Folding and Finding RNA Secondary Structure
Folding and Finding RNA Secondary Structure
复制标题
DOI：
10.1101/cshperspect.a003665
复制
发表时间：
2010-12-01
影响因子：
7.2
通讯作者：
Turner, Douglas H.
中科院分区：
文献类型：
--
作者：
Mathews, David H.;Moss, Walter N.;Turner, Douglas H.
对不断扩大的序列数据库的优化利用需要快速找到和折叠RNA。综述了利用将热力学与化学作图、核磁共振和/或序列比较相结合的算法自动折叠和发现RNA的方法。通过序列比较和假设功能性非编码RNA具有比其他RNA更有利的折叠自由能，可以在基因组序列中发现新的功能性非编码RNA。当发现新的RNA时，实验和序列比较可以限制折叠空间，从而可以借助预测的自由能快速确定二级结构。反过来，二级结构限制了三维折叠，从而允许对三维结构进行建模。描述了一个来自反转录转座子结构域的例子。新的RNA及其结构的发现将为进化、生物学和治疗设计提供洞察力。并对其在进化论研究中的应用进行了综述。
Optimal exploitation of the expanding database of sequences requires rapid finding and folding of RNAs. Methods are reviewed that automate folding and discovery of RNAs with algorithms that couple thermodynamics with chemical mapping, NMR, and/or sequence comparison. New functional noncoding RNAs in genome sequences can be found by combining sequence comparison with the assumption that functional noncoding RNAs will have more favorable folding free energies than other RNAs. When a new RNA is discovered, experiments and sequence comparison can restrict folding space so that secondary structure can be rapidly determined with the help of predicted free energies. In turn, secondary structure restricts folding in three dimensions, which allows modeling of three-dimensional structure. An example from a domain of a retrotransposon is described. Discovery of new RNAs and their structures will provide insights into evolution, biology, and design of therapeutics. Applications to studies of evolution are also reviewed.