title: Discrimination between perfect and mismatched duplexes with oligonucleotide gel microchips: role of thermodynamic and kinetic effects during hybridization.
abstract: The efficiency of discrimination between perfect and mismatched duplexes during hybridization on microchips depends on the concentrations of target DNA in solution and immobilized probes, buffer composition, and temperature of hybridization and is determined by both thermodynamic relationships and hybridization kinetics. In this work, optimal conditions of discrimination were studied using hybridization of fluorescently labeled target DNA with custom-made gel-based oligonucleotide microchips. The higher the concentration of immobilized probes and the higher the association constant, the higher the concentration of the formed duplexes and the stronger the corresponding fluorescence signal, but, simultaneously, the longer the time needed to reach equilibrium. Since mismatched duplexes hybridize faster than their perfect counterparts, perfect-to-mismatch signal ratio is lower in transient regime, and short hybridization times may hamper the detection of mutations. The saturation time can be shortened by decreasing the probe concentration or augmenting the gel porosity. This improves the detection of mutations in transient regime. It is shown that the decrease in the initial concentration of oligonucleotide probes by an order of magnitude causes only 1.5-2.5-fold decrease of fluorescence signals after hybridization of perfect duplexes for 3-12 h. At the same time, these conditions improve the discrimination between perfect and mismatched duplexes more than two-fold. A similar improvement may be obtained using an optimized dissociation procedure.
authors.affiliation: Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Vavilov str. 32, Moscow, Russia 119991.
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: Livshits
authors.forename: S V
authors.initials: SV
authors.lastname: Pan'kov
authors.forename: M Y
authors.initials: MY
authors.lastname: Donnikov
authors.forename: D A
authors.initials: DA
authors.lastname: Gryadunov
authors.forename: S A
authors.initials: SA
authors.lastname: Lapa
authors.forename: A S
authors.initials: AS
authors.lastname: Zasedatelev
mesh_terms: D001482:Base Composition; D020137:Base Pair Mismatch; D004247:DNA / Q000737:chemistry*; D015342:DNA Probes; D005782:Gels; D007700:Kinetics; D008856:Microscopy, Fluorescence; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry*; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D009841:Oligonucleotides / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
chemical_list: D015342:DNA Probes; D005782:Gels; D009692:Nucleic Acid Heteroduplexes; D009841:Oligonucleotides; D004247:DNA