Theoretical Characterization of the H-Bonding and Stacking Potential of Two Non-Standard Nucleobases Expanding the Genetic Alphabet
dc.contributor.author | Chawla, Mohit | |
dc.contributor.author | Credendino, Raffaele | |
dc.contributor.author | Chermak, Edrisse | |
dc.contributor.author | Oliva, Romina | |
dc.contributor.author | Cavallo, Luigi | |
dc.date.accessioned | 2016-02-21T14:16:57Z | |
dc.date.available | 2016-02-21T14:16:57Z | |
dc.date.issued | 2016-02-25 | |
dc.identifier.citation | Theoretical Characterization of the H-Bonding and Stacking Potential of Two Non-Standard Nucleobases Expanding the Genetic Alphabet 2016 The Journal of Physical Chemistry B | |
dc.identifier.issn | 1520-6106 | |
dc.identifier.issn | 1520-5207 | |
dc.identifier.pmid | 26882210 | |
dc.identifier.doi | 10.1021/acs.jpcb.6b00125 | |
dc.identifier.uri | http://hdl.handle.net/10754/596860 | |
dc.description.abstract | We report a quantum chemical characterization of the non-natural (synthetic) H-bonded base pair formed by 6-amino-5-nitro-2(1H)-pyridone (Z) and 2-amino-imidazo [1,2-a]-1,3,5-triazin-4(8H)-one (P). The Z:P base pair, orthogonal to the classical G:C base pair, has been introduced in DNA molecules for expanding the genetic code. Our results indicate that the Z:P base pair closely mimics the G:C base pair both in terms of structure and stability. To clarify the role of the NO2 group on the C5 position of the Z base, we compared the stability of the Z:P base pair with that of base pairs having different functional group on the C5 position of Z. Our results indicate that the electron donating/withdrawing properties of the group in the C5 position has a clear impact on the stability of the Z:P base pair, with the strong electron withdrawing nitro group achieving the largest stabilizing effect on the H-bonding interaction, and the strong electron donating NH2 group destabilizing the Z:P pair by almost 4 kcal/mol. Finally, our gas phase and in water calculations confirm that the Z-nitro group reinforce the stacking interaction with its adjacent purine or pyrimidine ring. | |
dc.description.sponsorship | The research reported in this publication was supported by funding from King Abdullah University of Science and Technology (KAUST). | |
dc.language.iso | en | |
dc.publisher | American Chemical Society (ACS) | |
dc.relation.url | http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b00125 | |
dc.rights | This document is the Accepted Manuscript version of a Published Work that appeared in final form in The Journal of Physical Chemistry B, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b00125. | |
dc.title | Theoretical Characterization of the H-Bonding and Stacking Potential of Two Non-Standard Nucleobases Expanding the Genetic Alphabet | |
dc.type | Article | |
dc.contributor.department | Chemical Science Program | |
dc.contributor.department | KAUST Catalysis Center (KCC) | |
dc.contributor.department | Physical Science and Engineering (PSE) Division | |
dc.identifier.journal | The Journal of Physical Chemistry B | |
dc.eprint.version | Post-print | |
dc.contributor.institution | Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143, Naples, Italy | |
dc.contributor.affiliation | King Abdullah University of Science and Technology (KAUST) | |
kaust.person | Chawla, Mohit | |
kaust.person | Credendino, Raffaele | |
kaust.person | Chermak, Edrisse | |
kaust.person | Cavallo, Luigi | |
refterms.dateFOA | 2017-02-16T00:00:00Z | |
dc.date.published-online | 2016-02-25 | |
dc.date.published-print | 2016-03-10 |
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