Brush Effects on DNA Chips: Thermodynamics, Kinetics, and Design Guidelines

• Published in: Biophysical journal 2005-08, Vol.89 (2), p.796-811
• Main Authors: Halperin, A., Buhot, A., Zhulina, E.B.
• Format: Article
• Language: English
• Subjects: Biophysical Theory and Modeling; Biotechnology; Computer Simulation; Computer-Aided Design; Deoxyribonucleic acid; DNA; DNA - analysis; DNA - chemistry; DNA Probes - analysis; DNA Probes - chemistry; Equipment Design - methods; Equipment Failure Analysis; Gene expression; Hybridization; In Situ Hybridization - methods; Kinetics; Life Sciences; Models, Chemical; Nucleic Acid Denaturation; Oligonucleotide Array Sequence Analysis - instrumentation; Oligonucleotide Array Sequence Analysis - methods; Thermodynamics
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1529/biophysj.105.063479

In biology experiments, oligonucleotide microarrays are contacted with a solution of long nucleic acid targets. The hybridized probes thus carry long tails. When the surface density of the oligonucleotide probes is high enough, the progress of hybridization gives rise to a polyelectrolyte brush due to mutual crowding of the nucleic acid tails. The free-energy penalty associated with the brush modifies both the hybridization isotherms and the rate equations: the attainable hybridization is lowered significantly as is the hybridization rate. When the equilibrium hybridization fraction, x eq, is low, the hybridization follows a Langmuir type isotherm, x eq/(1 - x eq) = c t K where c t is the target concentration and K is the equilibrium constant. K is smaller than its bulk value by a factor ( n/ N) 2/5 due to wall effects where n and N denote the number of bases in the probe and the target. At higher x eq, when the brush is formed, the leading correction is x eq / ( 1 − x eq ) = c t K ⁡ exp ⁡ − c o n s t ' x eq 2 / 3 − x B 2 / 3 where x B corresponds to the onset of the brush regime. The denaturation rate constant in the two regimes is identical. However, the hybridization rate constant in the brush regime is lower, the leading correction being exp ⁡ − c o n s t ' x 2 / 3 − x B 2 / 3