Theoretical characterization of the conformational features of unnatural oligonucleotides containing a six nucleotide genetic alphabet
| Autor: | Shaolong Zhang, Dezhan Chen, Xie-Huang Sheng, Jian-Biao Liu, Wenjuan Wang, Fang Huang, Chuanzhi Sun |
|---|---|
| Rok vydání: | 2016 |
| Předmět: |
Models
Molecular 0301 basic medicine chemistry.chemical_classification Nucleotides Oligonucleotide Base pair Oligonucleotides Stacking General Physics and Astronomy 010402 general chemistry 01 natural sciences Quantum chemistry 0104 chemical sciences Nucleobase 03 medical and health sciences Crystallography Molecular dynamics 030104 developmental biology chemistry Nucleic Acid Conformation Nucleotide Artificially Expanded Genetic Information System Physical and Theoretical Chemistry Base Pairing |
| Zdroj: | Physical Chemistry Chemical Physics. 18:28492-28501 |
| ISSN: | 1463-9084 1463-9076 |
| DOI: | 10.1039/c6cp05594j |
| Popis: | The addition of the unnatural P:Z base pair to the four naturally occurring DNA bases expands the genetic alphabet and yields an artificially expanded genetic information system (AEGIS). Herein, the structural feature of oligonucleotides containing a novel unnatural P:Z base pair is characterized using both molecular dynamics and quantum chemistry. The results show that the incorporation of the novel artificial base pair (P:Z) preserves the global conformational feature of duplex DNA except for some local structures. The Z-nitro group imparts new properties to the groove width, which widens the major groove. The unnatural oligonucleotides containing mismatched base pairs exhibit low stability. This ensures efficient and high-fidelity replication. In general, the incorporation of the P:Z pair strengthens the stability of the corresponding DNA duplex. The calculated results also show that the thermostability originates from both hydrogen interaction and stacking interaction. The Z-nitro group plays an important role in enhancing the stability of the H-bonds and stacking strength of the P:Z pair. Overall, the present results provide theoretical insights in the exploration of artificially expanded genetic information systems. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|