BMRB Entry 30255

Name: Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A - A6-DNAm1A16 structure
Published: 2017-04-03

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PDB ID: 5uzi
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30255
MolProbity Validation Chart

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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:

Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A - A6-DNAm1A16 structure

Deposition date:

2017-02-26

Original release date:

2017-04-03

Authors:

Sathyamoorthy, B.; Shi, H.; Xue, Y.; Al-Hashimi, H.

Citation:

Citation: Sathyamoorthy, B.; Shi, H.; Zhou, H.; Xue, Y.; Rangadurai, A.; Merriman, D.; Al-Hashimi, H.. "Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A" Nucleic Acids Res. 45, 5586-5601 (2017).
PubMed: 28369571

Assembly members:

Assembly members:
entity_1, polymer, 12 residues, 3659.387 Da.
entity_2, polymer, 12 residues, 3679.467 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: CGATTTTTTGGC
entity_2: GCCXAAAAATCG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	115
15N chemical shifts	10
1H chemical shifts	160
31P chemical shifts	20

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 12 residues - 3659.387 Da.

1

DC

DG

DA

DT

DG

2

DG

DC

Entity 2, entity_2 12 residues - 3679.467 Da.

1

DG

DC

MA7

DA

DT

2

DC

DG

Samples:

sample_1: DNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3') 3.0 ± 0.5 mM; DNA (5'-D(*GP*CP*CP*(M1A)P*AP*AP*AP*AP*AP*TP*CP*G)-3') 3.0 ± 0.5 mM; sodium phosphate buffer 15 mM; sodium chloride 25 mM; EDTA 0.1 mM

sample_2: DNA (5'-D(*CP*GP*AP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3') 3.25 ± 0.25 mM; DNA (5'-D(*GP*CP*CP*(M1A)P*AP*AP*AP*AP*AP*TP*CP*G)-3') 3.25 ± 0.25 mM; sodium phosphate buffer 15 mM; sodium chloride 25 mM; EDTA 0.1 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 100 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N SOFAST-HMQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C SOFAST-HMQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
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
2D 1H-31P HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C TROSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C TROSY	sample_2	anisotropic	sample_conditions_2

Software:

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

TOPSPIN, Bruker Biospin - collection

VNMR, Varian - collection

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Varian INOVA 800 MHz
Bruker AvanceII 600 MHz