BMRB Entry 34054

Title:
Structure of DNA tetrameric AGCGA-quadruplex adopted by 15-mer d(GCGAGGGAGCGAGGG), VK34, oligonucleotide found in regulatory region of the PLEKHG3 human gene
Deposition date:
2016-10-13
Original release date:
2017-05-25
Authors:
Kocman, V.; Plavec, J.
Citation:

Citation: Kocman, V.; Plavec, J.. "Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions."  Nat. Commun. 8, 15355-15355 (2017).
PubMed: 28513602

Assembly members:

Assembly members:
entity_1, polymer, 15 residues, 4765.084 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):
entity_1: GCGAGGGAGCGAGGG

Data sets:
Data typeCount
1H chemical shifts103

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_1, 11
2entity_1, 21
3entity_1, 31
4entity_1, 41

Entities:

Entity 1, entity_1, 1 15 residues - 4765.084 Da.

1   DGDCDGDADGDGDGDADGDC
2   DGDADGDGDG

Samples:

sample_1: DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3') 1.0 mM; sodium chloride 150 mM

sample_2: DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), residue specific 15N and 13C, 1 mM; sodium chloride 150 mM

sample_3: DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), D8 residue specific labeled, 1 mM; sodium chloride 150 mM

sample_4: DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), uniformly labeled with D8, 1 mM; sodium chloride 150 mM

sample_conditions_1: ionic strength: 150 mM; pH: 6; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
1D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
2D 1H-1H NOESYsample_4isotropicsample_conditions_1

Software:

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

SPARKY, Goddard - chemical shift assignment

spar - peak picking

NMR spectrometers:

  • Agilent-Varian Uniform NMR System 600 MHz
  • Agilent-Varian Uniform NMR System 800 MHz