El origen de la vida en la Tierra es una de las preguntas más difíciles presentadas a la ciencia. En los últimos 60 años, ha habido un progreso considerable en entender cómo moléculas relativamente sencillas, que son relevantes para la vida, pueden ser generadas espontáneamente o pueden llegar a la Tierra desde el espacio. Además, los análisis de la evolución de la historia de ácidos nucleicos, los cuales almacenan la información genética, apuntan a un ancestro común universal ya extinto. Los estudios del origen de la vida ofrecen muchas pistas que apuntan hacia un origen común, quizás no solo en el Tierra sino también en algún otro punto del sistema solar. Debido al largo tiempo transcurrido desde que la Tierra empezó a albergar vida, las pistas más antiguas de los primeros organismos se han perdido. Es muy poco probable encontrar exactamente cómo fue este primer organismo. Sin embargo, en los últimos años la biología sintética ha logrado progresar mucho en la modificación de biomoléculas, en particular, los ácidos nucleicos. Es posible que pronto podamos construir y comprender un sistema minimalista en el cual las moléculas puedan copiarse a sí mismas dentro de una célula rudimentaria. El estudio de un sistema así podría permitirnos develar el origen de los primeros organismos. / The origin of life on Earth is one of the most challenging questions in science. In the last 60 years, considerable progress has been made in understanding how simple molecules relevant to life can be generated spontaneously or are known to arrive to Earth from space. Additionally, analysis of the evolution history of nucleic acids, which are the repository of genetic information, points to a now extinct, universal common ancestor for all life on Earth. The studies of the origin of life offer many clues towards a common origin, perhaps not just on Earth but somewhere else in the solar system. However due to the length of time that the Earth has harbored life, the oldest clues of the first organisms are mostly gone. It is unlikely to find exactly what this first organism was like. Nevertheless, in the last few years, synthetic biology has made remarkable progress at modifying biomolecules, particularly nucleic acids. It is possible that soon we will be able to construct and understand a minimalistic system in which molecules can copy themselves in a protocell. The study of such systems could shed light into the origin of the first organisms.

In the past 30 years, the discovery of capabilities of nucleic acids far beyond their well-known information-bearing capacity has profoundly influenced our understanding of these polymers. The discovery by the Cech and Altman labs that nucleic acids could perform catalytic functions, coupled with the Gold and Szostak groups’ demonstration of the de novo evolution of nucleic acids that bind arbitrary ligands, has resulted in a proliferation of newfound roles for these molecules. Nucleic acids have found utility in both engineered systems, such as aptamer therapeutics, as well as in newly appreciated roles in extant organisms, such as riboswitches. As a result of these discoveries, many have pondered the potential importance of the dual (catalytic and informational) roles of nucleic acids in early evolution. A high-yielding synthetic route for the nonenzymatic polymerization of nucleic acids, based on the aqueous self-assembly of their components, would provide a powerful tool in nucleic acid chemistry, with potential utility in prebiotic and contemporary nucleic acid systems alike – however, such a route remains elusive. In this thesis, I describe several steps towards such a synthetic route. In these systems, a nucleic-acid binding ligand drives the assembly of short DNA and RNA duplexes, promoting the production of long nucleic acid polymers, while suppressing the production of short, cyclic species. Additionally, the use of a reversible covalent linkage allows for the production of long polymers, as well as the incorporation of previously cyclized products into these polymers. I also report several explorations of novel base pairings, nucleic acid-ligand interactions, and nucleic acid-ion interactions that have informed our studies of self-assembling nucleic acid systems.

The origin of the first RNA polymers is central to most current theories regarding the origin of life. However, difficulties associated with the prebiotic formation of RNA have lead many researchers to conclude that simpler polymers, or proto-RNAs, preceded RNA. These earlier polymers would have been replaced by RNA over the course of evolution. A remaining difficulty for this theory is that the de novo synthesis of a feasible proto-RNA has not yet been demonstrated by plausible prebiotic reactions. This thesis focuses on two problems associated with prebiotic proto-RNA synthesis: The formation of nucleosides and the necessity of reversible backbone linkages for error correction in nucleic acid polymers. "The Nucleoside Problem", or the lack of success in forming pyrimidine nucleosides by plausible prebiotic reactions, represents a significant stumbling block to the RNA world hypothesis. Nearly four decades ago Orgel and coworkers demonstrated that the purine nucleosides adenosine and inosine are synthesized by heating and drying their respective bases and ribose in the presence of magnesium, but these reaction conditions do not yield the pyrimidine nucleosides uridine or cytidine from their respective bases. In this thesis a potential solution to The Nucleoside Problem is hypothesized based upon a proposed chemical mechanism for nucleoside formation. This hypothesis is supported by the successful synthesis of 2-pyrimidinone nucleosides by a plausible prebiotic reaction in good yield, demonstrating that pyrimidine nucleosides could have been available in the prebiotic chemical inventory, but that uridine and cytidine were likely not abundant. Reversible backbone linkages are necessary to provide a mechanism for error correction in non-enzymatic template-directed syntheses of proto-RNAs. In this thesis, acetals are explored as low-energy, reversible linkage groups for nucleosides in polymers. The synthesis of glyoxylate-acetal nucleic acids (gaNAs) through simple heating-drying reactions from neutral aqueous solutions is demonstrated, and these linkages are shown to be hydrolytically stable under a considerable range of solution conditions. Computational models demonstrate that the glyoxylate linkage is an excellent electronic and isosteric replacement for phosphate. Molecular dynamics simulations also indicate that a gaNA duplex would have structural properties that closely match a phosphate-linked RNA helix, suggesting the possibility for cross-pairing between gaNAs and RNAs, allowing for sequence transfer and genetic continuity through the evolution from proto-RNAs to RNA. The principles illustrated in this thesis by 2-pyrimidinone nucleoside and gaNA synthesis can be extended to other prebiotic condensation reactions. Factors affecting condensation yield, such as thermodynamics, kinetics, reactant solubility, and salt effects, are summarized herein.