Andronescu Mirela, Condon Anne, Turner Douglas H, Mathews David H
Department of Genome Sciences, University of Washington, Seattle, WA, USA.
Methods Mol Biol. 2014;1097:45-70. doi: 10.1007/978-1-62703-709-9_3.
The stability of RNA secondary structure can be predicted using a set of nearest neighbor parameters. These parameters are widely used by algorithms that predict secondary structure. This contribution introduces the UV optical melting experiments that are used to determine the folding stability of short RNA strands. It explains how the nearest neighbor parameters are chosen and how the values are fit to the data. A sample nearest neighbor calculation is provided. The contribution concludes with new methods that use the database of sequences with known structures to determine parameter values.
RNA二级结构的稳定性可以通过一组最近邻参数来预测。这些参数被广泛用于预测二级结构的算法中。本文介绍了用于确定短RNA链折叠稳定性的紫外光热解实验。它解释了如何选择最近邻参数以及如何将这些值与数据拟合。文中还提供了一个最近邻计算的示例。本文最后介绍了一些新方法，这些方法利用具有已知结构的序列数据库来确定参数值。
