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 18199

Title: Structural Basis for Bifunctional Zn(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA. Structure of a Thymine bulge.   PubMed: 22507054

Authors: Morrow, Janet; Fountain, Matthew; del Mundo, Imee Marie; Siter, Kevin

Citation: Del Mundo, Imee Marie A; Siters, Kevin; Fountain, Matthew; Morrow, Janet. "Structural Basis for Bifunctional Zinc(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA."  Inorg. Chem. 51, 5444-5457 (2012).

Assembly members:
DNA_1, polymer, 12 residues, 3664.409 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: GGCCGCAGTGCC

Data sets:
Data typeCount
1H chemical shifts55

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1DNA_11

Entities:

Entity 1, DNA_1 12 residues - 3664.409 Da.

1   DGDGDCDCDGDCDADGDTDG
2   DCDC

Samples:

sample_1: DNA_1 1.8 mM; D2O 100%; NaCl 0.1 M; HEPES 0.02 M

sample_2: DNA_1 1.8 mM; H2O 90%; D2O 10%; NaCl 0.1 M; HEPES 0.02 M

sample_conditions_1: ionic strength: 0.1 M; pD: 7.9; pressure: 1 atm; temperature: 273 K

sample_conditions_2: ionic strength: 0.1 M; pD: 7.9; pressure: 1 atm; temperature: 288 K

Experiments:

NameSampleSample stateSample conditions
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_2

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - geometry optimization

SPARKY v3.14, Goddard - chemical shift assignment, data analysis

NMR spectrometers:

  • Varian INOVA 500 MHz

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