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 19917

Title: Solution NMR structure of DNA dodecamer containing the 5-hydroxycytosine

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

Citation: Szulik, Marta. "Characterization of 5-hydroxycytosine in DNA"  Not known ., .-..

Assembly members:
DNA_(5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3'), polymer, 12 residues, 3355.223 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: chemical synthesis

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

Data sets:
Data typeCount
1H chemical shifts70

Additional metadata:

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

Assembly:

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

Entities:

Entity 1, DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3')_1 12 residues - 3355.223 Da.

1   DCDGDCDGDADADTDT5OCDG
2   DCDG

Samples:

sample_1: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3') 100 mM; D2O 10%; sodium phosphate 10 mM; sodium chloride 100 mM; sodium azide 11 mM; EDTA 0.05 mM; H2O 90%

sample_conditions_1: pH: 7; pressure: 1 atm; temperature: 288 K

Experiments:

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

Software:

SPARKY, Goddard - chemical shift assignment

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

TOPSPIN, Bruker Biospin - processing

NMR spectrometers:

  • Bruker INOVA 900 MHz

Related Database Links: