FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, United States.
J Am Chem Soc. 2013 Jan 9;135(1):354-66. doi: 10.1021/ja3095558. Epub 2012 Dec 21.
Nonenzymatic, template-directed synthesis of nucleic acids is a paradigm for self-replicating systems. The evolutionary dynamics of such systems depend on several factors, including the mutation rates, relative replication rates, and sequence characteristics of mutant sequences. We measured the kinetics of correct and incorrect monomer insertion downstream of a primer-template mismatch (mutation), using a range of backbone structures (RNA, DNA, and LNA templates and RNA and DNA primers) and two types of 5'-activated nucleotides (oxyazabenzotriazolides and imidazolides, i.e., nucleoside 5'-phosphorimidazolides). Our study indicated that for all systems studied, an initial mismatch was likely to be followed by another error (54-75% of the time), and extension after a single mismatch was generally 10-100 times slower than extension without errors. If the mismatch was followed by a matched base pair, the extension rate recovered to nearly normal levels. On the basis of these data, we simulated nucleic acid replication in silico, which indicated that a primer suffering an initial error would lag behind properly extended counterparts due to a cascade of subsequent errors and kinetic stalling, with the typical mutational event consisting of several consecutive errors. Our study also included different sequence contexts, which suggest the presence of cooperativity among monomers affecting both absolute rate (by up to 2 orders of magnitude) and fidelity. The results suggest that molecular evolution in enzyme-free replication systems would be characterized by large "leaps" through sequence space rather than isolated point mutations, perhaps enabling rapid exploration of diverse sequences. The findings may also be useful for designing self-replicating systems combining high fidelity with evolvability.
非酶、模板指导的核酸合成是自我复制系统的典范。此类系统的进化动态取决于多个因素,包括突变率、相对复制率以及突变序列的序列特征。我们使用一系列骨架结构(RNA、DNA 和 LNA 模板和 RNA 和 DNA 引物)和两种 5'-活化核苷酸(氧杂氮杂苯并三唑和咪唑,即核苷 5'-磷酸咪唑)测量了在引物-模板错配(突变)下游正确和错误单体插入的动力学。我们的研究表明,对于所有研究的系统,最初的错配很可能会被另一个错误所跟随(54-75%的时间),并且在单个错配之后的延伸通常比没有错误的延伸慢 10-100 倍。如果错配后面跟着一个匹配的碱基对,延伸速率会恢复到接近正常水平。根据这些数据,我们在计算机上模拟了核酸复制,这表明由于随后的错误和动力学停滞的级联,最初发生错误的引物会落后于正确延伸的引物,典型的突变事件由几个连续的错误组成。我们的研究还包括不同的序列背景,这表明单体之间存在协同作用,影响绝对速率(高达 2 个数量级)和保真度。研究结果表明,无酶复制系统中的分子进化将以序列空间中的大“跳跃”为特征,而不是孤立的点突变,这可能使对不同序列的快速探索成为可能。这些发现对于设计结合高保真度和可进化性的自我复制系统可能也很有用。