BMRB Entry 16225

Title:
Solution Structure of cis-5R,6S-thymine glycol opposite complementary adenine in duplex DNA
Deposition date:
2009-03-24
Original release date:
2010-05-27
Authors:
Brown, Kyle
Citation:

Citation: Brown, Kyle; Roginskaya, Marina; Zou, Yue; Altamirano, Alvin; Basu, Ashis; Stone, Michael. "Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5R-thymine glycol lesion and structure of the cis-(5R,6S) thymine glycol epimer in the 5'-GTgG-3' sequence: destabilization of two base pairs at the lesion site"  Nucleic Acids Res. 38, 428-440 (2010).
PubMed: 19892827

Assembly members:

Assembly members:
DNA_(5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3'), polymer, 12 residues, 3392.232 Da.
DNA_(5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DAP*DCP*DGP*DCP*DAP*DC)-3'), polymer, 12 residues, 3609.425 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(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3'): GTGCGXGTTTGT
DNA_(5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DAP*DCP*DGP*DCP*DAP*DC)-3'): ACAAACACGCAC

Data sets:
Data typeCount
1H chemical shifts231
31P chemical shifts20

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3')1
2DNA (5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DAP*DCP*DGP*DCP*DAP*DC)-3')2

Entities:

Entity 1, DNA (5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3') 12 residues - 3392.232 Da.

1   DGDTDGDCDGCTGDGDTDTDT
2   DGDT

Entity 2, DNA (5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DAP*DCP*DGP*DCP*DAP*DC)-3') 12 residues - 3609.425 Da.

1   DADCDADADADCDADCDGDC
2   DADC

Samples:

sample_1: DNA_(5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3') 1 mM; DNA_(5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DAP*DCP*DGP*DCP*DAP*DC)-3') 1 mM; sodium phosphate 20 mM; sodium chloride 100 mM; sodium azide 10 uM; EDTA 50 uM

sample_2: DNA_(5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3') 1 mM; DNA_(5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DAP*DCP*DGP*DCP*DAP*DC)-3') 1 mM; sodium phosphate 20 mM; sodium chloride 100 mM; sodium azide 10 uM; EDTA 50 uM

sample_conditions_1: ionic strength: 0.1 M; pH: 7.0; pressure: 1 atm; temperature: 303 K

sample_conditions_2: ionic strength: 0.1 M; pH: 7.0; pressure: 1 atm; temperature: 278 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D 31P-1H COSYsample_1isotropicsample_conditions_1

Software:

AMBER v9, Delaglio, Zhengrong and Bax - refinement

SPARKY, Goddard - chemical shift assignment, data analysis

TOPSPIN, Bruker Biospin - processing

MARDIGRAS, Borgias, B.A. & James, T.L. - restraint generation

CORMA, James T.L. - structure validation

CURVES, Lavery, R. and Sklenar, H - data analysis, structure analysis

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz