A Biocomputational Study of Water-Nucleobase Stacking Contacts in Functional RNAs
KAUST DepartmentPhysical Science and Engineering (PSE) Division
Embargo End Date2019-12-03
Permanent link to this recordhttp://hdl.handle.net/10754/630130
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Access RestrictionsAt the time of archiving, the student author of this thesis opted to temporarily restrict access to it. The full text of this thesis became available to the public after the expiration of the embargo on 2019-12-03.
AbstractRecent structural studies evidenced the presence of a recurring well-known interaction between an oxygen atom and an aromatic nucleobase ring in structural motifs of nucleic acids. In particular, this type of interaction is observed between the O4' atom of the (deoxy)ribose moiety and the aromatic nucleobase in Z-DNA molecules and in a variety of structural RNA molecules. In this thesis, we comprehensively examine the hitherto undetected stacking interactions between an oxygen atom of a water (Ow) molecule and the aromatic nucleobase ring, using structural bioinformatics along with quantum mechanics. On the basis of the structural analysis of the high-resolution X-ray structures, we found out that the stacking distance between the Ow atom and the nucleobase plane varies between 3.1 and 4.0 Å. Further, the contact between the Ow-nucleobase plane can be categorized either as a lonepair-π type, where the Ow atom interacts directly with the aromatic surface of the nucleobase, or as an OH-π interaction, where one of the hydrogen atoms of the Ow points towards the nucleobase. Our quantum chemical analysis evidenced that the OH-π interaction is clearly favored in terms of energetics when compared to the lonepair-π, except for the uracil, where the lonepair-π kind of interaction seems to be energetically more stable, as also supported by electrostatic potential map calculations.
CitationKalra, K. (2018). A Biocomputational Study of Water-Nucleobase Stacking Contacts in Functional RNAs. KAUST Research Repository. https://doi.org/10.25781/KAUST-TY700