Thermodynamic properties of DNA sequences: characteristic values for the human genome
Thermodynamic properties of DNA sequences: characteristic values for the human genome
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DOI：
10.1093/bioinformatics/bti530
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发表时间：
2005-08-15
期刊：
影响因子：
5.8
通讯作者：
Peyret, N
中科院分区：
文献类型：
--
作者：
Koehler, RT;Peyret, N
动机：许多分子生物学技术如PCR和Southern印迹普遍存在的核心是具有特定热力学性质的寡核苷酸（oligo）探针和/或引物的设计。在这里，我们使用经过验证的理论方法来生成各种长度的DNA寡核苷酸的预测热力学性质的分布。这些分布有利于立即赞赏典型的热力学值为oligosofvariouslength.Results：熔解温度（Tm），自由能（Δ G（T）（o）），和分数杂交或分数结合（Fb）的分布，提出了长度为10-50碱基的oligos从人类基因组中取样。举例说明了改变温度、寡聚物和盐浓度、约束G+C含量和引入错配的影响。我们的研究结果提供了第一次调查的典型和限制的热力学值在基因组规模上进行评估。所描述的数字包括适用于依赖于DNA寡核苷酸设计的大多数技术的有用的“经验法则”。
Motivation: Central to many molecular biology techniques as ubiquitous as PCR and Southern blotting is the design of oligonucleotide (oligo) probes and/or primers possessing specific thermodynamic properties. Here, we use validated theoretical methods to generate distributions of predicted thermodynamic properties for DNA oligos of various lengths. These distributions facilitate immediate appreciation of typical thermodynamic values for oligos of various lengths.Results: Distributions of melting temperature (T-m), free energy (Delta G(T)(o)), and fraction hybridized or fraction bound (Fb), are presented for oligos of length 10-50 bases sampled from the human genome. The effects of changing temperature, oligo and salt concentrations, constraining G+C content, and introducing mismatches are exemplified. Our results provide the first survey of typical and limiting thermodynamic values evaluated on a genomic scale. Described numbers comprise useful 'rules of thumb' that are applicable to most technologies dependent upon DNA oligo design.