uu.seUppsala University Publications
Change search
ReferencesLink to record
Permanent link

Direct link
3'-endo/4'-exo Locked Thymidine in the Dickerson-Drew Dodecamer Causes Local Base Pairing Distortions – An NMR Structure and Hydration Study
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
Show others and affiliations
2005 In: Nucleic Acids ResArticle in journal (Refereed) Submitted
Place, publisher, year, edition, pages
URN: urn:nbn:se:uu:diva-93247OAI: oai:DiVA.org:uu-93247DiVA: diva2:166673
Available from: 2005-06-01 Created: 2005-06-01 Last updated: 2015-05-19Bibliographically 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

Open Access in DiVA

No full text

Search in DiVA

By author/editor
Plashkevych, Oleksandr
By organisation
Department of Bioorganic Chemistry

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Total: 203 hits
ReferencesLink to record
Permanent link

Direct link