RNA Chemistry and the RNA World

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The presence of RNA at the core of the ribosome, the extensive use of nucleotide cofactors, and the synthesis of DNA and some amino acids from RNA precursors suggests that RNA was once the dominant catalytic and genetic polymer early in the evolution of life. This 'RNA World' hypothesis assumes that RNA is capable of all the reactions required to maintain and evolve a 'ribo-organism'. One of my laboratories long term objectives is to select and evolve an RNA replicase ribozyme capable of sustaining RNA based evolution in the laboratory. Such a system could be called 'alive' and would marry the underlying simplicity of chemistry to the complexity of biology. Identifying the minimal complexity required to produce an RNA replicace would inform as never before about the difficulties faced on the early Earth in transitioning from an abiotic to biotic world.** Aims I&II: Towards an RNA replicase ribozyme: We will use conventional and emulsion based in vitro selection methodologies to isolate superior RNA polymerase ribozymes that are highly processive. The current state of the art polymerase ribozyme is capable of rapid phosphodiester bond formation, but is nearly unable to appropriately hold the primer-template substrate it extends. Overcoming this central problem has the potential to increase polymerization rates by factors of ten or more and offers the prospect of extending a template by hundreds of nucleotides in a time scale measured in hours - an exciting prospect if realized!** Aim II: Translocation mechanism & homopolymer polymerases: We will select for polymerase ribozymes that processively incorporate poly(A) tails onto the end of an RNA primer. Such polymerases are interesting as the processive synthesis of a long homopolymer requires a translocation mechanism that, after the incorporation of a nucleotide, must reset the polymerase complex to look exactly like the initial state so as to allow iterative polymerization. Such a mechanism ultimately could prove very useful in displacing a non-template strand during RNA replication and thus play an important role in developing a replicase ribozyme.********