BMRB Entry 19695

Title:
NMR studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations
Deposition date:
2013-12-20
Original release date:
2014-03-31
Authors:
Rodriguez, Fabian; Liu, Zhi; Lin, Chin; Ding, Shuang; Cai, Yuqin; Kolbanovskiy, Alexander; Kolbanovskiy, Marina; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas
Citation:

Citation: Rodriguez, Fabian; Liu, Zhi; Lin, Chin; Ding, Shuang; Cai, Yuqin; Kolbanovskiy, Alexander; Kolbanovskiy, Marina; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas. "Nuclear Magnetic Resonance Studies of an N(2)-Guanine Adduct Derived from the Tumorigen Dibenzo[a,l]pyrene in DNA: Impact of Adduct Stereochemistry, Size, and Local DNA Sequence on Solution Conformations"  Biochemistry 53, 1827-1841 (2014).
PubMed: 24617538

Assembly members:

Assembly members:
DNA_(5'-D(*CP*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3'), polymer, 11 residues, 3254.165 Da.
DNA_(5'-D(*GP*GP*TP*AP*GP*GP*AP*TP*GP*G)-3'), polymer, 10 residues, 3165.103 Da.
(11R,12R,13R)-11,12,13,14-tetrahydronaphtho[1,2,3,4-pqr]tetraphene-11,12,13-triol, non-polymer, 354.398 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*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3'): CCATCGCTACC
DNA_(5'-D(*GP*GP*TP*AP*GP*GP*AP*TP*GP*G)-3'): GGTAGGATGG

Data sets:
Data typeCount
1H chemical shifts151

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*CP*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3')1
2DNA (5'-D(*GP*GP*TP*AP*GP*GP*AP*TP*GP*G)-3')2
3(11R,12R,13R)-11,12,13,14-tetrahydronaphtho[1,2,3,4-pqr]tetraphene-11,12,13-triol3

Entities:

Entity 1, DNA (5'-D(*CP*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3') 11 residues - 3254.165 Da.

1   DCDCDADTDCDGDCDTDADC
2   DC

Entity 2, DNA (5'-D(*GP*GP*TP*AP*GP*GP*AP*TP*GP*G)-3') 10 residues - 3165.103 Da.

1   DGDGDTDADGDGDADTDGDG

Entity 3, (11R,12R,13R)-11,12,13,14-tetrahydronaphtho[1,2,3,4-pqr]tetraphene-11,12,13-triol - C24 H18 O3 - 354.398 Da.

1   2QL

Samples:

sample_1: DB[a,l]P covalently bound to 11mer DNA duplex 1.5 mM; NaCl 100 mM; Na2HPO4 10 mM; DSS 25 mM; D2O 100%

sample_2: DB[a,l]P covalently bound to 11mer DNA duplex 1.5 mM; NaCl 100 mM; Na2HPO4 10 mM; DSS 25 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.8

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment, data analysis

TOPSPIN, Bruker Biospin - collection

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

NMR spectrometers:

  • Bruker Avance 500 MHz