Structural Properties of Hachimoji Nucleic Acids and Their Building Blocks: Comparison of Genetic Systems with Four, Six and Eight Alphabets
| العنوان: | Structural Properties of Hachimoji Nucleic Acids and Their Building Blocks: Comparison of Genetic Systems with Four, Six and Eight Alphabets |
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| المؤلفون: | Indu Negi, Bimaldeep Singh, Amanpreet Singh Mahmi, Purshotam Sharma |
| المصدر: | ChemPhysChem. 24 |
| بيانات النشر: | Wiley, 2022. |
| سنة النشر: | 2022 |
| مصطلحات موضوعية: | Physical and Theoretical Chemistry, Atomic and Molecular Physics, and Optics |
| الوصف: | Expansion of the genetic alphabet is an ambitious goal. A recent breakthrough has led to the eight-base (hachimoji) genetics having canonical and unnatural bases. However, very little is known on the molecular-level features that facilitate the candidature of unnatural bases as genetic alphabets. Here we amalgamated DFT calculations and MD simulations to analyse the properties of the constituents of hachimoji DNA and RNA. DFT reveals the dominant syn conformation for isolated unnatural deoxyribonucleosides and at the 5'-end of oligonucleotides, although an anti/syn mixture is predicted at the nonterminal and 3'-terminal positions. However, isolated ribonucleotides prefer an anti/syn mixture, but mostly prefer anti conformation at the nonterminal positions. Further, the canonical base pairing combinations reveals significant strength, which may facilitate replication of hachimoji DNA. We also identify noncanonical base pairs that can better tolerate the substitution of unnatural pairs in RNA. Stacking strengths of 51 dimers reveals higher average stacking stabilization of dimers of hachimoji bases than canonical bases, which provides clues for choosing energetically stable sequences. A total of 14.4 μs MD simulations reveal the influence of solvent on the properties of hachimoji oligonucleotides and point to the likely fidelity of replication of hachimoji DNA. Our results pinpoint the features that explain the experimentally observed stability of hachimoji DNA. |
| تدمد: | 1439-7641 1439-4235 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::278d3af2a5669da971e18801e15b7c1d https://doi.org/10.1002/cphc.202200714 |
| حقوق: | CLOSED |
| رقم الأكسشن: | edsair.doi.dedup.....278d3af2a5669da971e18801e15b7c1d |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 14397641 14394235 |
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