title: A competitive kinetic model of nucleic acid surface hybridization in the presence of point mutants.
abstract: Microarray analysis has become increasingly complex due to the growing size of arrays and the inherent cross-binding of targets. In this work, we explore the effects of matched and mismatched target species concentrations, temperature, and the time of hybridization on sensing specificity in two-component systems. A finite element software is used to simulate the diffusion of DNA through a microfluidic chamber to the sensing surface where hybridization of DNA is modeled using the corresponding kinetic equation. Comparison between a single-component system, where only one target is allowed to bind to a specific zone, and a two-component system, where more than one target can hybridize in a sensing zone, uncovers significant kinetic disparities during the transitory state; however, at thermodynamic equilibrium a modified Langmuir isotherm governs the bound amount of both species. The results presented suggest that it may be more appropriate to consider collective rather than quasi-independent interaction of targets in multicomponent systems.
authors.affiliation: Department of Electrical and Computer Engineering University of Utah, Salt Lake City, Utah, USA.
authors.forename: J
authors.initials: J
authors.lastname: Bishop
authors.forename: S
authors.initials: S
authors.lastname: Blair
authors.forename: A M
authors.initials: AM
authors.lastname: Chagovetz
mesh_terms: D001667:Binding, Competitive; D001703:Biophysics / Q000379:methods*; D015342:DNA Probes; D004058:Diffusion; D020342:Finite Element Analysis; D005821:Genetic Techniques; D007700:Kinetics; D044085:Microfluidics; D008954:Models, Biological; D008962:Models, Theoretical; D009154:Mutation; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D015345:Oligonucleotide Probes; D017354:Point Mutation; D020641:Polymorphism, Single Nucleotide; D012984:Software; D013696:Temperature; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D015342:DNA Probes; D015345:Oligonucleotide Probes