KINETICS OF INTERFACIAL NUCLEIC-ACID HYBRIDIZATION STUDIED BY ACOUSTIC NETWORK ANALYSIS

A novel acoustic network analysis technique has been developed to study DNA hybridization kinetics at a sensor-solution interface. The series resonant frequency change is related to the DNA hybridization process through the DNA concentration-dependent viscosity change in the acoustic wave decay length region. The kinetics of hybridization of pPT-2 cDNA probe to ss DNA immobilized on thickness-shear-mode (TSM) acoustic wave sensors has been examined. The process measured by this device does not conform to the generally assumed theoretical second order reaction in solution and one-step mechanism on a typical membrane filter. The pseudo-first order effective rate (8.0 +/- 0. 5) x 10(-5) s(-1) when hybridization is performed in solution without the presence of moieties employed to prevent non-specific effects (blocking agnets), and (3.8 +/- 0.1) x 10(-5) s(-1) with them. The calculated Mark-Houwink constant, alpha, is 1.8, and the intrinsic viscosity is 9.0 x 10(4) (M(-1)) under the hybridization conditions. Inflection points due to the formation of intermediate hybrids are observed during continuous measurement of series resonant frequency with time.