BMRB Entry 36003

Name: Solution NMR structure of a 16-mer DNA duplex containing quadruple GC mismatches showing staggered base pairing, and consequent rescue of canonical double helical characteristics
Published: 2025-10-10

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PDB ID: 5b81
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36003
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution NMR structure of a 16-mer DNA duplex containing quadruple GC mismatches showing staggered base pairing, and consequent rescue of canonical double helical characteristics

Deposition date:

2016-07-05

Original release date:

2025-10-10

Authors:

De, M.; Chatterjee, S.

Citation:

Citation: De, M.; Chatterjee, S.. "Solution NMR structure of a 16-mer DNA duplex containing quadruple GC mismatches showing staggered base pairing, and consequent rescue of canonical double helical characteristics" .

Assembly members:

Assembly members:
DNA (5'-D(*GP*CP*GP*CP*AP*TP*GP*CP*GP*CP*TP*AP*CP*GP*CP*G)-3'), polymer, 16 residues, 4900.167 Da.
DNA (5'-D(*CP*GP*CP*GP*TP*AP*CP*GP*CP*GP*AP*TP*GP*CP*GP*C)-3'), polymer, 16 residues, 4900.167 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis Host organism: unidentified

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*GP*CP*GP*CP*AP*TP*GP*CP*GP*CP*TP*AP*CP*GP*CP*G)-3'): GCGCATGCGCTACGCG
DNA (5'-D(*CP*GP*CP*GP*TP*AP*CP*GP*CP*GP*AP*TP*GP*CP*GP*C)-3'): CGCGTACGCGATGCGC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	158

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 16 residues - 4900.167 Da.

1

DG

DC

DG

DC

DA

DT

DG

DC

DG

DC

2

DT

DA

DC

DG

DC

DG

Entity 2, entity_2 16 residues - 4900.167 Da.

1

DC

DG

DC

DG

DT

DA

DC

DG

DC

DG

2

DA

DT

DG

DC

DG

DC

Samples:

sample_1: DNA (5'-D(*GP*CP*GP*CP*AP*TP*GP*CP*GP*CP*TP*AP*CP*GP*CP*G)-3') 350 ± 0.5 uM; DNA (5'-D(*CP*GP*CP*GP*TP*AP*CP*GP*CP*GP*AP*TP*GP*CP*GP*C)-3') 350 ± 0.5 uM; sodium chloride 50 mM; H2O 95%; D2O, [U-2H], 5%

sample_2: DNA (5'-D(*GP*CP*GP*CP*AP*TP*GP*CP*GP*CP*TP*AP*CP*GP*CP*G)-3') 350 ± 0.5 uM; DNA (5'-D(*CP*GP*CP*GP*TP*AP*CP*GP*CP*GP*AP*TP*GP*CP*GP*C)-3') 350 ± 0.5 uM; sodium chloride 50 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 50 mM; pH: 7.2; pressure: 1 atm; temperature: 288 K

sample_conditions_2: ionic strength: 50 mM; pH: 7.2 pD; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_2

Software:

AMBER v14, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

AMBER v14, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation

SPARKY v3.114, Goddard - chemical shift assignment

SPARKY v3.114, Goddard - peak picking

NMR spectrometers:

Bruker AvanceIII 500 MHz
Bruker AvanceIII 700 MHz