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 19440

Title: NMR structure of DNA duplex   PubMed: 24361616

Deposition date: 2013-08-20 Original release date: 2014-01-23

Authors: Brzezinska, Jolanta; Gdaniec, Zofia; Popenda, Lukasz; Markiewicz, Wojciech

Citation: Brzezinska, Jolanta; Gdaniec, Zofia; Popenda, Lukasz; Markiewicz, Wojciech. "Polyaminooligonucleotide: NMR structure of duplex DNA containing a nucleoside with spermine residue, N-[4,9,13-triazatridecan-1-yl]-2'-deoxycytidine."  Biochim. Biophys. Acta 1840, 1163-1170 (2014).

Assembly members:
DNA_(5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3'), polymer, 8 residues, 2458.635 Da.
DNA_(5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3'), polymer, 8 residues, 2396.614 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(*GP*TP*CP*GP*GP*CP*TP*G)-3'): GTCGGCTG
DNA_(5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3'): CAGCCGAC

Data sets:
Data typeCount
1H chemical shifts160
31P chemical shifts14

Additional metadata:

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

Assembly:

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

Entities:

Entity 1, DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3') 8 residues - 2458.635 Da.

1   DGDTDCDGDGDCDTDG

Entity 2, DNA (5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3') 8 residues - 2396.614 Da.

1   DCDADGDCDCDGDADC

Samples:

sample_1: DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3') 0.5 mM; DNA (5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3') 0.5 mM; D2O, [U-100% 2H], 100%; sodium chloride 50 mM; sodium phosphate 10 mM; EDTA 0.1 mM

sample_2: DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3') 0.5 mM; DNA (5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3') 0.5 mM; D2O, [U-100% 2H], 10%; H2O 90%; sodium chloride 50 mM; sodium phosphate 10 mM; EDTA 0.1 mM

sample_conditions_1: ionic strength: 60 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 60 mM; pH: 7.0; pressure: 1 atm; temperature: 283 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-31P HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2

Software:

X-PLOR_NIH vv2.22, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

TOPSPIN vv2.0, Bruker Biospin - collection, processing

Felix vv2002, Accelrys Software Inc. - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Bruker Avance 600 MHz