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Significant pKa Perturbation of Nucleobases Is an Intrinsic Property of the Sequence Context in DNA and RNA
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2004 In: J. Am. Chem. Soc., ISSN 0002-7863, Vol. 126, 8674-8681 p.Article in journal (Refereed) Published
Place, publisher, year, edition, pages
2004. Vol. 126, 8674-8681 p.
URN: urn:nbn:se:uu:diva-93249OAI: oai:DiVA.org:uu-93249DiVA: diva2:166675
Available from: 2005-06-01 Created: 2005-06-01Bibliographically approved
In thesis
1. Studies on Nucleic Acids – Structure and Dynamics
Open this publication in new window or tab >>Studies on Nucleic Acids – Structure and Dynamics
2005 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis is based on six papers, Papers I-VI, focusing on the interplay between the stabilizing elements of nucleic acids self-assembly; hydrogen bonding, stacking and solvent effects. In Paper I we investigate how the substitution of the O4' for CH2 in the sugar moiety of adenosine (2'-deoxyaristeromycin) at the A6 position of the Dickerson-Drew dodecamer makes the two modified bases exist in a dynamic equilibrium between Hoogsteen and Watson-Crick base pairing in the NMR time scale. Paper II is a structural study of the incorporation of 1-(1',3'-O-anhydro-β-D-psicofuranosyl)thymine in the T7 position of the Dickerson-Drew dodecamer. NMR constrained molecular dynamics and hydration studies show the base-base distortions caused by the introduction of a North-type locked sugar in an otherwise B-type DNA•DNA duplex. Paper III shows that the stacking distortion caused by the 1-(1',3'-O-anhydro-β-D-psicofuranosyl)thymine building block perturbs the charge transfer similar to a DNA mismatch. Paper IV highlights how the sequence context affects the physico-chemical properties, monitored by the pKa of guanine itself as well as how the charge perturbation is experienced by the neighboring bases, in ssDNA and ssRNA. Paper V focuses on the differences between the structural equilibria of single-stranded ssDNA and ssRNA. Directional differences in single-stranded stacking between ssDNA and ssRNA are identified and provide a basis to explain directional differences in pKa modulation and dangling-end stabilization. In Paper VI the thermodynamic gains of dangling ends on DNA and RNA core duplexes are found to correlate with the X-ray geometries of dangling nucleobases relative to the hydrogen bonds of the closing base pairs.

Place, publisher, year, edition, pages
Uppsala: Institutionen för bioorganisk kemi, 2005. 75 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 71
Bioorganic chemistry, nucleic acids, modified nucleotides, NMR, structure, dangling-end, single-stranded, thermodynamics, hydration, Bioorganisk kemi
National Category
Organic Chemistry
urn:nbn:se:uu:diva-5867 (URN)91-554-6293-6 (ISBN)
Public defence
2005-09-16, Room C10:305 (floor 3), Biomedical Center (BMC), Uppsala, 10:00
Available from: 2005-06-01 Created: 2005-06-01Bibliographically approved

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