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Catalytic RNAs

Gene regulatory RNAs

RNA in signal transduction

RNA-protein interactions

RNA analogs of GFP

Small molecule recognition by RNA

RNA folding and dynamics

Molecular evolution

Methods

 

Ferré-D'Amaré Lab Research > Molecular evolution

The process of evolution can readily be studied in vitro with RNA because this nucleic acid can function both as a repository of genetic information and as a catalyst. We have developed methodology that combines in vitro selection of RNA with next-generation DNA sequencing technology that allows the rapid analysis of the fitness landscape of RNAs. This approach can be extended to the study of clinically important biological systems in which diversity is generated, for instance the immune system and virus-host genetic interactions. Our structural and biochemical studies also have resulted in the comparison of mechanistic strategies employed by naturally an artificially evolved RNAs, and of the delineation of the evolutionary history of RNA-modifying enzymes.

• Lau, M.W.L & Ferré-D'Amaré, A.R. An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence. Nature Chemical Biology 9, 805-810 (2013). [abstract]

• Pitt, J.N. & Ferré-D'Amaré, A.R. Rapid construction of empirical RNA fitness landscapes. Science 330, 376-379 (2010). [abstract]

• Pitt, J.N. & Ferré-D'Amaré, A.R. Structure-guided engineering of the regioselectivity of RNA ligase ribozymes. J. Am. Chem. Soc. 131, 3532-3540 (2009). [abstract]

• Xiao, H., Murakami, E., Suga, H. & Ferré-D'Amaré, A.R. Structural basis for specific tRNA aminoacylation by a small in vitro selected ribozyme. Nature 454, 358-361 (2008). [abstract]

• Xiao, H., Edwards, T.E. & Ferré-D'Amaré, A.R. Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch. Chem. Biol. 15, 1125-1137 (2008). [abstract]