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Insight into the functional versatility of RNA through model-making with applications to data fitting

Published online by Cambridge University Press:  29 March 2007

Philip C. Bevilacqua ,
Andrea L. Cerrone-Szakal  and
Nathan A. Siegfried
Philip C. Bevilacqua*
Affiliation:
Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
Andrea L. Cerrone-Szakal
Affiliation:
Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
Nathan A. Siegfried
Affiliation:
Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
*
*Author for correspondence: Dr P. C. Bevilacqua, Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA. Tel.: (814) 863–3812; Fax: (814) 863–8403; E-mail: [email protected]
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Abstract

The RNA World hypothesis posits that life emerged from self-replicating RNA molecules. For any single biopolymer to be the basis for life, it must both store information and perform diverse functions. It is well known that RNA can store information. Advances in recent years have revealed that RNA can exhibit remarkable functional versatility as well. In an effort to judge the functional versatility of RNA and thereby the plausibility that RNA was at one point the basis for life, a statistical chemical approach is adopted. Essential biological functions are reduced to simple molecular models in a minimalist, biopolymer-independent fashion. The models dictate requisite states, populations of states, and physical and chemical changes occurring between the states. Next, equations are derived from the models, which lead to complex phenomenological constants such as observed and functional constants that are defined in terms of familiar elementary chemical descriptors: intrinsic rate constants, microscopic ligand equilibrium constants, secondary structure stability, and ligand concentration. Using these equations, simulations of functional behavior are performed. These functional models provide practical frameworks for fitting and organizing real data on functional RNAs such as ribozymes and riboswitches. At the same time, the models allow the suitability of RNA as a basis for life to be judged. We conclude that RNA, while inferior to extant proteins in most, but not all, functional respects, may be more versatile than proteins, performing a wider range of elementary biological functions at a tolerable level. Inspection of the functional models and various RNA structures uncovers several surprising ways in which the nucleobases can conspire to afford chemical catalysis and evolvability. These models support the plausibility that RNA, or a closely related informational biopolymer, could serve as the basis for a fairly simple form of life.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 40 , Issue 1 , February 2007 , pp. 55 - 85
Copyright
Copyright © Cambridge University Press 2007

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