BMRB Entry 19925

Title:
Solution NMR structure of DNA dodecamer with A:C mismatch
Deposition date:
2014-04-18
Original release date:
2014-09-08
Authors:
Donahue, Patrick; Szulik, Marta; Stone, Michael
Citation:

Citation: Szulik, Marta; Donahue, Patrick; Stone, Michael. "Characterization of 5-hydroxycytosine in DNA"  .

Assembly members:

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:

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

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

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
  • Hide all

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