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Issue 41, 2016
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Theoretical characterization of the conformational features of unnatural oligonucleotides containing a six nucleotide genetic alphabet

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Abstract

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.

Graphical abstract: Theoretical characterization of the conformational features of unnatural oligonucleotides containing a six nucleotide genetic alphabet

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Publication details

The article was received on 12 Aug 2016, accepted on 19 Sep 2016 and first published on 20 Sep 2016


Article type: Paper
DOI: 10.1039/C6CP05594J
Phys. Chem. Chem. Phys., 2016,18, 28492-28501

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    Theoretical characterization of the conformational features of unnatural oligonucleotides containing a six nucleotide genetic alphabet

    W. Wang, X. Sheng, S. Zhang, F. Huang, C. Sun, J. Liu and D. Chen, Phys. Chem. Chem. Phys., 2016, 18, 28492
    DOI: 10.1039/C6CP05594J

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