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 11608

Title: SOLUTION STRUCTURE OF DNA CONTAINING METALLO-BASE-PAIR   PubMed: 27505707

Authors: Dairaku, Takenori; Furuita, Kyoko; Sato, Hajime; Sebera, Jakub; Nakashima, Katsuyuki; Kondo, Jiro; Yamanaka, Daichi; Kondo, Yoshinori; Okamoto, Itaru; Ono, Akira; Sychrovsky, Vladimir; Kojima, Chojiro; Tanaka, Yoshiyuki

Citation: Dairaku, Takenori; Furuita, Kyoko; Sato, Hajime; Sebera, Jakub; Nakashima, Katsuyuki; Kondo, Jiro; Yamanaka, Daichi; Kondo, Yoshinori; Okamoto, Itaru; Ono, Akira; Sychrovsky, Vladimir; Kojima, Chojiro; Tanaka, Yoshiyuki. "Structure Determination of an AgI-Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with 1H/15N/109Ag NMR Spectroscopy"  Chem. Eur. J. ., .-. (2016).

Assembly members:
DNA_(5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3'), polymer, 15 residues, 4566.059 Da.
DNA_(5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3'), polymer, 15 residues, 4566.059 Da.
SILVER ION, non-polymer, 107.868 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):
DNA_(5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3'): TAATATACTTAATTA
DNA_(5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3'): TAATTAACTATATTA

Data sets:
Data typeCount
1H chemical shifts244

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3')1
2DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3')2
3SILVER ION3

Entities:

Entity 1, DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3') 15 residues - 4566.059 Da.

1   DTDADADTDADTDADCDTDT
2   DADADTDTDA

Entity 2, DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3') 15 residues - 4566.059 Da.

1   DTDADADTDTDADADCDTDA
2   DTDADTDTDA

Entity 3, SILVER ION - Ag - 107.868 Da.

1   AG

Samples:

sample_1: DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3') 2 mM; DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3') 2 mM; AgNO3 2.1 mM; NaNO3 100 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3') 2 mM; DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3') 2 mM; AgNO3 2.1 mM; NaNO3 100 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 0.1 M; pH: 6.9; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.1 M; pH: 7.1; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D DQF-COSYsample_2isotropicsample_conditions_2
2D 1H-13C HSQCsample_2isotropicsample_conditions_2

Software:

SPARKY, Goddard - chemical shift assignment, peak picking

MARDIGRAS, Thomas L. James - data analysis, structure solution

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

NMR spectrometers:

  • Bruker Avance 950 MHz

Related Database Links: