Vainrub Arnold, Pettitt B Montgomery
Department of Chemistry, University of Houston, Houston, TX 77204-5003, USA.
J Am Chem Soc. 2003 Jul 2;125(26):7798-9. doi: 10.1021/ja035020q.
We report a new theoretical approach to optimize the performance and quantify the results of gene expression oligonucleotide microarrays which are widely used in biomedical research. An on-array hybridization isotherm that takes into account the screened Coulomb repulsion between the assayed nucleic acid target and the layer of surface tethered oligonucleotide probes is presented. The hybridization efficiency is found as a function of the genomic target (sequence, length, and concentration), array parameters (probe sequence and length, surface probe density), and hybridization conditions (temperature and buffer ionic strength). We present simple relations for the hybridization signal maximum and the linear dynamic detection range and show explicit criteria for optimization. The approach is based on an extension of our recently published theory (Vainrub, A.; Pettitt, B. M. Phys. Rev. E 2002, 66, art. no.-041905) which we generalize here for the cases of target depletion effects and arbitrary target length.
我们报告了一种新的理论方法，用于优化基因表达寡核苷酸微阵列的性能并量化其结果，该微阵列在生物医学研究中广泛使用。提出了一种阵列上的杂交等温线，该等温线考虑了被检测核酸靶标与表面固定寡核苷酸探针层之间的屏蔽库仑排斥力。杂交效率是基因组靶标（序列、长度和浓度）、阵列参数（探针序列和长度、表面探针密度）以及杂交条件（温度和缓冲液离子强度）的函数。我们给出了杂交信号最大值和线性动态检测范围的简单关系，并展示了优化的明确标准。该方法基于我们最近发表的理论（Vainrub, A.; Pettitt, B. M. Phys. Rev. E 2002, 66, art. no.-041905）的扩展，我们在此将其推广到靶标耗尽效应和任意靶标长度的情况。
