BMRB Entry 18762

Title:
NMR solution structure of an N2-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: Intercalation from the minor groove with ruptured Watson-Crick base pairing
Deposition date:
2012-10-04
Original release date:
2012-11-20
Authors:
Tang, Yijin; Liu, Zhi; Ding, Shuang; Lin, Chin; Cai, Yuqin; Rodriguez, Fabian; Sayer, Jane; Jerina, Donald; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas
Citation:

Citation: Tang, Yijin; Liu, Zhi; Ding, Shuang; Lin, Chin; Cai, Yuqin; Rodriguez, Fabian; Sayer, Jane; Jerina, Donald; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas. "Nuclear Magnetic Resonance Solution Structure of an N(2)-Guanine DNA Adduct Derived from the Potent Tumorigen Dibenzo[a,l]pyrene: Intercalation from the Minor Groove with Ruptured Watson-Crick Base Pairing."  Biochemistry 51, 9751-9762 (2012).
PubMed: 23121427

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*CP*GP*AP*TP*GP*G)-3')_, polymer, 11 residues, 3454.286 Da.
1,3-DIAMINOBENZYL PHENYLALANINE, non-polymer, 122.168 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*CP*GP*AP*TP*GP*G)-3')_: GGTAGCGATGG

Data sets:
Data typeCount
1H chemical shifts154

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*CP*GP*AP*TP*GP*G)-3')2
31,3-DIAMINOBENZYL PHENYLALANINE3

Entities:

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

C14 ATOM OF DB[a,l]P LINKED TO N2 ATOM OF DG6

1   DCDCDADTDCDGDCDTDADC
2   DC

Entity 2, DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3') 11 residues - 3454.286 Da.

1   DGDGDTDADGDCDGDADTDG
2   DG

Entity 3, 1,3-DIAMINOBENZYL PHENYLALANINE - C7 H10 N2 - 122.168 Da.

1   DBP

Samples:

sample_1: DNA duplex 1.5 mM; sodium phosphate 10 mM; sodium chloride 100 mM; DSS 25 nM; D2O 100%

sample_2: DNA duplex 1.5 mM; sodium phosphate 10 mM; sodium chloride 100 mM; DSS 25 nM; 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

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, data analysis

NMR spectrometers:

  • Bruker Avance 500 MHz