2RVP

Solution structure of DNA Containing Metallo-Base-Pair

Summary for 2RVP

• Entry DOI: 10.2210/pdb2rvp/pdb
• NMR Information: BMRB: 11608
• Descriptor: DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3'), DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3'), SILVER ION (3 entities in total)
• Functional Keywords: dna, metallo-dna, metallo-base-pair, c-ag(i)-c base-pair
• Biological source: synthetic construct; More
• Total number of polymer chains: 2
• Total formula weight: 9239.91

Authors

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. (deposition date: 2016-03-22, release date: 2016-08-31, Last modification date: 2024-05-15)

Primary citation

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.
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.
Chemistry, 22:13028-13031, 2016

PubMed Abstract: 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.

PubMed: 27505707
DOI: 10.1002/chem.201603048

Experimental method

SOLUTION NMR