Free energy of DNA duplex formation on short oligonucleotide microarrays
Free energy of DNA duplex formation on short oligonucleotide microarrays
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DOI：
10.1093/nar/gkl1064
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发表时间：
2007-02-01
影响因子：
14.9
通讯作者：
Zhao, Haitao
中科院分区：
文献类型：
--
作者：
Zhang, Li;Wu, Chunlei;Zhao, Haitao
DNA/DNA双链体形成是用于由Affytechnology制造的基因组平铺阵列和SNP阵列的基本机制。然而，物理过程的详细知识仍然缺乏。在这项研究中，我们显示了一个自由能分析的DNA/DNA双链体形成这些阵列的基础上的位置依赖最近邻（PDNN）模型，这是以前开发的描述DNA/RNA双链体形成表达微阵列。我们的研究结果表明，探针的两端有助于减少双链体的稳定性，并有一个微阵列表面结合亲和力的影响。我们还表明，一个单一的错配的自由能成本取决于碱基相邻的错配位点，并获得了一个全面的表下的所有可能的组合相邻碱基的单一错配的成本。错配成本被发现与在水溶液中确定的那些相关。我们进一步证明了从SNP阵列估计的DNA拷贝数与靶长度负相关;这可能是由于长片段的低效PCR扩增引起的。这些结果为微阵列技术的分子机制提供了重要的见解，并对微阵列设计和观察数据的解释产生了影响。
DNA/DNA duplex formation is the basic mechanism that is used in genome tiling arrays and SNP arrays manufactured by Affymetrix. However, detailed knowledge of the physical process is still lacking. In this study, we show a free energy analysis of DNA/DNA duplex formation these arrays based on the positional-dependent nearest-neighbor (PDNN) model, which was developed previously for describing DNA/RNA duplex formation on expression microarrays. Our results showed that the two ends of a probe contribute less to the stability of the duplexes and that there is a microarray surface effect on binding affinities. We also showed that free energy cost of a single mismatch depends on the bases adjacent to the mismatch site and obtained a comprehensive table of the cost of a single mismatch under all possible combination of adjacent bases. The mismatch costs were found to be correlated with those determined in aqueous solution. We further demonstrate that the DNA copy number estimated from the SNP array correlates negatively with the target length; this is presumably caused by inefficient PCR amplification for long fragments. These results provide important insights into the molecular mechanisms of microarray technology and have implications for microarray design and the interpretation of observed data.