ISDA

Deposition Date 2016-03-22

Release Date 2016-08-31

Last Version Date 2024-05-15

Entry Detail

PDB ID:

2RVP

Keywords:

DNA

Title:

Solution structure of DNA Containing Metallo-Base-Pair

Biological Source:

Source Organism:

synthetic construct (Taxon ID: 32630)

Method Details:

Experimental Method:

SOLUTION NMR

Conformers Calculated:

100

Conformers Submitted:

Selection Criteria:

structures with the lowest energy

Download Validation Report

Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3')
Chain IDs:A (auth: 1)
Chain Length:15
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3')
Chain IDs:B (auth: 2)
Chain Length:15
Number of Molecules:1
Biological Source:synthetic construct

Ligand Molecules

Primary Citation

Structure Determination of an Ag(I) -Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with (1) H/(15) N/(109) Ag NMR Spectroscopy.

Dairaku, T, Furuita, K, Sato, H, Sebera, J, Nakashima, K, Kondo, J, Yamanaka, D, Kondo, Y, Okamoto, I, Ono, A, Sychrovsky, V, Kojima, C, Tanaka, Y.Show

Chemistry 22 13028 13031 (2016)

PMID: 27505707 DOI: 10.1002/chem.201603048

Abstact

The structure of an Ag(I) -mediated cytosine-cytosine base pair, C-Ag(I) -C, was determined with NMR spectroscopy in solution. The observation of 1-bond (15) N-(109) Ag J-coupling ((1) J((15) N,(109) Ag): 83 and 84 Hz) recorded within the C-Ag(I) -C base pair evidenced the N3-Ag(I) -N3 linkage in C-Ag(I) -C. The triplet resonances of the N4 atoms in C-Ag(I) -C demonstrated that each exocyclic N4 atom exists as an amino group (-NH2), and any isomerization and/or N4-Ag(I) bonding can be excluded. The 3D structure of Ag(I) -DNA complex determined with NOEs was classified as a B-form conformation with a notable propeller twist of C-Ag(I) -C (-18.3±3.0°). The (109) Ag NMR chemical shift of C-Ag(I) -C was recorded for cytidine/Ag(I) complex (δ((109) Ag): 442 ppm) to completed full NMR characterization of the metal linkage. The structural interpretation of NMR data with quantum mechanical calculations corroborated the structure of the C-Ag(I) -C base pair.

Legend

Protein

Chemical

Disease

Primary Citation of related structures