Department of Chemistry, North-Eastern Hill University, Shillong, 793022, India.
J Mol Model. 2012 Aug;18(8):3805-20. doi: 10.1007/s00894-012-1385-4. Epub 2012 Mar 8.
Codon degeneracy is a key feature of the genetic code, explained by Crick (J Mol Biol 19:548-555, 1966) in terms of imprecision of base pairing at the codon third position (the wobble position) of the codon-anticodon duplex. The Crick wobble rules define, but do not explain, which base pairs are allowed/disallowed at the wobble position of this duplex. This work examines whether the H-bonded configurations of solitary RNA base pairs can in themselves help decide which base pairs are allowed at the wobble position during codon-anticodon pairing. Taking the purine-type bases guanine, hypoxanthine, queuine and adenine as anticodon wobble bases, H-bonded pairing energies and optimized configurations of numerous RNA base pairs are calculated in gas and modeled aqueous phase at the B3LYP/6-31 G(d,p) level. Calculated descriptors of alignment of these solitary base pairs are able to screen between allowed and disallowed base pairs for all cases studied here, except two cases which invoke base-sugar interactions in the codon wobble nucleoside. The exclusion of adenine from the anticodon wobble position cannot be explained on the basis of pairing facility or base pair geometry. These DFT results thus account for the specificity and degeneracy of the genetic code for all cases involving guanine, hypoxanthine and queuine as anticodon wobble bases.
密码子简并性是遗传密码的一个关键特征，克里克（J Mol Biol 19:548-555, 1966）用密码子-反密码子双链的密码子第三位（摆动位）碱基配对不精确来解释。克里克摆动规则定义了但没有解释哪些碱基对在这个双链的摆动位是允许的/不允许的。这项工作研究了单独的 RNA 碱基对的氢键构象本身是否有助于决定在密码子-反密码子配对过程中哪些碱基对可以在摆动位出现。以嘌呤型碱基鸟嘌呤、次黄嘌呤、Queuine 和腺嘌呤作为反密码子摆动碱基，在 B3LYP/6-31 G(d,p)水平下，在气相和模拟水相计算了许多 RNA 碱基对的氢键配对能和优化构型。这些孤立碱基对的排列描述符能够筛选出所有研究案例中允许和不允许的碱基对，除了两个案例涉及到密码子摆动核苷中的碱基-糖相互作用。腺嘌呤不能从反密码子摆动位置排除，不能基于配对能力或碱基对几何形状来解释。因此，这些 DFT 结果解释了涉及鸟嘌呤、次黄嘌呤和 Queuine 作为反密码子摆动碱基的所有情况下遗传密码的特异性和简并性。
