A competitive kinetic model of nucleic acid surface hybridization in the presence of point mutants.
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.
Bishop
J
J
Department of Electrical and Computer Engineering University of Utah, Salt Lake City, Utah, USA.
Blair
S
S
Chagovetz
A M
AM
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
D015342:DNA Probes; D015345:Oligonucleotide Probes