Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson–Crick‐like T–Hg^II–T Base Pairs

Abstract

The metallo DNA duplex containing mercurymediated 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 Bform 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 . The relatively short Hg II -Hg II distance (3.3 ) 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 IIinduced structural switching from the nonhelical form to the Bform provide the basis for structure-based design of metalconjugated nucleic acid nanomaterials.

The structure of metallo-DNA with consecutive thymine–HgII–thymine base pairs explains positive entropy for the metallo base pair formation

“…The Hg–Hg distance derived solely with NOEs was ∼4 Å. When we applied the Hg–Hg distance constraint at 3.3 Å reflecting our X-ray diffraction analysis of a DNA duplex with tandem T–Hg II –T base pairs ( 53 ) ( Supplementary Figure S6 and Supplementary Material ), the derived model structure of duplex 1 • 2 ( Supplementary Figure S7 ) was consistent with the NOE constraints. …”

Application of mercury–mediated thymine–base pairs for successful voltammetric detection of HPV 18

“…It is known that the presence of mercury(II)-mediated thymine base pairs leads to the formation of a double helix between two partially complementary DNA strands. Moreover, the metallophilic attraction between Hg(II) ions in consecutive T-Hg(II)-T base pairs, resulting from the relatively short Hg(II) -Hg(II) distance, stabilized the structure of the formed double helix [41]. The progress in the hybridization process and the ability of thymine residues to form mercury(II)-mediated thymine base pairs was confirmed by voltammetric and spectroscopic measurements.…”

Self-pairing of 1-methylthymine mediated by two and three Ag(i) ions: a gas phase study using infrared dissociation spectroscopy and density functional theory

“…9 Thymine (T) containing DNA strands are prone to dimerize and stabilize by deprotonation (T-H) with a parallel selective uptake of Hg II ions forming neutral (T-H)-Hg II -(T-H) metal base pairs (MBPs), representing one of the best documented examples of specific metal complexation by a nucleobase pair. 7,[10][11][12] By vibrational analysis in solution, a Raman ''fingerprint'' band has been identified for the mercury coordinated (T-H) using a thymidylyl-3 0 -5 0 -thymidine (TpT) model compound. 13 On the other hand, DNA strands containing cytosine-cytosine (C-C) mispairs show a tendency to preferentially incorporate Ag I ions in solution forming cationic C-Ag I -C MBPs.…”