BMRB Entry 19375

Title:
NMR Structure of N2-IQ-dG at the G3 position in the NarI recognition sequence
Deposition date:
2013-07-19
Original release date:
2014-05-12
Authors:
Stavros, Kallie; Hawkins, Edward; Rizzo, Carmelo; Stone, Michael
Citation:

Citation: Stavros, Kallie; Hawkins, Edward; Rizzo, Carmelo; Stone, Michael. "Base-displaced intercalation of the 2-amino-3-methylimidazo[4,5-f]quinolone N2-dG adduct in the NarI DNA recognition sequence"  Nucleic Acids Res. 42, 3450-3463 (2014).
PubMed: 24366876

Assembly members:

Assembly members:
DNA_(5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3'), polymer, 12 residues, 3777.5 Da.
DNA_(5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3'), polymer, 12 residues, 3711.459 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(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3'): CTCGGCXCCATC
DNA_(5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3'): GATGGCGCCGAG

Data sets:
Data typeCount
1H chemical shifts213
homonuclear NOE values334

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*CP*TP*CP*GP*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*GP*GP*CP*GP*CP*CP*AP*TP*C)-3') 12 residues - 3777.5 Da.

Oligo was synthesized as described in J. Stover, C. Rizzo [Chem. Res. Toxicol., 2007, 20, 1972-1979]

1   DCDTDCDGDGDCIQGDCDCDA
2   DTDC

Entity 2, DNA (5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3') 12 residues - 3711.459 Da.

Oligo was obtained from Midland Certified Reagent Co. and purified by RP-HPLC.

1   DGDADTDGDGDCDGDCDCDG
2   DADG

Samples:

sample_1: DNA (5'-D(*CP*TP*CP*GP*GP*CP*IQGP*CP*CP*AP*TP*C)-3') 560 nM; DNA (5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3') 560 nM

sample_2: DNA (5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3') 560 mM; DNA (5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3') 560 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 v3.2, Bruker Biospin - collection, processing

SPARKY v3.115, Goddard - chemical shift assignment, data analysis, peak picking

AMBER v10, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure solution

CORMA, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

MARDIGRAS, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - data analysis

NMR spectrometers:

  • Bruker DRX 800 MHz