Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur, India.
PLoS One. 2013;8(1):e54753. doi: 10.1371/journal.pone.0054753. Epub 2013 Jan 21.
Microarrays have been widely used for various biological applications, such as, gene expression profiling, determination of SNPs, and disease profiling. However, quantification and analysis of microarray data have been a challenge. Previously, by taking into account translational and rotational diffusion of the target DNA, we have shown that the rate of hybridization depends on its size. Here, by mathematical modeling of surface diffusion of transcript, we show that the dynamics of hybridization on DNA microarray surface is inherently oscillatory and the amplitude of oscillation depends on fluid velocity. We found that high fluid velocity enhances the signal without affecting the background, and reduces the oscillation, thereby reducing likelihood of inter- and intra-experiment variability. We further show that a strong probe reduces dependence of signal-to-noise ratio on probe strength, decreasing inter-microarray variability. On the other hand, weaker probes are required for SNP detection. Therefore, we recommend high fluid velocity and strong probes for all microarray applications except determination of SNPs. For SNP detection, we recommend high fluid velocity with weak probe on the spot. We also recommend a surface with high adsorption and desorption rates of transcripts.
微阵列已被广泛应用于各种生物学应用，如基因表达谱分析、单核苷酸多态性（SNP）的测定和疾病分析。然而，微阵列数据的定量和分析一直是一个挑战。此前，我们考虑到靶 DNA 的平移和旋转扩散，已经表明杂交速率与其大小有关。在这里，通过对转录物表面扩散的数学建模，我们表明 DNA 微阵列表面上杂交的动力学是固有振荡的，并且振荡的幅度取决于流体速度。我们发现高流速可以增强信号而不影响背景，并且减少振荡，从而减少实验内和实验间变异性的可能性。我们进一步表明，强探针减少了信号与噪声比对探针强度的依赖性，从而降低了微阵列间的变异性。另一方面，SNP 检测需要较弱的探针。因此，我们建议在所有微阵列应用中（除 SNP 检测外）使用高流速和强探针。对于 SNP 检测，我们建议在该点处使用高流速和弱探针。我们还建议使用具有高转录物吸附和解吸速率的表面。
