Functional and Templating Ability of Fluorescent RNA Aptamers in Possible Prebiotic Conditions

Abstract

RNA is believed to have been central to the origin of life and may form the basis for simple synthetic cells. Herein, we investigate the role of two possible prebiotic conditions on the functional and templating ability of fluorescent RNA aptamers. Early protocells likely consisted of RNA functioning inside vesicles made of simple lipids. However, little is known about how encapsulation would affect the activity and folding of RNA. We find that confinement of the Malachite green RNA aptamer inside fatty acid vesicles increases binding affinity and locally stabilizes the bound conformation of the RNA (1). The vesicle effectively ‘chaperones’ the aptamer, consistent with an excluded volume mechanism due to confinement. Protocellular organization thereby leads to a direct benefit for the RNA. Coupled with previously described mechanisms by which encapsulated RNA aids membrane growth, this effect illustrates how the membrane and RNA might cooperate for mutual benefit. Second, Intriguing prebiotic syntheses of ribonucleotides, amino acids, and even iron-sulfur clusters rely on reactions driven by UV radiation. We irradiated two fluorescent RNA aptamers and monitored the loss of activity, folding, and the kinetics of lesion accumulation. The loss of activity differed depending on the aptamer, with the Spinach2 aptamer retaining substantial activity after long exposure times (2). The binding pocket was particularly susceptible to damage, and melting of duplex regions increased susceptibility, consistent with the view that duplex formation is protective. At the same time, susceptibility was highly variable depending on context, emphasizing the importance of studying many different RNAs to understand UV hardiness.