Synthesis and RNA-Binding Properties of Extended Nucleobases for Triplex-Forming Peptide Nucleic Acids
Synthesis and RNA-Binding Properties of Extended Nucleobases for Triplex-Forming Peptide Nucleic Acids
复制标题
DOI：
10.1021/acs.joc.9b01133
复制
发表时间：
2019-11-01
影响因子：
3.6
通讯作者：
Rozners, Eriks
中科院分区：
文献类型：
--
作者：
Kumpina, Ilze;Brodyagin, Nikita;Rozners, Eriks
利用三链体形成寡核苷酸的Hoogsteen氢键形成三链体，代表了用于双链核酸的序列特异性识别的有吸引力的方法。然而，使用三螺旋形成寡核苷酸及其类似物的实际应用限于长的同型嘌呤序列。嘧啶识别的关键问题是它们在大沟中只存在一个氢键受体或供体基团。在此，我们报告了我们的第一次尝试，以克服这个问题，通过使用肽核酸（PNA）修饰与延长的核碱基形成三个氢键沿着整个Hoogsteen边缘的沃森-克里克碱基对。设计了5个新的碱基三联体，并通过从头计算证实了它们的氢键可行性。合成携带修饰的核碱基的PNA单体并将其掺入短模型PNA序列中。等温滴定量热法表明，这些核碱基具有适度的结合亲和力，其双链RNA（dsRNA）的目标。最后，PNA-dsRNA螺旋中修饰的三联体的分子建模表明，适度的结合亲和力是由与理想氢键排列的细微结构偏差或扩展的核碱基支架的破坏的预堆叠引起的。
Triple-helix formation, using Hoogsteen hydrogen bonding of triplex-forming oligonucleotides, represents an attractive method for sequence-specific recognition of double-stranded nucleic acids. However, practical applications using triple-helix-forming oligonucleotides and their analogues are limited to long homopurine sequences. The key problem for recognition of pyrimidines is that they present only one hydrogen-bond acceptor or donor group in the major groove. Herein, we report our first attempt to overcome this problem by using peptide nucleic acids (PNAs) modified with extended nucleobases that form three hydrogen bonds along the entire Hoogsteen edge of the Watson-Crick base'pair. New nucleobase triples (five) were designed, and their hydrogen bonding feasibility was confirmed by ab initio calculations. PNA monomers carrying the modified nucleobases were synthesized and incorporated in short model PNA sequences. Isothermal titration calorimetry showed that these nucleobases had a modest binding affinity for their double-stranded RNA (dsRNA) targets. Finally, molecular modeling of the modified triples in PNA-dsRNA helix suggested that the modest binding affinity was caused by subtle structural deviations from ideal hydrogen-bonding arrangements or disrupted pr-stacking of the extended nucleobase scaffolds.