The effects of sequence characteristics on competitive hybridization kinetics
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DNA and RNA profiling technologies have a promising role in elucidating the genetic component of various pathological conditions such as human cancers. The increasing demand for such technologies has motivated research into the design of highly sensitive, accurate and cost-efficient nucleic acid detection systems. We employed double-stranded DNA probes, formed by the hybridization of DNA primary targets to single-stranded probes, in order to detect the presence of targets in solution via competitive hybridization events. In our approach, displacement of the original hybridization partner is driven by the affinity differences of the primary and the competitive target for the immobilized strand. Hence, unlike conventional nucleic acid detection technologies such as microarrays, which rely on elevated temperatures for improved detection specificity, our system design imposes specificity at isothermal, room temperature conditions. We report our investigation of competitive hybridization kinetics as a function of double-stranded sequence in which the parameters of length and base-pair mismatch are used to tune affinity of the double-stranded probes. Better understanding of competitive hybridization kinetics will aid the development of highly specific nucleic acid detection systems.