2RT8

Structure of metallo-dna in solution

Summary for 2RT8

• Entry DOI: 10.2210/pdb2rt8/pdb
• NMR Information: BMRB: 11528
• Descriptor: DNA (5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3'), MERCURY (II) ION (3 entities in total)
• Functional Keywords: dna, metallo-base-pair, t-hg(ii)-t base-pair
• Total number of polymer chains: 2
• Total formula weight: 6474.15

Authors

Yamaguchi, H.,Sebera, J.,Kondo, J.,Oda, S.,Komuro, T.,Kawamura, T.,Dairaku, T.,Kondo, Y.,Okamoto, I.,Ono, A.,Burda, J.V.,Kojima, C.,Sychrovsky, V.,Tanaka, Y. (deposition date: 2013-06-18, release date: 2014-03-05, Last modification date: 2024-05-15)

Primary citation

Yamaguchi, H.,Sebera, J.,Kondo, J.,Oda, S.,Komuro, T.,Kawamura, T.,Dairaku, T.,Kondo, Y.,Okamoto, I.,Ono, A.,Burda, J.V.,Kojima, C.,Sychrovsky, V.,Tanaka, Y.
The structure of metallo-DNA with consecutive thymine-HgII-thymine base pairs explains positive entropy for the metallo base pair formation.
Nucleic Acids Res., 42:4094-4099, 2014

PubMed Abstract: We have determined the three-dimensional (3D) structure of DNA duplex that includes tandem Hg(II)-mediated T-T base pairs (thymine-Hg(II)-thymine, T-Hg(II)-T) with NMR spectroscopy in solution. This is the first 3D structure of metallo-DNA (covalently metallated DNA) composed exclusively of 'NATURAL' bases. The T-Hg(II)-T base pairs whose chemical structure was determined with the (15)N NMR spectroscopy were well accommodated in a B-form double helix, mimicking normal Watson-Crick base pairs. The Hg atoms aligned along DNA helical axis were shielded from the bulk water. The complete dehydration of Hg atoms inside DNA explained the positive reaction entropy (ΔS) for the T-Hg(II)-T base pair formation. The positive ΔS value arises owing to the Hg(II) dehydration, which was approved with the 3D structure. The 3D structure explained extraordinary affinity of thymine towards Hg(II) and revealed arrangement of T-Hg(II)-T base pairs in metallo-DNA.

PubMed: 24371287
DOI: 10.1093/nar/gkt1344

Experimental method

SOLUTION NMR