Hybridization kinetics mismatches

The effect of temperature on fluorescence has been studied, as has the effect of salt concentration and water-soluble conjugated polymers. A method for the quantification of ssDNA dsDNA is described, as well as kinetics of mismatch hybridization and the kinetics of collision in short ss-nucleic acids. Fluorescence quenching of Cy-5 labelled oligonucleotides by poly(phenylene ethynylene) particles has been shown to be a more sensitive method than excitation of the Cy-5 fluorophore. An ultrasensitive method for the detection of DNA uses highly fluorescent conjugated nanoparticles, and detection limits below IfM were achieved. DNA transport through a carbon nanotube has also been observed using fluorescence microscopy. " ... 

Other methods have been developed that allow the detection of point mutations in non-hybridization based assays. An effective alternative electrochemical method harnesses differences in the kinetics of the reaction of Ru(bpy)3 with gnanine in the context of base mismatches to report base substitutions [47]. In addition, altered patterns of chemical reactivity have been detected in RNA-DNA hybrids containing 2-NH2 modifications in an RNA complement at mispaired positions [48]. Extension of this approach to an immobilized system has not yet been demonstrated, but it may hold pronfise for any applications where alterations in chemical, rather than electrochanical, reactivity are required. 

More important from an application point of view is the quantitative difference of the observed kinetic behavior upon injecting T2, the mismatch 0 target, which is fully complementary to the recognition sequence of the probe strand. Both the association, as well as the dissociation data is given in Figure 12. The ccxresponding rate constants are also presented in Table II. It is clear that the numbers of these rate constants are not as reliable as for the P2/T1 hybrid because for this concentration, i.e., the... 

The electrochemical detection of mismatches and DNA hybridization relies on ET from the redox reporter to the transducer sinface. Thus, gaining a thorough imderstanding of the ET kinetics involved in the sensing process is crucial in order to optimize the detection, and eliminate potential flaws of this method. 

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