4L25

Crystal structure of DNA duplex containing consecutive T-T mispairs

PDB DOI: https://doi.org/10.2210/pdb4L25/pdb
NAKB: 4L25

Classification: DNA
Mutation(s): No

Deposited: 2013-06-04 Released: 2014-03-05
Deposition Author(s): Kondo, J., Yamada, T., Hirose, C., Tanaka, Y., Ono, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.240
R-Value Work: 0.231

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs

Kondo, J., Yamada, T., Hirose, C., Okamoto, I., Tanaka, Y., Ono, A.

(2014) Angew Chem Int Ed Engl 53: 2385-2388

PubMed: 24478025 Search on PubMed
DOI: https://doi.org/10.1002/anie.201309066
Primary Citation of Related Structures:
4L24, 4L25, 4L26

PubMed Abstract:
The metallo DNA duplex containing mercury-mediated T-T base pairs is an attractive biomacromolecular nanomaterial which can be applied to nanodevices such as ion sensors. Reported herein is the first crystal structure of a B-form DNA duplex containing two consecutive T-Hg(II)-T base pairs. The Hg(II) ion occupies the center between two T residues. The N3-Hg(II) bond distance is 2.0 Å. The relatively short Hg(II)-Hg(II) distance (3.3 Å) observed in consecutive T-Hg(II)-T base pairs suggests that the metallophilic attraction could exist between them and may stabilize the B-form double helix. To support this, the DNA duplex is largely distorted and adopts an unusual nonhelical conformation in the absence of Hg(II). The structure of the metallo DNA duplex itself and the Hg(II)-induced structural switching from the nonhelical form to the B-form provide the basis for structure-based design of metal-conjugated nucleic acid nanomaterials.

Organizational Affiliation

Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo (Japan). j.kondo@sophia.ac.jp.