BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 18050

Title: Structure of a bis-naphthalene bound to a thymine-thymine DNA mismatch   PubMed: 22362757

Authors: Jourdan, Muriel; Granzhan, Anton; Guillot, Regis; Dumy, Pascal; Teulade-Fichou, Marie-Paule

Citation: Jourdan, Muriel; Granzhan, Anton; Guillot, Regis; Dumy, Pascal; Teulade-Fichou, Marie-Paule. "Double threading through DNA: NMR structural study of a bis-naphthalene macrocycle bound to a thymine-thymine mismatch."  Nucleic Acids Res. 40, 5115-5128 (2012).

Assembly members:
DNA_1, polymer, 11 residues, 3365.224 Da.
DNA_2, polymer, 11 residues, 3334.213 Da.
LLJ, non-polymer, 516.717 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_1: CGTCGTAGTGC
DNA_2: GCACTTCGACG

Data sets:
Data typeCount
1H chemical shifts179
31P chemical shifts9

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA_11
2DNA_22
3bis-naphthalene3

Entities:

Entity 1, DNA_1 11 residues - 3365.224 Da.

1   DCDGDTDCDGDTDADGDTDG
2   DC

Entity 2, DNA_2 11 residues - 3334.213 Da.

1   DGDCDADCDTDTDCDGDADC
2   DG

Entity 3, bis-naphthalene - C32 H44 N4 O2 - 516.717 Da.

1   LLJ

Samples:

sample_1: DNA_1 1.5 mM; DNA_2 1.5 mM; 2_7-bisnaphthalene 1.5 mM; H2O 90%; D2O 10 *

sample_conditions_1: ionic strength: 0.06 M; pH: 6; pressure: 1 atm; temperature: 283 K

Experiments:

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

Software:

AMBER v10.1, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - structure solution

NMR spectrometers:

  • Varian UnityPlus 500 MHz
  • Varian Unity 800 MHz

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