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 19925

Title: Solution NMR structure of DNA dodecamer with A:C mismatch

Authors: Donahue, Patrick; Szulik, Marta; Stone, Michael

Citation: Szulik, Marta; Donahue, Patrick; Stone, Michael. "Characterization of 5-hydroxycytosine in DNA"  Not known ., .-..

Assembly members:
DNA_(5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*CP*GP*CP*G)-3'), polymer, 12 residues, 3647.422 Da.

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: Homo sapiens

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
DNA_(5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*CP*GP*CP*G)-3'): CGCAAATTCGCG

Data sets:
Data typeCount
1H chemical shifts66

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*CP*GP*CP*G)-3')_11
2DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*CP*GP*CP*G)-3')_21

Entities:

Entity 1, DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*CP*GP*CP*G)-3')_1 12 residues - 3647.422 Da.

1   DCDGDCDADADADTDTDCDG
2   DCDG

Samples:

sample_1: DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*CP*GP*CP*G)-3') 100 mM; sodium phosphate 10 mM; sodium chloride 100 mM; D2O 100%; sodium azide 11 mM; EDTA 0.5 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 6.0; pressure: 1 atm; temperature: 288 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1

Software:

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

SPARKY, Goddard - chemical shift assignment

TOPSPIN, Bruker Biospin - processing

NMR spectrometers:

  • Bruker Avance 900 MHz

Related Database Links: