BMRB Entry 18862

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18862
MolProbity Validation Chart

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Title:
Parallel human telomeric quadruplex containing 2'F-ANA substitutions
Deposition date:
2012-11-27
Original release date:
2013-05-06
Authors:
Martin-Pintado, Nerea; Yahyaee-Anzahaee, Maryam; Portella, Guillem; Orozco, Modesto; Damha, Masad; Gonzalez, Carlos
Citation:

Citation: Martin-Pintado, Nerea; Yahyaee-Anzahaee, Maryam; Deleavey, Glen; Portella, Guillem; Orozco, Modesto; Damha, Masad; Gonzalez, Carlos. "Dramatic effect of furanose c2' substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom"  J. Am. Chem. Soc. 135, 5344-5347 (2013).
PubMed: 23521511

Assembly members:

Assembly members:
DNA_(5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3'), polymer, 12 residues, 3791.484 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):
DNA_(5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3'): TAGGGTTAXGGT

Data sets:
Data typeCount
1H chemical shifts111

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3')_11
2DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3')_21

Entities:

Entity 1, DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3')_1 12 residues - 3791.484 Da.

1   DTDADGDGDGDTDTDAGFLDG
2   DGDT

Samples:

sample_1: DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3') 0.7 mM; potassium chloride 5 mM; potassium phosphate 10 mM

sample_2: DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3') 0.7 mM; potassium chloride 10 mM; potassium phosphate 5 mM

sample_conditions_1: ionic strength: 15 mM; pH: 7.0; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D DQF-COSYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1

Software:

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

SPARKY, Goddard - chemical shift assignment

Molmol, Koradi, Billeter and Wuthrich - data analysis

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 700 MHz