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 30255

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

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

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. ., .-. (2017).

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

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

Experimental source:   Production method: chemical synthesis

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

Data sets:
Data typeCount
13C chemical shifts115
15N chemical shifts10
1H chemical shifts160
31P chemical shifts20

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 12 residues - 3659.387 Da.

1   DCDGDADTDTDTDTDTDTDG
2   DGDC

Entity 2, entity_2 12 residues - 3679.467 Da.

1   DGDCDCMA7DADADADADADT
2   DCDG

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:

NameSampleSample stateSample conditions
2D 1H-15N SOFAST-HMQCsample_1isotropicsample_conditions_1
2D 1H-13C SOFAST-HMQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-31P HSQCsample_1isotropicsample_conditions_1
2D 1H-13C TROSYsample_1isotropicsample_conditions_1
2D 1H-13C TROSYsample_2anisotropicsample_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

Related Database Links: