Theoretical Characterization of the H-Bonding and Stacking Potential of Two Non-Standard Nucleobases Expanding the Genetic Alphabet

Handle URI:
http://hdl.handle.net/10754/596860
Title:
Theoretical Characterization of the H-Bonding and Stacking Potential of Two Non-Standard Nucleobases Expanding the Genetic Alphabet
Authors:
Chawla, Mohit; Credendino, Raffaele; Chermak, Edrisse ( 0000-0002-2716-5724 ) ; Oliva, Romina; Cavallo, Luigi ( 0000-0002-1398-338X )
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.
KAUST Department:
Physical Sciences and Engineering (PSE) Division; KAUST Catalysis Center (KCC)
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
Publisher:
American Chemical Society (ACS)
Journal:
The Journal of Physical Chemistry B
Issue Date:
16-Feb-2016
DOI:
10.1021/acs.jpcb.6b00125
Type:
Article
ISSN:
1520-6106; 1520-5207
Sponsors:
The research reported in this publication was supported by funding from King Abdullah University of Science and Technology (KAUST).
Additional Links:
http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b00125
Appears in Collections:
Articles; Physical Sciences and Engineering (PSE) Division; KAUST Catalysis Center (KCC)

Full metadata record

DC FieldValue Language
dc.contributor.authorChawla, Mohiten
dc.contributor.authorCredendino, Raffaeleen
dc.contributor.authorChermak, Edrisseen
dc.contributor.authorOliva, Rominaen
dc.contributor.authorCavallo, Luigien
dc.date.accessioned2016-02-21T14:16:57Zen
dc.date.available2016-02-21T14:16:57Zen
dc.date.issued2016-02-16en
dc.identifier.citationTheoretical Characterization of the H-Bonding and Stacking Potential of Two Non-Standard Nucleobases Expanding the Genetic Alphabet 2016 The Journal of Physical Chemistry Ben
dc.identifier.issn1520-6106en
dc.identifier.issn1520-5207en
dc.identifier.doi10.1021/acs.jpcb.6b00125en
dc.identifier.urihttp://hdl.handle.net/10754/596860en
dc.description.abstractWe 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.en
dc.description.sponsorshipThe research reported in this publication was supported by funding from King Abdullah University of Science and Technology (KAUST).en
dc.language.isoenen
dc.publisherAmerican Chemical Society (ACS)en
dc.relation.urlhttp://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b00125en
dc.rightsThis 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.en
dc.titleTheoretical Characterization of the H-Bonding and Stacking Potential of Two Non-Standard Nucleobases Expanding the Genetic Alphabeten
dc.typeArticleen
dc.contributor.departmentPhysical Sciences and Engineering (PSE) Divisionen
dc.contributor.departmentKAUST Catalysis Center (KCC)en
dc.identifier.journalThe Journal of Physical Chemistry Ben
dc.eprint.versionPost-printen
dc.contributor.institutionDepartment of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143, Naples, Italyen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorChawla, Mohiten
kaust.authorCredendino, Raffaeleen
kaust.authorChermak, Edrisseen
kaust.authorCavallo, Luigien
All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.