BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 18835

Title: Structure of perimidinone-derived synthetic nucleoside paired with guanine in DNA duplex   PubMed: 23748954

Authors: Kowal, Ewa; Lad, Rahul; Pallan, Pradeep; Muffly, Elizabeth; Wawrzak, Zdzislaw; Egli, Martin; Sturla, Shana; Stone, Michael

Citation: Kowal, Ewa; Lad, Rahul; Pallan, Pradeep; Dhummakupt, Elizabeth; Wawrzak, Zdzislaw; Egli, Martin; Sturla, Shana; Stone, Michael. "Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction."  Nucleic Acids Res. 41, 7566-7576 (2013).

Assembly members:
5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3', polymer, 12 residues, 2755.845 Da.

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

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3': CGCGAATTXGCG

Data sets:
Data typeCount
1H chemical shifts107
homonuclear NOE values153

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1strand 11
2strand 21

Entities:

Entity 1, strand 1 12 residues - 2755.845 Da.

1   DCDGDCDGDADADTDTD3NDG
2   DCDG

Samples:

sample_1: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3' 0.53 mM; D2O, [U-100% 2H], 100%; sodium chloride 100 mM; EDTA 50 uM; sodium phosphate 10 mM

sample_2: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3' 0.53 mM; D2O, [U-100% 2H], 90%; H2O 10%; sodium phosphate 10 mM; EDTA 50 uM; sodium chloride 100 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 283 K

sample_conditions_2: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 278 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2

Software:

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

TOPSPIN, Bruker Biospin - collection, processing

CORMA, Thomas L. James - data analysis

CURVES v5.3, Ravishankar, G. et al. - data analysis

MARDIGRAS, Thomas L. James - processing

SPARKY, Goddard - chemical shift assignment, chemical shift calculation

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz

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