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Measurement of nucleobase pKa values in model mononucleotides shows RNA-RNA duplexes to be more stable than DNA-DNA duplexes
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Biochemistry and Organic Chemistry.
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2004 In: J. Am. Chem. Soc., Vol. 126, 2862-2869 p.Article in journal (Refereed) Published
Place, publisher, year, edition, pages
2004. Vol. 126, 2862-2869 p.
URN: urn:nbn:se:uu:diva-96570OAI: oai:DiVA.org:uu-96570DiVA: diva2:171191
Available from: 2007-12-20 Created: 2007-12-20Bibliographically approved
In thesis
1. Physicochemical and Structural Aspects of Nucleic Acids
Open this publication in new window or tab >>Physicochemical and Structural Aspects of Nucleic Acids
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis consists of seven research publications concerning (i) pKa studies of nucleobases in model nucleotides to understand why RNA duplexes are more stable than DNA duplexes (Paper I), (ii) the role of Me(T)-π interactions in the relative stability of DNA-RNA heteroduplexes (Paper II), (iii) pKa measurements in nucleotides with different 2′-substituents (paper III), (iv) a conformation study of constrained sugars and a pKa study of 1-thyminyl to reveal effect of sugar constraints on the pKa of the nucleobase (paper IV), (v) NMR and MD studies of 1′, 2′-oxetane constrained thymidine incorporated Dickerson Drew dodecamer (paper V), (vi) the sequence dependent pKa perturbation of 9-guaninyl moeity in single stranded (ss) DNA and RNA (paper VI), (vii) the non identical chemical nature of internucleotidic phosphates in (ss) RNA using 31P NMR (paper VI), and an alkaline hydrolysis study of phosphodiesters in ssRNAs (paper VII). The architecture of DNA and RNA molecules is determined by (a) hydrogen bonding (b) base stacking (c) a variety of additional non-covalent interactions. In paper (I) we showed that A-U and G-C base pairings in RNA are more stable than A-T and G-C base pairings in DNA by 4.3 and 1 kJ mol-1 respectively. Me(T)-π interaction plays a dominant role in the relative stability of DNA-RNA duplexes (paper II). In paper III and IV, we have shown that 1′ , 2′- oxetane and azetidine rings have strong inductive effect on pyrimidine bases, and that the H2′-sugar proton can be the marker to understand the pseudoaromaticity of pyrimidine bases, as well as increasing constraints in sugar reducing the basicity of nucleobases. A 1′, 2′-oxetane locked thymidine (T) moiety deforms the local structure of Dickerson-Drew dodecamer, d(CGCGAATTCGCG)2- investigated by High resolution NMR and MD study, as is discussed in the paper V. In papers VI and VII, we showed sequence context dependent pKa (N1) of 9-guaninyl perturbation in (ss) DNAs and RNAs and the non identical chemical nature of inter-nucleotidic phosphate groups in single stranded RNAs.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2007. 71 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 379
Organic chemistry, pKa, Hydrogen bonding, Stacking, NMR, MD, DNA, RNA, Pyrimidine, Organisk kemi
National Category
Organic Chemistry
urn:nbn:se:uu:diva-8360 (URN)978-91-554-7056-2 (ISBN)
Public defence
2008-01-11, 101a, B7, Husargatan 3, Uppsala, 13:30 (English)
Available from: 2007-12-20 Created: 2007-12-20 Last updated: 2013-09-26Bibliographically approved

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