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 25531

Title: N2-dG-IQ modified DNA at the G1 position of the NarI recognition sequence   PubMed: 26083477

Authors: Stavros, Kallie; Hawkins, Edward; Rizzo, Carmelo; Stone, Michael

Citation: Stavros, Kallie; Hawkins, Edward; Rizzo, Carmelo; Stone, Michael. "Base-Displaced Intercalated Conformation of the 2-Amino-3-methylimidazo[4,5-f]quinoline N(2)-dG DNA Adduct Positioned at the Nonreiterated G(1) in the NarI Restriction Site"  Chem. Res. Toxicol. 28, 1455-1468 (2015).

Assembly members:
DNA_(5'-D(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3'), polymer, 12 residues, 3251.149 Da.
DNA_(5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3'), polymer, 12 residues, 3728.459 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(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3'): CTCXGCGCCATC
DNA_(5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3'): GATGGCGCCGAG

Data sets:
Data typeCount
1H chemical shifts156

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3')1
2DNA (5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3')2

Entities:

Entity 1, DNA (5'-D(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3') 12 residues - 3251.149 Da.

1   DCDTDCIQGDGDCDGDCDCDA
2   DTDC

Entity 2, DNA (5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3') 12 residues - 3728.459 Da.

1   DGDADTDGDGDCDGDCDCDG
2   DADG

Samples:

sample_1: DNA (5'-D(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3') 430 mM; DNA (5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3') 430 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 7; pressure: 1 atm; temperature: 288 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, data analysis

MARDIGRAS, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - chemical shift calculation

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure solution

NMR spectrometers:

  • Bruker Avance 900 MHz

Related Database Links: