BMRB Entry 36379

Title:
NMR solution structures of the DNA minidumbbell formed by two CmCTG repeats at pH 5
Deposition date:
2020-09-12
Original release date:
2021-08-02
Authors:
Wan, L.; Guo, P.; Lam, S.
Citation:

Citation: Wan, Liqi; Yi, Jie; Lam, Sik; Lee, Hung; Guo, Pei. "5-Methylcytosine Substantially Enhances the Thermal Stability of DNA Minidumbbell"  Chemistry 27, 6740-6747 (2021).
PubMed: 33501691

Assembly members:

Assembly members:
DNA (5'-D(*(DCZ)P*(5CM)P*TP*GP*CP*(5CM)P*TP*G)-3'), polymer, 8 residues, 2326.641 Da.
SODIUM ION, non-polymer, 22.990 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*(DCZ)P*(5CM)P*TP*GP*CP*(5CM)P*TP*G)-3'): XXTGCXTG

Data sets:
Data typeCount
1H chemical shifts85

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22
3unit_32
4unit_42
5unit_52
6unit_62

Entities:

Entity 1, unit_1 8 residues - 2326.641 Da.

1   DCZ5CMDTDGDC5CMDTDG

Entity 2, unit_2 - Na - 22.990 Da.

1   NA

Samples:

sample_1: DNA 0.2 ± 0.02 mM; DSS 0.02 ± 0.005 mM; NaCl 10 ± 1 mM; D2O, [U-2H], 99.96%

sample_conditions_1: ionic strength: 10 mM; pH: 5; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1

Software:

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

TopSpin, Bruker Biospin - chemical shift assignment

NMR spectrometers:

  • Bruker AVANCE 700 MHz
  • Bruker AVANCE 500 MHz