BMRB Entry 11437

Title:
DNA oligmer containing propylene cross-linked cyclic 2' -deoxyuridylate dimer
Deposition date:
2011-03-24
Original release date:
2011-06-24
Authors:
Furuita, Kyoko; Murata, Shunpei; Jee, JunGoo; Ichikawa, Satoshi; Matsuda, Akira; Kojima, Chojiro
Citation:

Citation: Furuita, Kyoko; Murata, Shunpei; Jee, Jun Goo; Ichikawa, Satoshi; Matsuda, Akira; Kojima, Chojiro. "Structural feature of bent DNA recognized by HMGB1."  J. Am. Chem. Soc. 133, 5788-5790 (2011).
PubMed: 21443191

Assembly members:

Assembly members:
Propylene-DNA, polymer, 28 residues, 111.103 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: not available   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):
Propylene-DNA: CCTTCAXTACATCCGGATGT AATGAAGG

Data sets:
Data typeCount
1H chemical shifts213

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Propylene-DNA1

Entities:

Entity 1, Propylene-DNA 28 residues - 111.103 Da.

1   DCDCDTDTDCDAJDTDTDADC
2   DADTDCDCDGDGDADTDGDT
3   DADADTDGDADADGDG

Samples:

sample_1: sodium phosphate 50 mM; sodium chloride 100 mM; Propylene-DNA 0.5 mM; H2O 90%; D2O 10%

sample_2: sodium phosphate 50 mM; sodium chloride 100 mM; Propylene-DNA 0.5 mM; D2O 100%

sample_conditions_1: pH: 6.8; temperature: 283 K

sample_conditions_2: pH: 6.8; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_2

Software:

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment

MARDIGRAS, Brandan A. Borgias, Paul D. Thomas, He Liu and Anil Kumar - structure solution

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker DRX 800 MHz