The chemical versatility of RNA

Hiller, David A.; Strobel, Scott A.

doi:10.1098/rstb.2011.0143

Cited by 29 publications

(25 citation statements)

References 60 publications

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“…Although RNA in extant biology is seen to catalyze only RNA cutting and ligation along with peptidyl transfer (within the ribosome), a wide variety of chemical transformations can be catalyzed by ribozymes selected in vitro (Cech 2002;Hiller and Strobel 2011;Robertson and Ellington 2000;Sczepanski and Joyce 2014;Seelig and Jaschke 1999;Silverman and Begley 2007). Sustained experimental efforts have attempted to show that RNA is capable of self-replication (Attwater et al 2013;Sczepanski and Joyce 2014;Shechner and Bartel 2011;Vaidya et al 2012;Wochner et al 2011).…”

Section: Support For An Rna Worldmentioning

confidence: 99%

The Ribosome Challenge to the RNA World

2015

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An RNA World that predated the modern world of polypeptide and polynucleotide is one of the most widely accepted models in origin of life research. In this model, the translation system shepherded the RNA World into the extant biology of DNA, RNA, and protein. Here, we examine the RNA World Hypothesis in the context of increasingly detailed information available about the origins, evolution, functions, and mechanisms of the translation system. We conclude that the translation system presents critical challenges to RNA World Hypotheses. Firstly, a timeline of the RNA World is problematic when the ribosome is incorporated. The mechanism of peptidyl transfer of the ribosome appears distinct from evolved enzymes, signaling origins in a chemical rather than biological milieu. Secondly, we have no evidence that the basic biochemical toolset of life is subject to substantive change by Darwinian evolution, as required for the transition from the RNA world to extant biology. Thirdly, we do not see specific evidence for biological takeover of ribozyme function by protein enzymes. Finally, we can find no basis for preservation of the ribosome as ribozyme or the universality of translation, if it were the case that other information transducing ribozymes, such as ribozyme polymerases, were replaced by protein analogs and erased from the phylogenetic record. We suggest that an updated model of the RNA World should address the current state of knowledge of the translation system.

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Section: Support For An Rna Worldmentioning

confidence: 99%

The Ribosome Challenge to the RNA World

2015

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“…Despite the limited complexity of the RNA building blocks (the four canonical ribonucleotides), RNA enzymes and aptamers are capable of efficiently performing a wide range of biochemical functions (for review, see Cochrane and Strobel 2008a;Hiller and Strobel 2011). Small self-cleaving ribozymes promote acid-base-catalyzed autolytic reactions at rates comparable to protein enzymes (Nakano et al 2000;Bevilacqua et al 2004;Cochrane and Strobel 2008a).…”

Section: Biochemical Functions and Mechanisms Of Chemical Diversificamentioning

confidence: 99%

Role of tautomerism in RNA biochemistry

Singh

Fedeles

Essigmann

2014

RNA

121

116

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Heterocyclic nucleic acid bases and their analogs can adopt multiple tautomeric forms due to the presence of multiple solventexchangeable protons. In DNA, spontaneous formation of minor tautomers has been speculated to contribute to mutagenic mispairings during DNA replication, whereas in RNA, minor tautomeric forms have been proposed to enhance the structural and functional diversity of RNA enzymes and aptamers. This review summarizes the role of tautomerism in RNA biochemistry, specifically focusing on the role of tautomerism in catalysis of small self-cleaving ribozymes and recognition of ligand analogs by riboswitches. Considering that the presence of multiple tautomers of nucleic acid bases is a rare occurrence, and that tautomers typically interconvert on a fast time scale, methods for studying rapid tautomerism in the context of nucleic acids under biologically relevant aqueous conditions are also discussed.

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“…They are no longer viewed as molecules whose key function is only to code the genomic information of DNA in the process of generation of the primary sequence of proteins. They are now recognized an essential part for regulation of protein function and catalysis [1,2] control of gene expression [3][4][5][6][7] and crucial players in the transcription and translation process [8][9][10]. Recent discovery of a large number of small non coding RNA molecules called micro RNAs further substantiated the crucial roles played by RNA molecules in various life processes inside the cells [11][12][13][14][15][16][17][18][19][20].…”

Section: Introductionmentioning

confidence: 99%