Halperin A, Buhot A, Zhulina E B
UMR 5819 SPrAM (UJF, CNRS, CEA), DRFMC, CEA Grenoble, France.
Biophys J. 2005 Aug;89(2):796-811. doi: 10.1529/biophysj.105.063479. Epub 2005 May 20.
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 - const'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 -const' x(2/3) - x(B)(2/3).
在生物学实验中，寡核苷酸微阵列与长核酸靶标的溶液接触。由此杂交的探针带有长尾巴。当寡核苷酸探针的表面密度足够高时，由于核酸尾巴的相互拥挤，杂交过程会产生聚电解质刷。与该刷相关的自由能惩罚会改变杂交等温线和速率方程：可达到的杂交显著降低，杂交速率也是如此。当平衡杂交分数x(eq)较低时，杂交遵循朗缪尔型等温线，x(eq)/(1 - x(eq)) = c(t)K，其中c(t)是靶标浓度，K是平衡常数。由于壁效应，K比其本体值小一个因子(n/N)(2/5)，其中n和N分别表示探针和靶标中的碱基数。在较高的x(eq)时，当形成刷时，主要的校正为x(eq)/(1 - x(eq)) = c(t)K exp - const'x(eq)(2/3) - x(B)(2/3)，其中x(B)对应于刷状区域的起始。两种情况下的变性速率常数相同。然而，刷状区域中的杂交速率常数较低，主要校正为exp -const' x(2/3) - x(B)(2/3)。
