Computational biochemical study of the prebiotic selection of nucleic acids

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dc.contributor.advisor Matta, Chérif F.
dc.creator Monteserín Castanedo, Lázaro Andrés
dc.date.accessioned 2024-03-20T15:22:52Z
dc.date.available 2024-03-20T15:22:52Z
dc.date.issued 2024-01-31
dc.identifier.uri http://library2.smu.ca/xmlui/handle/01/31893
dc.description 1 online resource (509 pages) : illustrations (some colour), charts (some colour), graphs (some colour)
dc.description Includes abstract and appendices.
dc.description Includes bibliographical references (pages 88-110, 139-146, 254-270, 378-385, 478-482, 490-496, 504-509).
dc.description.abstract This thesis addresses fundamental questions related to the prebiotic evolutionary selection of the building blocks of nucleic acids. The structural tendencies and propensities in today’s nucleic acids are rationalized based on thermodynamics as a principal driver of evolutionary selection. The free energies of the possible reaction paths available to prebiotic Nature are calculated from quantum chemistry. As one example (of many), the β-anomers of the nucleosides(tides) - predominant in modern nucleic acids - are found to be slightly more stable than their α-counterparts. This small thermodynamic advantage operating over millennia may have contributed to the observed dominance of today’s canonical forms. Calculations also suggest the possibility that non-canonical N-(2-aminoethyl)glycine (AEG) and glycerol nucleosides(tides) may have assisted in the synthesis of today’s nucleosides(tides) if the prebiotic environment has been aqueous. Energetic comparisons of ancestral nucleic acids containing arsenate instead of phosphate indicate no thermodynamic advantage for the phosphate, raising an important open question as to the reason for Nature’s selection of the latter. It is also found, computationally, that barbituric acid may have well been a prebiotic precursor of today’s nucleobases reinforcing earlier proposals. A more fundamental question may be about the choice of nucleic acids as the carriers of genetic information, in the first place, instead of other contenders such as proteins. A partial answer is formulated by proposing a quantitative account of the “<i>value</i>” of information as a new dimension to be added to the traditional “<i>amount</i>” (bits) in Shannon’s information theory. Thus, the thesis addresses certain aspects of evolutionary biochemistry from the standpoint of thermodynamics under differing conditions of solvation. Meanwhile, the rates (kinetics) were not considered in this work since the synthetic and mechanistic steps from reactants to products of most of the proposed reactions remain largely unknown. Several other potential factors have not been considered but, with these variables being constant, our results remain valid and so are the questions they open for future investigations. en_CA
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dc.description.provenance Made available in DSpace on 2024-03-20T15:22:52Z (GMT). No. of bitstreams: 1 Castanedo_Lazaro_PHD_2024.pdf: 26992910 bytes, checksum: 3bc52ec4172143b33e56db647e9dc4bb (MD5) Previous issue date: 2024-01-31 en
dc.language.iso en en_CA
dc.publisher Halifax, N.S. : Saint Mary's University
dc.subject.lcsh Prebiotics -- Evolution
dc.subject.lcsh Nucleic Acids
dc.subject.lcsh Biochemistry -- Computer simulation
dc.subject.lcsh Biochemistry -- Mathematical models
dc.title Computational biochemical study of the prebiotic selection of nucleic acids en_CA
dc.type Text en_CA
thesis.degree.name Doctor of Philosophy in Applied Science
thesis.degree.level Doctoral
thesis.degree.discipline Chemistry
thesis.degree.grantor Saint Mary's University (Halifax, N.S.)
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