BMRB Entry 15376

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15376

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Title:
SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING THE UNIVERSAL BASE 5-NITROINDOLE-3-CARBOXAMIDE
Deposition date:
2007-07-12
Original release date:
2007-09-04
Authors:
Gallego, Jose; Loakes, David
Citation:

Citation: Gallego, Jose; Loakes, David. "Solution structure and dynamics of DNA duplexes containing the universal base analogues 5-nitroindole and 5-nitroindole-3-carboxamide"  NUCLEIC ACIDS RES. 35, 2904-2912 (2007).
PubMed: 17438041

Assembly members:

Assembly members:
5'-D(*GP*TP*AP*CP*(NCX)P*AP*CP*GP*CP*GP*TP*TP*GP*TP*AP*C)-3'_(1)_, polymer, 16 residues, Formula weight is not available

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):
5'-D(*GP*TP*AP*CP*(NCX)P*AP*CP*GP*CP*GP*TP*TP*GP*TP*AP*C)-3'_(1)_: GTACXACGCGTTGTAC

Data sets:
Data typeCount
1H chemical shifts170
31P chemical shifts15

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1modified DNA monomer1
2modified DNA monomer1

Entities:

Entity 1, modified DNA monomer 16 residues - Formula weight is not available

THE STRUCTURE OF ONE SYMMETRICAL HALF OF THE SELF-COMPLEMENTARY (5'-D(*GP*TP*AP*CP*(NCX)P*AP*CP*GP*CP*GP*TP*TP*GP*TP*AP*C)-3')2 DUPLEX IS PROVIDED

1   DGDTDADCNCXDADCDGDCDG
2   DTDTDGDTDADC

Samples:

sample_1: 5'-D(*GP*TP*AP*CP*(NCX)P*AP*CP*GP*CP*GP*TP*TP*GP*TP*AP*C)-3' 1.9 mM; phosphate buffer 20 mM; NaCL 100 mM; EDTA 0.2 mM; D2O 100%

sample_2: 5'-D(*GP*TP*AP*CP*(NCX)P*AP*CP*GP*CP*GP*TP*TP*GP*TP*AP*C)-3' 1.9 mM; phosphate buffer 20 mM; NaCL 100 mM; EDTA 0.2 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 120 mM; pH: 6.9; pressure: 1 atm; temperature: 311 K

sample_conditions_2: ionic strength: 120 mM; pH: 6.9; pressure: 1 atm; temperature: 287 K

Experiments:

NameSampleSample stateSample conditions
2D NOESYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D TOCSYsample_1isotropicsample_conditions_1
2D 1H-31P HETCORsample_1isotropicsample_conditions_1
2D ROESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2

Software:

TOPSPIN v1.3, Bruker biospin corporation - collection

NMRPipe v2004, F. Delaglio, S. Grzesiek, G. Zhu, G.W. Vuister, J. Pfeifer and A. Bax - processing

SPARKY v3.110, T.D. Goddard and D.G. Kneller - data analysis

AMBER v8.0, D.A. Case et al. - refinement

NMR spectrometers:

  • Bruker AVANCE 600 MHz