Issue 11, 2008
From the journal:

New Journal of Chemistry

Hydrogen bonding of 3- and 5-methyl-6-aminouracil with natural DNA bases†

Gábor Paragi,*a   Emília Szájli,b   Ferenc Bogár,a   Lajos Kovács,c   Célia Fonseca Guerrad  and  F. Matthias Bickelhaupt*d  

* Corresponding authors

a Supramolecular and Nanostructured Materials Research Group of the Hungarian Academy of Sciences at the University of Szeged, Dóm tér 8, Szeged, Hungary
E-mail: paragi@sol.cc.u-szeged.hu
Fax: 36 62 545971
Tel: 36 62 544593

b Proteomics Research Group at the Biological Research Center of the Hungarian Academy of Science, Temesvári krt. 62, Szeged, Hungary

c University of Szeged, Department of Medicinal Chemistry, Dóm tér 8., Szeged, Hungary

d Theoretische Chemie and Amsterdam Center for Multiscale Modeling, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, Amsterdam, The Netherlands
E-mail: FM.Bickelhaupt@few.vu.nl
Fax: +31 20 5987617

Abstract

We have theoretically analyzed the hydrogen bonding of two artificial nucleobases (3- and 5-methyl-6-aminouracil) with the natural DNA bases using the generalized gradient approximation (GGA) of density functional theory at BP86/TZ2P level. The analysis of the monomers provides the possibility to distinguish the different active parts of molecules and the interactions with natural nucleobases have been determined. Another purpose of this work is to clarify the relative importance of electrostatic interaction vs. orbital interaction in the hydrogen bonds between the artificial base and the natural DNA base. At variance with widespread belief, the orbital interaction component in these hydrogen bonds is found to contribute about 40% of the attractive interactions and is thus of the same order of magnitude as the electrostatic component, which provides the remaining attraction. According to our theoretical results both candidates are potential artificial nucleobases for incorporation in DNA.

Graphical abstract: Hydrogen bonding of 3- and 5-methyl-6-aminouracil with natural DNA bases

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Article information

DOI
https://doi.org/10.1039/B803593H
Article type
Paper
Submitted
03 Mar 2008
Accepted
12 Jun 2008
First published
11 Aug 2008

New J. Chem., 2008,32, 1981-1987

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Hydrogen bonding of 3- and 5-methyl-6-aminouracil with natural DNA bases

G. Paragi, E. Szájli, F. Bogár, L. Kovács, C. F. Guerra and F. M. Bickelhaupt, New J. Chem., 2008, 32, 1981 DOI: 10.1039/B803593H

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