title: Kinetics of hybridization on the oligonucleotide microchips with gel pads.
abstract: The kinetics of hybridization on the oligonucleotide microchip with gel pads is studied both theoretically and experimentally. The monitoring of kinetics was performed with the measurements of fluorescence intensity produced by the labeled target oligonucleotides. As is shown, the hybridization time depends on the stability of the formed duplexes, the concentrations of target and probe oligonucleotides, and the diffusion of target oligonucleotides in solution and gel pad. The initial stage of hybridization is determined by the flow of target oligonucleotides from solution, then, followed by the diffusive propagation with approximately constant concentration of oligonucleotides at the boundary of gel pad and, finally, by the exponential saturation. The theoretical predictions of hybridization kinetics reveal a good correspondence with the experimental results and may be used for the choice of the optimal hybridization conditions. The possible applications of kinetic hybridization curves to the discrimination problems and assessment of diffusion coefficients in gel pads are briefly discussed. Finally, we discuss the relationships between the binding kinetics and the general functioning of biomolecular microchips.
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str 32, 119991 Moscow, Russia.
authors.forename: N V
authors.initials: NV
authors.lastname: Sorokin
authors.forename: V R
authors.initials: VR
authors.lastname: Chechetkin
authors.forename: M A
authors.initials: MA
authors.lastname: Chechetkin
authors.forename: V A
authors.initials: VA
authors.lastname: Vasiliskov
authors.forename: A Y
authors.initials: AY
authors.lastname: Turygin
authors.forename: A D
authors.initials: AD
authors.lastname: Mirzabekov
mesh_terms: D000465:Algorithms; D005782:Gels / Q000737:chemistry*; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009841:Oligonucleotides / Q000737:chemistry*; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D005782:Gels; D009841:Oligonucleotides