Astrobiological implications of guanosine gels and analysis of abiotic RNA polymerization

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Cassidy, Lauren
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A robust analytical procedure is required in order to study model systems for abiotic RNA polymerization. Matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry (MALDI-TOF-MS) has been used as a platform to characterize the efficiency of polymerization in sodium-titrated montmorillonite clay. After incubation with sodium-titrated montmorillonite clay, imidazole-activated nucleotide monomers are analyzed, in parallel, using high performance liquid chromatography (HPLC) and MALDI-TOF-MS. In following the prescribed methodology for the detection of abiotically derived nucleotide polymers, it was observed that the desorption surface played a role in the efficiency of desorption. This was a previously un-characterized phenomena. While subsequent research by the McGown group revealed that the utilization of a non-metal platform can also enhance the detection of non- polymer aggregates, it it still a novel that silica surfaces appear to promote the detection of anionic polymers more than conventionally used metal surfaces.
The bulk properties of nucleotides, in particular GMP, their interaction with a well-characterized catalytic surface, and the analytical techniques applied to these discoveries are presented in this dissertation. These interactions have important implications for potential involvement in early abiotic processes, in particular the implications that guanosine species could have been mediating forces on the early Earth and could have served as proto-regulatory systems.
The implications for this new GMP/XMP class of guanosine gels in the context of astrobiology and origins of life research led to interest in the gels' tolerance of non-nucleotide inclusions. Gels were synthesized in the presence of a previously well-characterized polymer catalyst, sodium-titrated montmorillonite clay. Other non-nucleotide species of astrobiological importance, such as carbon nanotubes and amino acids, were included in gel preparation. The second part of this dissertation discusses the impact of a nucleotide gel on the abiotic polymerization of activated nucleotide species and the implications thereof for environments experiencing wet/dry cycling.
Beyond the previously well-characterized behavior of homo-guanosine gels, this dissertation will discuss the observation that guanosine 5'-monophosphate (GMP) based gels, as previously reported by members of the McGown group, are far more diverse than previously reported. In addition to homo-nucleotide gelation, GMP can also act to bring other nucleotides (XMP, where X = adenosine, guanosine, cytidine, or uridine) and amino acids into solution. GMP/XMP gels show a higher tolerance to pH than previously observed GMP/guanosine gels. Stability of the gels correlates to relative concentration of GMP to XMP and the overall nucleotide concentration in solution as well as the form: disodium salt (dss) or free acid (fa). It is imperative to the stability of the gels to have either a mismatch of species (dss/fa or fa/dss), to adjust the pH in the presence of a Gquadruplex stabilizing counter ion (sodium hydroxide [NaOH] for fa/fa and hydrochloric acid [HCl] for dss/dss), or a suitably high concentration of salts present. This behavior was studied over a temperature range of 5-75 °C via visual inspection, circular dichroism (CD) spectroscopy (CD), and CD thermal melts. Of particular interest regarding these gels is the observation that they are, in many ways, dissimilar to previously characterized GMP/guanosine gels and solutions at similar concentrations involving the standard library of nucleosides.
A philispohically interesting question, which science has made strides toward piecing together for a long time has been the understanding of early terrestrial biological processes. Even simple biological systems are complex and have a number of componants, but a thourough understanding of terrestrial life is necessacary in order to understand the possible development of extraterrestrial life. Part of the puzzle lies with the nucleosides and nucleotides, which are responsible for storing the "data" of life.
Of the nucleosides, guanosine species are of great interest to the astrobiological community due to their unique ability to self-assemble under possible early Earth conditions. In solution, monomeric guanosine nucleotides, unlike other nucleotides, have a great deal of versatility regarding their hydrogen bonding arrangements. This versatility is exemplified by the formation of a gel-like liquid crystalline phase, which comes about through Hoogsteen hydrogen bonding between guanosine species and pi-pi stacking of the purine rings, and is mediated by the presence of cations involved in cation-dipole interactions. This behavior has been widely observed and well characterized by previous members of the McGown lab group as well as in the literature.
May 2014
School of Science
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Rensselaer Polytechnic Institute, Troy, NY
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