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Probing folding/unfolding kinetics, reaction mechanism and thermodynamic stability of nucleic acid hairpins

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dc.contributor.authorNayak, Rajesh Kumar, author
dc.contributor.authorVan Orden, Alan, advisor
dc.contributor.authorBarisas, George B., committee member
dc.contributor.authorChen, Eugene, committee member
dc.contributor.authorMcNaughton, Brian, committee member
dc.contributor.authorYalin, Azer, committee member
dc.date.accessioned2007-01-03T06:08:53Z
dc.date.available2007-01-03T06:08:53Z
dc.date.issued2013
dc.description.abstractNucleic acid hairpins play pivotal roles in biological and cellular processes. The functions of the DNA and RNA hairpins depend upon the conformational changes they adopt during the biological process. Therefore, a clear understanding of their conformational dynamics such as folding and unfolding kinetics, reaction mechanism as well as thermodynamic stability is essential to understand their biological functions. This dissertation describes folding kinetics, reaction mechanism and thermodynamic stability of stem-loop nucleic acid hairpins by using rapid-mixing stopped-flow kinetics and other spectroscopic techniques. Firstly, the folding kinetics and reaction mechanism of a five base-paired stem and twenty one polythymidine loop DNA hairpin as a function of varying monovalent counter ion concentrations have been discussed. The important observation of this investigation is that the DNA hairpin folding is not simply a two-state process, and based on our experiments and kinetic modeling, we proposed a three-state reaction mechanism, wherein, the intermediate formation occurs on microsecond time scale and the complete hairpin formation occurs on millisecond time scale. Secondly, the loop length and counter ion dependent thermodynamic stability and folding of DNA hairpins have been described. This investigation provides a detailed understanding of how the stability and folding changes as a function of loop length and counter ion concentrations. The most important conclusion of this part of the investigation is that the thermodynamic stability of tetraloop hairpins depend upon counter ion concentration regimes and we explained the exceptional stability of a tetraloop hairpin in the higher concentration regime, compared to longer loop length hairpins on the basis of base-stacking effect. Finally, the folding and unfolding kinetics of RNA hairpins with identical four base-paired stem but different nucleotide loop sequence is discussed. Here we observed that the RNA hairpin folding and unfolding can be much more complex than previously thought and also RNA hairpin folding process can be different than DNA hairpin folding process.
dc.format.mediumborn digital
dc.format.mediumdoctoral dissertations
dc.identifierNayak_colostate_0053A_12014.pdf
dc.identifierETDF2013500318CHEM
dc.identifier.urihttp://hdl.handle.net/10217/80961
dc.languageEnglish
dc.language.isoeng
dc.publisherColorado State University. Libraries
dc.relation.ispartof2000-2019
dc.rightsCopyright and other restrictions may apply. User is responsible for compliance with all applicable laws. For information about copyright law, please see https://libguides.colostate.edu/copyright.
dc.subjectfolding
dc.subjectnucleic acid hairpins
dc.titleProbing folding/unfolding kinetics, reaction mechanism and thermodynamic stability of nucleic acid hairpins
dc.typeText
dcterms.rights.dplaThis Item is protected by copyright and/or related rights (https://rightsstatements.org/vocab/InC/1.0/). You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s).
thesis.degree.disciplineChemistry
thesis.degree.grantorColorado State University
thesis.degree.levelDoctoral
thesis.degree.nameDoctor of Philosophy (Ph.D.)

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