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On the prebiotic selection of nucleotide anomers: A computational study
Lázaro A M Castanedo1,2, Chérif F Matta1,2,3,4
1Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada.
Heliyon
|July 5, 2022
Summary
Thermodynamic analysis explains why beta-nucleosides dominate and uracil/thymine are in RNA/DNA. Quantum chemical calculations reveal how thermodynamics guided the natural selection of life's building blocks.
Area of Science:
- Biochemistry
- Quantum Chemistry
- Astrobiology
Background:
- The predominant forms of nucleosides and nucleotides in modern biology are beta-anomers.
- The specific incorporation of uracil into RNA and thymine into DNA is a fundamental aspect of genetic material.
- The origin of these biochemical specificities is often attributed to a combination of kinetic and thermodynamic factors during early life evolution.
Purpose of the Study:
- To investigate the thermodynamic basis for the observed predominance of beta-anomers over alpha-anomers in nucleosides and nucleotides.
- To explore the thermodynamic control mechanisms that may have driven the evolutionary selection of uracil for RNA and thymine for DNA.
- To utilize quantum chemical calculations to understand the role of thermodynamics in the
- natural selection
- of life's fundamental molecular components.
Main Methods:
- Thermodynamic analysis of the assembly of nucleosides and nucleotides from their constituent parts (bases, sugars, phosphate group).
- Quantum chemical calculations to model and predict the energetic favorability of different molecular configurations and incorporations.
- Comparative analysis of the thermodynamic stability of various nucleoside/nucleotide structures and base-sugar pairings.
Main Results:
- Thermodynamic analysis successfully predicts the prevalence of beta-anomers over alpha-anomers in nucleosides and nucleotides.
- Calculations indicate that thermodynamic principles favor the incorporation of uracil into RNA and thymine into DNA.
- The study highlights the significant role of thermodynamic control in the selection of key biomolecules.
Conclusions:
- Thermodynamic factors provide a strong explanation for the observed stereochemistry of nucleosides and nucleotides.
- The specific base composition of RNA and DNA is likely a consequence of thermodynamic selection pressures.
- Quantum chemical insights into thermodynamics offer a powerful lens for understanding the origins and evolution of life's molecular machinery.
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