Mismatch discrimination, thermodynamics

Forman, J.E., et al. Thermodynamics of duplex formation and mismatch discrimination on photolithographically synthesized oligonucleotide arrays. ACS Symposium Series, 1998, 682, p. 206-228. 

Gel pads of MAGIChips could serve as micro cuvettes, which would enable massive parallel or multiplex thermodynamical studies for any DNA duplexes, triplexes, DNA binding ligands, proteins, and so forth. Thousands of melting curves could be obtained simultaneously, which cannot be accomplished with the usual UV-VIS spectrophotometer. This fact demonstrates that all mismatch discrimination and mutation detection is based on the sohd theoretical foundation of classical DNA thermodynamics. 

Thermodynamics of Duplex Formation and Mismatch Discrimination on Photolithographically Synthesized Oligonucleotide Arrays... 

Melt temperature measurements indicated that the thermodynamic stability of the probe molecules can be adjusted using the oligomer matrix to achieve lower Tm values by as much as 5 °C, with retention of selectivity for discrimination of single base pair mismatches [14]. The enhanced temperature sensitivity may ultimately provide for the development of analytical devices of extremely high selectivity. Devices containing immobilized... 

A full parallel screening of thermodynamic parameters of stacking between all possible interface bases XIY was done by using our microchip, and the results were monitored using a fluorescent microscope (unpublished results). It was shown, that adenine had maximum stacking [26], but in all other cases discrimination of stacking between perfect and mismatched bases was sufficiently enough for mutation... 

The thermodynamic ratio Oq < 1 is connected to the free energy of discrimination, AG > 0, between the correct and incorrect nucleotides (ksT is the thermal energy unit, with kgT 2.5 kJ mol at room temperature). The kinetic ratio y depends on the bond formation rate W and the effective off-rates. It approaches the value 1 when the bond formation rate W is negligibly slow compared to both off-rates. Furthermore, as long as the off-rate for the correct nucleotide is not larger than that for the mismatched one (a reasonable assumption), the kinetic ratio cannot... 

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