The biophysics of DNA hybridization with immobilized oligonucleotide probes
The biophysics of DNA hybridization with immobilized oligonucleotide probes
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DOI：
10.1016/s0006-3495(95)80095-0
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发表时间：
1995-12-01
影响因子：
3.4
通讯作者：
McKenzie, SE
中科院分区：
文献类型：
--
作者：
Chan, V;Graves, DJ;McKenzie, SE
基于细胞表面受体-配体相互作用的数学模型被改进和进一步发展，以表示固体表面上的异质DNA-DNA杂交，在该模型中，具有已知序列的固定DNA分子称为探针，而具有未知序列的溶液中的DNA分子称为靶标。完全互补目标的捕获被建模为一个联合反应-扩散限制不可逆反应。在该模型中，有两种不同的机制可以使目标与互补探针杂交：来自溶液的直接杂交和非特异性吸附然后表面扩散到探针的分子杂交。结果表明，单链DNA在表面的非特异性吸附和随后的二维扩散可以显著提高整体反应速率。非均相杂交在很大程度上取决于DNA在表面非探针覆盖区域的吸附/解吸速率常数、二维（2D）扩散系数以及探针和靶标的大小。该模型表明，对于物理上真实的二维扩散系数、靶标浓度和表面探针密度而言，DNA在固体载体上杂交的总体动力学可能是一个非常有效的过程。对DNA杂交表面设计和操作的启示是，当二维扩散发生时，存在一个最佳表面探针密度；高于最佳值的值不会增加捕获率。我们的模型预测捕获率与最近的实验文献一致。我们的分析结果预测，可以做几件事来改善非均相杂交：1)溶液相目标分子的大小应该在100个碱基左右或更小，以加速溶液相和表面扩散；2)在DNA探针分子之间的表面区域创造可逆吸附和二维扩散的条件；3)如果满足2)，则稀疏探针覆盖的结果等于或优于表面完全被DNA探针覆盖的结果。
A mathematical model based on receptor-ligand interactions at a cell surface has been modified and further developed to represent heterogeneous DNA-DNA hybridization on a solid surface, The immobilized DNA molecules with known sequences are called probes, and the DNA molecules in solution with unknown sequences are called targets in this model. Capture of the perfectly complementary target is modeled as a combined reaction-diffusion limited irreversible reaction. In the model, there are two different mechanisms by which targets can hybridize with the complementary probes: direct hybridization from the solution and hybridization by molecules that adsorb nonspecifically and then surface diffuse to the probe. The results indicate that nonspecific adsorption of single-stranded DNA on the surface and subsequent two-dimensional diffusion can significantly enhance the overall reaction rate. Heterogeneous hybridization depends strongly on the rate constants for DNA adsorption/desorption in the non-probe-covered regions of the surface, the two-dimensional (2D) diffusion coefficient, and the size of probes and targets, The model shows that the overall kinetics of DNA hybridization to DNA on a solid support may be an extremely efficient process for physically realistic 2D diffusion coefficients, target concentrations, and surface probe densities. The implication for design and operation of a DNA hybridization surface is that there is an optimal surface probe density when 2D diffusion occurs; values above that optimum do nor increase the capture rate. Our model predicts capture rates in agreement with those from recent experimental literature. The results of our analysis predict that several things can be done to improve heterogeneous hybridization: 1) the solution phase target molecules should be about 100 bases or less in size to speed solution-phase and surface diffusion; 2) conditions should be created such that reversible adsorption and two-dimensional diffusion occur in the surface regions between DNA probe molecules; 3) provided that 2) is satisfied, one can achieve results with a sparse probe coverage that are equal to or better than those obtained with a surface totally covered with DNA probes.