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CALTECH CS 191A - Evolutionary origins and directed evolution of RNA

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The International Journal of Biochemistry & Cell Biology 41 (2009) 254–265Contents lists available at ScienceDirectThe International Journal of Biochemistry& Cell Biologyjournal homepage: www.elsevier.com/locate/biocelReviewEvolutionary origins and directed evolution of RNAAndrew D. Ellington∗, Xi Chen, Michael Robertson, Angel SyrettDepartment of Chemistry and Biochemistry, Institute for Cell and Molecular Biology,University of Texas at Austin, Austin, TX 78712, United Statesarticle infoArticle history:Available online 19 August 2008Keywords:OriginsIn vitro selectionSELEXAptamerRibozymePolymeraseTranslationFitness landscapeabstractIn vitro selection experiments show first and foremost that it is possible that functional nucleic acids canarise from random sequence libraries. Indeed, even simple sequence and structural motifs can prove tobe robust binding species and catalysts, indicating that it may have been possible to transition from eventhe earliest self-replicators to a nascent, RNA-catalyzed metabolism. Because of the diversity of aptamersand ribozymes that can be selected, it is possible to construct a ‘fossil record’ of the evolution of the RNAworld, with in vitro selected catalysts filling in as doppelgangers for molecules long gone. In this way aplausible pathway from simple oligonucleotide replicators to genomic polymerases can be imagined, ascan a pathway from basal ribozyme activities to the ribosome. Most importantly, though, in vitro selectionexperiments can give a true and quantitative idea of the likelihood that these scenarios could have playedout in the RNA world. Simple binding species and catalysts could have evolved into other structures andfunctions. As replicating sequences grew longer, new, more complex functions or faster catalytic activitiescould have been accessed. Some activities may have been isolated in sequence space, but others couldhave been approached along large, interconnected neutral networks. As the number, type, and lengthof ribozymes increased, RNA genomes would have evolved and eventually there would have been noarea in a fitness landscape that would have been inaccessible. Self-replication would have inexorably ledto life.© 2008 Elsevier Ltd. All rights reserved.Contents1. Background on the RNA world hypothesis and in vitro selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2552. What in vitro selection tells us about functional RNAs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2552.1. Binding species .............................................................................................................................. 2552.2. Catalysts ................................................................................................................................ . . . . . 2552.3. Cofactors................................................................................................................................ . . . . . 2552.4. Structural complexity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2573. Doppelgangers for recapitulating the RNA world . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2583.1. Recapitulation of the evolution of self-replication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2583.2. Recapitulation of the development of translation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2614. What in vitro selection reveals about fitness landscapes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2624.1. Tyranny of short motifs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2624.2. Diversity in sequence space . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . …


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