1: DNA_1 1 mM; DNA_2 1 mM; (2E,4R)-4-HYDROXYNON-2-ENAL 1 mM; D2O 100%

sample_conditions_1: ionic strength: 100 mM; pH: 7.3; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1

Software:

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

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 800 MHz