Analytical Sciences

Electrochemical Impedimetric Study of Non-Watson–Crick Base Pairs of DNA

Rodtichoti WANNAPOB,* Surachada CHUAYCHOB,*,** Masahiro FUJITA,* and Mizuo MAEDA*,**

*Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
**Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan

Electrochemical impedance spectroscopy (EIS) was used to detect non-Watson–Crick base pairs of DNA. Thiol-modified DNA as a probe and mercaptohexanol (MCH) were co-immobilized to form a DNA/MCH mixed self-assembled monolayer on a gold electrode surface and then hybridized with complementary DNAs. The DNA layers were measured by the EIS method and interpreted by equivalent circuits. Every terminal base mismatch of the DNA duplex brought about an increase in the charge-transfer resistance (R_ct), unlike the case with a fully matched DNA duplex. The value of R_ct was highly sensitive to the number of base mismatches for both unpaired and overhang DNA at the terminal. For internal base mismatches, however, no significant increase in R_ct was observed. These experimental results proved that the charge transfer of redox molecules to the electrode surface is largely hindered by an end fraying motion due to base unpairing and dangling overhang. EIS was able to detect these steric properties of DNA strands. Furthermore, an electrode modified with G-quadruplex (G4) DNA demonstrated the influences of bulkiness and loop structure on the accessibility of the redox probe to the electrode.

J-STAGE: View this article in J-STAGE