Novel Strategy for Single Nucleotide Polymorphism (Snp) Genotyping by Heteroduplex Analysis: Specific Stabilization of Tt Mismatch Base Pair by Mercury (Ii) Cation and Cc Mismatch Base Pair by Silver (I) Cation

Effects of metal binding to mismatched base pairs on DNA-mediated charge transfer

“…Thermally melting profile of DNA 1/DNA 2 is indicative that Hg 2+ does not affect T m of the duplex, thus non-site-specific Hg 2+ -binding to complete duplex DNA is negligible. As reported previously, Hg 2+ coordinates to N3 of thymine both in a free solution and in a mismatched duplex [12][13][14][15][16]. The stabilization effect by Hg 2+ was observed by monitoring T m values of TT-mismatched duplex DNA 1/DNA 4, where the addition of the first one equivalent of Hg 2+ increased T m by DT m = 6.6°C, but further addition did not change the T m (Supplementary information).…”

“…In this regard, mercury (II) ions (Hg 2+ ) preferentially bind to thymine-thymine (TT) mismatch base pairs, in which imino protons of the bases are replaced by Hg 2+ , and generate stable non-hydrogen-bonding base pairs [12][13][14]. Based on the preferential bindings of Hg 2+ to a TT site and of Ag + to a cytosinecytosine (CC) site, novel nanoscale sensors have been developed recently [15,16]. Such interactions may alter inherent charge conductivity of DNA molecule, since the charge transfer efficiency is sensitive to the conformation of DNA as well as the electronic properties [3][4][5]7,17].…”

“…First, we chose a duplex DNA 1/DNA 3 containing single CC-mismatched base pair as a Ag + binding site [16]. As increasing the concentration of Ag + from 1 to 5 equivalents of the CC site, hole transfer was dramatically suppressed (Figs.…”

Mismatch Base Pair Detection by Fluorescence Spectral Change Upon Addition of Metal Cation—Toward Efficient Analysis of Single Nucleotide Polymorphism

“…When the molar ratio of silver (I) cation to the duplex with X:Y=C:C was increased, the intensity of Fam emission at 520 nm was decreased. Each strand of the duplex may be separated due to the C:C mismatch base pair without silver (I) cation, but addition of silver (I) cation may induce the assembly of each strand by the C-Ag-C formation, [4] which decreases the distance between the fluorophore (Fam) and the quencher (Dab). The Dab-mediated quenching may decrease the intensity at 520 nm.…”

“…We have already found that mercury (II) and silver (I) cations specifically bind to T:T and C:C mismatch base pairs in heteroduplexes, respectively, which significantly increased the melting temperature of a heteroduplex involving the corresponding mismatch base pair. [4,5] The result shows that addition of the metal cation is a promising strategy for mismatch base pair detection in a heteroduplex, but determination of the melting temperature by UV melting is time-consuming. Thus, in the present study, we examined fluorescence spectral change of fluorescent-labeled duplexes upon addition of the metal cation to develop a more convenient way for the mismatch base pair detection.…”