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 16226

Title: Solution Structure of cis-5R,6S-thymine glycol opposite complementary guanine in duplex DNA   PubMed: 19772348

Authors: Brown, Kyle

Citation: Brown, Kyle; Basu, Ashis; Stone, Michael. "The cis-(5R,6S)-thymine glycol lesion occupies the wobble position when mismatched with deoxyguanosine in DNA."  Biochemistry 48, 9722-9733 (2009).

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*DGP*DCP*DGP*DCP*DAP*DC)-3')_, polymer, 12 residues, 3625.425 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(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3')_: GTGCGXGTTTGT
DNA_(5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DGP*DCP*DGP*DCP*DAP*DC)-3')_: ACAAACGCGCAC

Data sets:
Data typeCount
1H chemical shifts230

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*DGP*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*DGP*DCP*DGP*DCP*DAP*DC)-3')_ 12 residues - 3625.425 Da.

1   DADCDADADADCDGDCDGDC
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*DGP*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')_ mM; DNA_(5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DGP*DCP*DGP*DCP*DAP*DC)-3')_ 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: 1.0 atm; temperature: 303 K

sample_conditions_2: ionic strength: 0.1 M; pH: 7.0; pressure: 1.0 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, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - 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

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

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz

Related Database Links: