DNA hybridization to mismatched templates: A chip study
DNA hybridization to mismatched templates: A chip study
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DOI：
10.1103/physreve.65.040902
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发表时间：
2002-04-01
影响因子：
2.4
通讯作者：
Magnasco, M
中科院分区：
文献类型：
--
作者：
Naef, F;Lim, DA;Magnasco, M
高密度寡核苷酸阵列是当今生物学中发展最快的技术之一。在基因芯片系统中，样本mRNA浓度的重建取决于通过将RNA与两个几乎相同的模板杂交产生的差异信号：包含确切生物序列的完美匹配探针（PM）;以及通过单个碱基取代与PM不同的单个错配（MM）。已经观察到，大部分的可重复结合靶标的能力比PM更好，这与序列特异性的明显预期相反。我们研究这个问题，通过大量的微阵列实验的统计分析。我们分类的探头根据其信号噪声（S/N）比，定义为（PM，MM）对的“轨迹”在许多实验的偏心率。在那些具有大S/N（>3）的探针中，只有一部分的行为与通常假设的杂交模型一致。我们的研究结果意味着，在微阵列中的DNA杂交的物理比预期的更复杂，并建议估计的目标RNA浓度。
High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the GeneChip system, the reconstruction of the sample mRNA concentrations depends upon the differential signal generated by hybridizing the RNA to two nearly identical templates: a perfect match probe (PM) containing the exact biological sequence; and a single mismatch (MM) differing from the PM by a single base substitution. It has been observed that a large fraction of MMs repeatably bind targets better than the PMs, against the obvious expectation of sequence specificity. We examine this problem via statistical analysis of a large set of microarray experiments. We classify the probes according to their signal to noise (S/N) ratio, defined as the eccentricity of a (PM,MM) pair's "trajectory" across many experiments. Of those probes having large S/N (>3) only a fraction behave consistently with the commonly assumed hybridization model. Our results imply that the physics of DNA hybridization in microarrays is more complex than expected, and suggest estimators for the target RNA concentration.