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Studies on Nucleic Acids – Structure and Dynamics
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
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. , p. 75
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 71
Keywords [en]
Bioorganic chemistry, nucleic acids, modified nucleotides, NMR, structure, dangling-end, single-stranded, thermodynamics, hydration
Keywords [sv]
Bioorganisk kemi
National Category
Organic Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-5867ISBN: 91-554-6293-6 (print)OAI: oai:DiVA.org:uu-5867DiVA, id: diva2:166678
Public defence
2005-09-16, Room C10:305 (floor 3), Biomedical Center (BMC), Uppsala, 10:00
Opponent
Supervisors
Available from: 2005-06-01 Created: 2005-06-01Bibliographically approved
List of papers
1. The First Example of a Hoogsteen Basepaired DNA Duplex in Dynamic Equilibrium with a Watson-Crick Basepaired Duplex –A Structural (NMR), Kinetic and Thermodynamic Study
Open this publication in new window or tab >>The First Example of a Hoogsteen Basepaired DNA Duplex in Dynamic Equilibrium with a Watson-Crick Basepaired Duplex –A Structural (NMR), Kinetic and Thermodynamic Study
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2001 In: J. Biomol. Struct. Dyn., ISSN 0739-1102, Vol. 18, p. 783-806Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-93246 (URN)
Available from: 2005-06-01 Created: 2005-06-01Bibliographically approved
2. 3'-endo/4'-exo Locked Thymidine in the Dickerson-Drew Dodecamer Causes Local Base Pairing Distortions – An NMR Structure and Hydration Study
Open this publication in new window or tab >>3'-endo/4'-exo Locked Thymidine in the Dickerson-Drew Dodecamer Causes Local Base Pairing Distortions – An NMR Structure and Hydration Study
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2005 In: Nucleic Acids ResArticle in journal (Refereed) Submitted
Identifiers
urn:nbn:se:uu:diva-93247 (URN)
Available from: 2005-06-01 Created: 2005-06-01 Last updated: 2015-05-19Bibliographically approved
3. An electrochemical probe of DNA stacking in an antisense oligonucleotide containing a C3'-endo-locked sugar
Open this publication in new window or tab >>An electrochemical probe of DNA stacking in an antisense oligonucleotide containing a C3'-endo-locked sugar
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2002 In: Angew. Chem. Int. Ed., ISSN 1433-7851, Vol. 41, p. 3402-3405Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-93248 (URN)
Available from: 2005-06-01 Created: 2005-06-01Bibliographically approved
4. Significant pKa Perturbation of Nucleobases Is an Intrinsic Property of the Sequence Context in DNA and RNA
Open this publication in new window or tab >>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, p. 8674-8681Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-93249 (URN)
Available from: 2005-06-01 Created: 2005-06-01Bibliographically approved
5. Single-Stranded Adenine-Rich DNA and RNA Retain Structural Characteristics of Their Respective Double-Stranded Conformations and Show Directional Differences in Stacking
Open this publication in new window or tab >>Single-Stranded Adenine-Rich DNA and RNA Retain Structural Characteristics of Their Respective Double-Stranded Conformations and Show Directional Differences in Stacking
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2004 In: Biochemistry, ISSN 0006-2960, Vol. 43, p. 15996-16010Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-93250 (URN)
Available from: 2005-06-01 Created: 2005-06-01Bibliographically approved
6. A Uniform Mechanism Correlating Dangling-End Stabilization and Stacking Geometry
Open this publication in new window or tab >>A Uniform Mechanism Correlating Dangling-End Stabilization and Stacking Geometry
2005 In: Biochemistry, ISSN 0006-2960, Vol. 44, p. 5390-5401Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-93251 (URN)
Available from: 2005-06-01 Created: 2005-06-01Bibliographically approved

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