Astrobiological exploration of RNA oligomerization and reaction product characterization for prebiotically based chemical reactions

Abstract

The formation of aggregates from circular and linear oligomers from conventional prebiotic reactions using activated nucleotides and montmorillonite clay catalysts are shown and characterized using MALDI-TOF mass spectrometry. These non-covalent aggregates can lead to misclassification of reaction products and may interfere with proper interpretation of results utilizing a number of analytical techniques. This aggregation was also shown to be enhanced under high pressure conditions of 5 and 10 kbar. This aggregation appears to not inhibit the formation of long oligomers for the investigated reactions at 5 kbar, but may play a significant role in inhibiting oligomerization at 10 kbar.

Overall, these results demonstrate that RNA oligomerization reactions are much more robust than previously thought, occurring under previously unexplored chemical and geochemical conditions. They also underline the need for care in application of analytical techniques for analyzing products of prebiotic reactions such as RNA polymerization and interpreting the results.

In addition to the increase in aggregation observed for the high pressure systems, minerals that were non-catalytic at ambient pressure showed catalytic activity at high pressures. Calcite showed the capability of producing 9-mers at 10 kbar, and nontronite produced 7-mers at 10 kbar, and 5-mers at 5 kbar. In addition, the sulfur-rich pyrrhotite and a black smoker sample (a modern hydrothermal vent system) showed increased catalytic activity as well. This potentially ground-breaking result increases possible environments for emergence of an RNA world from a select number of montmorillonite clays to a much broader host of mineral environments that were more likely to have been prevalent on early Earth.

Synthetic iron sulfide rich systems made under prebiotic conditions have previously been shown to catalyze synthesis of small organic molecules and be a rich source of chemical energy as well as abundant catalytic surfaces. My work demonstrates the formation of trimers utilizing RNA synthesis reactions using pre-activated nucleotides at synthetic hydrothermal chimney systems. These synthetic chimneys showed increased catalytic activity in the presence of montmorillonite clay by generating tetramers, even showing the capability to form dimers (and possibly trimers) when non-activated ribonucleotides were used. Catalytic activity was also enhanced with the presence of Al3+ during chimney growth, and also with the presence of stabilizing agents for the activated ribonucleotides.

The RNA World hypothesis is a major research area in the field of astrobiology. This hypothesis envisions a world in which organisms rely upon the unique properties of RNA to conduct their biochemical reactions instead of a mixture of RNA, DNA, and proteins seen in modern organisms. Evidence for such a world exists through the study of paleobiology and the preserved enzymatic activities seen in the ribozymes of all living organisms. If this RNA World was not preceded by a protein world or a more primitive proto-RNA world, mechanisms must exist to polymerize ribonucleotides to form catalytic RNA. This work focuses upon broadening the library of chemical and geochemical mechanisms which could lead to RNA oligomerization and improving the analytic techniques used to interpret the reaction products from prebiotic reactions in support of the de novo creation of an RNA World.

An alternative method to pre-activating ribonucleotides was investigated by using a carbodiimide to activate ribonucleotides in situ. This method provides a more realistic prebiotic pathway to activating ribonucleotides since it is performed in an aqueous environment rather than an organic solvent. The in situ activation was able to generate oligomers up to 8-mers in length compared to 10-mers for pre-activated ribonucleotides under identical reaction conditions, providing validation for this method.