Isambert H, Siggia E D
Center for Studies in Physics and Biology, The Rockefeller University, Box 25, 1230 York Avenue, New York, NY 10021, USA.
Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6515-20. doi: 10.1073/pnas.110533697.
A quantitative understanding of nucleic acid hybridization is essential to many aspects of biotechnology, such as DNA microarrays, as well as to the structure and folding kinetics of RNA. However, predictions of nucleic acid secondary structures have long been impeded by the presence of helices interior to loops, so-called pseudoknots, which impose complex three-dimensional conformational constraints. In this paper we compute the pseudoknot free energies analytically in terms of known standard parameters, and we show how the results can be included in a kinetic Monte Carlo code to follow the succession of secondary structures during quenched or sequential folding. For the hepatitis delta virus ribozyme, we predict several nonnative stems on the folding path, characterize a kinetically trapped state, interpret several experimentally characterized mutations in terms of the folding path, and suggest how hybridization with other parts of the genome inactivates the newly formed ribozyme.
对核酸杂交进行定量理解，对于生物技术的诸多方面（如DNA微阵列）以及RNA的结构和折叠动力学而言至关重要。然而，核酸二级结构的预测长期以来一直受到环内部螺旋（即所谓的假结）的阻碍，这些假结会施加复杂的三维构象限制。在本文中，我们根据已知的标准参数解析计算假结自由能，并展示如何将结果纳入动力学蒙特卡罗代码，以追踪猝灭或连续折叠过程中二级结构的演变。对于丁型肝炎病毒核酶，我们预测了折叠路径上的几个非天然茎，表征了一个动力学陷阱状态，根据折叠路径解释了几个经实验表征的突变，并提出了与基因组其他部分杂交如何使新形成的核酶失活的方式。
