BMRB Entry 16212

Name: Dimeric solution structure of the DNA loop d(TCGTTGCT)
Published: 2009-04-23

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PDB ID: 2k8z
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16212
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Dimeric solution structure of the DNA loop d(TCGTTGCT)

Deposition date:

2009-03-12

Original release date:

2009-04-23

Authors:

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

Citation:

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).
PubMed: 19321501

Assembly members:

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

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA_(5'-D(TP*CP*GP*TP*TP*GP*CP*T)-3'): TCGTTGCT

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	81

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D(TPCPGPTPTPGPCP*T)-3')_1	1
2	DNA (5'-D(TPCPGPTPTPGPCP*T)-3')_2	1

Entities:

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

1

DT

DC

DG

DT

DG

DC

DT

Samples:

sample_1: DNA (5'-D(*TP*CP*GP*TP*TP*GP*CP*T)-3') 0.1-2.0 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:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_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