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 16054

Title: Dimeric solution structure of the DNA loop d(TGCTTCGT)   PubMed: 19321501

Authors: Viladoms, Julia; Escaja, Nuria; Frieden, Miriam; Gomez-Pinto, Irene; Pedroso, Enrique; Gonzalez, Carlos

Citation: Viladoms, Julia; Escaja, Nuria; Frieden, Miriam; Gomez-Pinto, Irene; Pedroso, Enrique; Gonzalez, Carlos. "Self-association of short DNA loops through minor groove C:G:G:C tetrads"  Nucleic Acids Res. 37, 3264-3275 (2009).

Assembly members:
DNA_(5'-D(TP*GP*CP*TP*TP*CP*GP*T)-3'), polymer, 8 residues, 2408.610 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_(5'-D(TP*GP*CP*TP*TP*CP*GP*T)-3'): TGCTTCGT

Data sets:
Data typeCount
1H chemical shifts83

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA_(5'-D(TP*GP*CP*TP*TP*CP*GP*T)-3')_11
2DNA_(5'-D(TP*GP*CP*TP*TP*CP*GP*T)-3')_21

Entities:

Entity 1, DNA_(5'-D(TP*GP*CP*TP*TP*CP*GP*T)-3')_1 8 residues - 2408.610 Da.

1   DTDGDCDTDTDCDGDT

Samples:

sample_1: DNA_(5'-D(TP*GP*CP*TP*TP*CP*GP*T)-3')0.1 – 4.0 mM; sodium phosphate 25 mM; sodium chloride 100 mM; magnesium chloride 10 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 7; pressure: 1 atm; temperature: 278 K

Experiments:

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

Software:

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

DYANA, Guntert, Braun and Wuthrich - structure solution

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Bruker DMX 600 MHz
  • Bruker DPX 800 MHz

Related Database Links: