BMRB Entry 19925

Name: Solution NMR structure of DNA dodecamer with A:C mismatch
Published: 2014-09-08

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PDB ID: 2mo7
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19925
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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:

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:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	66

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D(CPGPCPAPAPAPTPTPCPGPCPG)-3')_1	1
2	DNA (5'-D(CPGPCPAPAPAPTPTPCPGPCPG)-3')_2	1

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

DC

DG

DC

DA

DT

DC

DG

2

DC

DG

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:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_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