The charge flow technique is used to study structure of nucleic acids. DNA-DNA duplexes and DNA-RNA heteroduplexes have been studied using charge transfer, yet little is known about RNA-RNA duplex conductivity. Both piperidine and aniline treatment on DNA-DNA duplexes with guanine-rich termini generated a large oxidative end-effect. Both DNA-DNA and RNA-RNA duplexes demonstrated similar findings. Sensitivity of the end-effect towards mismatches suggests its utility as sensitive reporter of mismatches. Various diseases are associated with polymorphic DNA trinucleotide repeats (TNR). Disease associated TNRs (CAG, CGG, CCG, CTG) can form alternative DNA structures in vitro with two Watson-Crick base pairs sandwiching single mismatches. Mismatches interrupt base stacking and hence are known to affect duplex conductivity. Charge flow through duplexes carrying TNRs did not show any statistically significant difference in damage. The increase in damage from 10 oC to 21 oC, was not statistically significant. Our approach could not be applied to TNRs.
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