Prebiotic assembly and replication of nucleic acids

One of the most researched hypotheses for the origins of life, known as the "RNA world", relies on replication of ribonucleic acid (RNA) before the advent of protein enzymes and deoxyribonucleic acid (DNA). Essentially, the hypothesis relies on what some researchers believe is a parsimonious claim that RNA was the central molecule of heredity and metabolic catalysis from which life evolved. To test this hypothesis, many critical steps in the formation of a replicating RNA have been attempted under purportedly plausible prebiotic conditions in the laboratory. For example, polymerization of monomer units of RNA directed by base pairing interactions with an RNA template strand has been achieved in the absence of enzymes through a process called template-directed synthesis. Despite such popularity and over half a century of laboratory experiments, there remain many problems in elucidating a pathway from formation of mononucleotides from small organic molecules to template-directed synthesis and replication of nucleic acids. This dissertation is primarily dedicated to resolving one of the outstanding problems of nucleic acid replication: The Strand Inhibition Problem. The interactions that allow assembly of mono- or oligonucleotides as substrates for a template-directed synthesis reaction are the same interactions that prevent further copying as the resulting product strand is bound to the template with greater affinity than that of shorter substrates. Effectively, the product strand inhibits further substrate assembly and synthesis, thus forming the problem of strand inhibition. The individual strands of the product-template duplex must be separated to allow substrate annealing to the free original template and product strands for further copying reactions. Attempts to separate the product-template and then anneal substrates, typically by heating and cooling, only result in reassociation of the product and template strands, establishing open ended template-directed replication as a problem of thermodynamics. In this dissertation, I will elaborate on the relevance of nucleic acid replication at the origins of life and the remaining challenges in replication of nucleic acids in Chapter 1. Then, I will discuss various kinetic solutions to overcoming strand inhibition to achieve nucleic acid replication in Chapter 2, using low-water solvents coupled to heating and cooling cycles, and in Chapter 3, using wet-dry cycles as a robust and efficient prebiotic method. In Chapter 4, I will explore nonenzymatic ligation of substrates once assembled on templates that is required to demonstrate a nucleic acid replication cycle in the absence of enzymes. In Chapter 5, I will present other interesting observations related to these chapters along with possible future directions that can be explored to demonstrate nucleic acid replication. Finally, in Chapter 6, we will draw our conclusions.

Level thesis:degree_level

Doctoral

Department dc:contributor.department

Chemistry and Biochemistry

Grantor dc:publisher

Georgia Institute of Technology

Year dc:date.issued

2023

Author dc:creator

• Clifton, Bryce E.

Advisors dc:contributor.advisor

• Hud, Nicholas V.
• Grover, Martha A.

Committee members dc:contributor.committeemember

• Schuster, Gary B.
• Williams, Loren D.
• Kim, Harold D.

• nucleic acid replication
• prebiotic chemistry

Language dc:language.iso

en_US

Handle dc:identifier.uri

https://hdl.handle.net/1853/72761

OAI identifier oai:identifier

oai:repository.gatech.edu:1853/72761