BMRB Entry 34623

Title:
A self-complementary DNA dodecamer duplex contaning 5-hydroxymethylcitosine
Deposition date:
2021-05-07
Original release date:
2021-10-30
Authors:
Battistini, F.; Dans, P.; Terrazas, M.; Castellazzi, C.; Portella, G.; Labrador, M.; Villegas, N.; Brun-Heath, I.; Gonzalez, C.; Orozco, M.
Citation:

Citation: Battistini, F.; Dans, P.; Terrazas, M.; Castellazzi, C.; Portella, G.; Labrador, M.; Villegas, N.; Brun-Heath, I.; Gonzalez, C.; Orozco, M.. "The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function"  PLoS Comput. Biol. 17, e1009547-e1009547 (2021).
PubMed: 34748533

Assembly members:

Assembly members:
entity_1, polymer, 12 residues, 3694.406 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: CGCGTXGACGCG

Data sets:
Data typeCount
1H chemical shifts105

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_21

Entities:

Entity 1, unit_1 12 residues - 3694.406 Da.

1   DCDGDCDGDT5HCDGDADCDG
2   DCDG

Samples:

sample_1: DNA (5'-D(*(DC5)P*GP*CP*GP*TP*(DH)P*GP*AP*CP*GP*CP*(DG3))-3') 1 mM

sample_conditions_1: ionic strength: 125 mM; pH: 7.0; pressure: 1 atm; temperature: 278 K

Experiments:

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

Software:

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

Sparky, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker AVANCE III 600 MHz