title: Theoretical characterization of the conformational features of unnatural oligonucleotides containing a six nucleotide genetic alphabet.
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.
authors.affiliation: College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China. dchen@sdnu.edu.cn shengxiehuang@sdnu.edu.cn.
authors.forename: Wenjuan
authors.initials: W
authors.lastname: Wang
authors.affiliation: College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China. dchen@sdnu.edu.cn shengxiehuang@sdnu.edu.cn.
authors.forename: Xiehuang
authors.initials: X
authors.lastname: Sheng
authors.affiliation: College of Physics and Electronics, Shandong Normal University, Jinan 250014, P. R. China.
authors.forename: Shaolong
authors.initials: S
authors.lastname: Zhang
authors.affiliation: College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China. dchen@sdnu.edu.cn shengxiehuang@sdnu.edu.cn.
authors.forename: Fang
authors.initials: F
authors.lastname: Huang
authors.affiliation: College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China. dchen@sdnu.edu.cn shengxiehuang@sdnu.edu.cn.
authors.forename: Chuanzhi
authors.initials: C
authors.lastname: Sun
authors.affiliation: College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China. dchen@sdnu.edu.cn shengxiehuang@sdnu.edu.cn.
authors.forename: Jianbiao
authors.initials: J
authors.lastname: Liu
authors.affiliation: College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China. dchen@sdnu.edu.cn shengxiehuang@sdnu.edu.cn.
authors.forename: Dezhan
authors.initials: D
authors.lastname: Chen
mesh_terms: D020029:Base Pairing; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry*
chemical_list: D009711:Nucleotides; D009841:Oligonucleotides