Thermodynamics of RNA/DNA hybridization in high-density oligonucleotide microarrays
Thermodynamics of RNA/DNA hybridization in high-density oligonucleotide microarrays
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DOI：
10.1016/j.physa.2005.09.067
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发表时间：
2006-04-01
影响因子：
3.3
通讯作者：
Heim, T
中科院分区：
文献类型：
--
作者：
Carlon, E;Heim, T
我们使用杂交过程的简单物理模型分析了 Affymetrix 高密度寡核苷酸微阵列上的一系列公开对照实验（拉丁方）。我们绘制了每个基因的信号强度与溶液中 RNA/DNA 双链体的杂交自由能的关系图，以实现完美匹配和错配探针。如果考虑到由于溶液中靶标与靶标杂交导致的有效靶标浓度的降低，这两个值往往会在一条主曲线上对齐，与朗缪尔吸附理论非常一致。我们给出了由于注释问题而导致探针组 1091_at 与预期热力学行为发生偏差的示例，即，由于设计阵列时公共数据库中存在错误，表面结合探针不是目标 RNA 序列的精确互补序列。我们表明，与之前的研究相比，使用 RNA/DNA 自由能对实验数据进行参数化提高了拟合质量并增强了拟合参数的稳定性。 (c) 2005 Elsevier B.V. 保留所有权利。
We analyze a series of publicly available controlled experiments (Latin square) on Affymetrix high-density oligonucleotide microarrays using a simple physical model of the hybridization process. We plot for each gene the signal intensity vs. the hybridization free energy of RNA/DNA duplexes in solution, for perfect matching and mismatching probes. Both values tend to align on a single master curve in good agreement with Langmuir adsorption theory, provided one takes into account the decrease of the effective target concentration due to target-target hybridization in solution. We give an example of a deviation from the expected thermodynamical behavior for the probe set 1091 _ at due to annotation problems, i.e., the surface-bound probe is not the exact complement of the target RNA sequence, because of errors present in public databases at the time when the array was designed. We show that the parametrization of the experimental data with RNA/DNA free energy improves the quality of the fits and enhances the stability of the fitting parameters compared to previous studies. (c) 2005 Elsevier B.V. All rights reserved.