Electrochemical detection of insertion/deletion mutations based on enhanced flexibility of bulge-containing duplexes on electrodes

Abstract

Ferrocene-modified DNA probes formed fully matched duplexes and bulge-containing ones with wild-type and insertion/deletion-type complements of clinical importance, respectively. Cyclic voltammetry measurements revealed that the bulge-containing duplexes showed an increased flexibility compared to the fully matched duplexes. The difference in the bending elasticity could be read out electrochemically by square wave voltammetry.

Electrochemical direct detection of DNA deamination catalyzed by APOBEC3G

“…Our method includes hybridization of an analyte DNA with a probe DNA that is chemically modified with a ferrocene/isoquinoline (Fc). 17 The hybridized DNA is immobilized on gold electrode and analyzed with an electrochemical technique, square-wave voltammetry (Fig. 1).…”

“…The frequency giving a peak is highly dependent on the elasticity of DNA hybrid immobilized on the electrode. 17,18 Optimization of the applied frequency refines specificity of the obtained electrochemical signal, and enables us to detect the amount of target DNA. Using this method, we successfully traced the time-course of A3G-catalyzed deamination.…”

“…The hybrids immobilized on the electrode undergo structural fluctuations at varying frequencies; in general, complementary hybrids indicates a slower fluctuation than mismatched hybrids. 17a When applied at a frequency synchronizing with a motional rate of the DNA hybrid, the pulse potential train induces a current peak on the electrogram. Therefore, a complementary hybrid generates a current peak when using a square-wave potential train at a relatively lower frequency, whereas a mismatched hybrid gives a signal peak at higher frequency.…”

Deformable nature of various damaged DNA duplexes estimated by an electrochemical analysis on electrodes

“…We have developed a conceptually new discrimination method for genomic variants, such as single nucleotide polymorphisms (SNPs) and insertion/deletion mutations, using electrochemical DNA probes. [6][7][8] The probes have a redox active ferrocene-isoquinoline-conjugate (FcIq) and a propane thiol linker connected to both the ends of a single-stranded DNA. After immobilization on gold electrodes using gold-thiol chemistry, the probe was hybridized with target DNAs and scanned by square wave voltammetry (SWV).…”

Development of acoustic wave biosensors for application in molecular diagnostics

“…This relatively new type of biosensors was initially presented for electrochemical and optical biosensing devices (188,189). This method exploits specific DNA probes, such as beacons (190), stem loops (191), flexible bulge-containing duplexes (192), hairpins (193), two single-stranded DNA pieces connected through PEGS (193), and clamp-like DNAs (194,195) all of which undergo a significant conformational change upon target binding. Nevertheless, in reality, both optical and electrochemical sensors do not measure the conformation of the surface-immobilized DNA per se; instead they exploit the sensor's sensitivity to the distance of a probe from another probe or the device surface, respectively, which changes as a result of target binding.…”