This report will focus on a combined treatment of the fields of RNA evolution and DNA computers. Using examples of in vitro selection of functional RNA molecules from large pools of random sequences, I show that these experiments can be viewed as an "RNA computer", in the language of DNA computation. By applying a strict set of criteria to a pool of heterogeneous DNA or RNA sequences, both types of experiments find sequences that contain solutions to hard molecular computational problems. These can even be nondigital problems that an electronic computer cannot solve. For example, a problem I addressed using a pool of RNA molecules was one of catalysis, or the ability to ligate a small substrate RNA molecule to itself. In vitro evolution searches for the best solution or class of solutions contained within a large library of approximately 10^15 unique sequences. The advantage of these "molecular computers" is their ability to examine and eliminate billions of possible solutions in parallel. We also describe an example of a cellular paradigm for RNA-based computing: RNA editing.
From the Second Annual DIMACS Meeting on DNA Based Computers, June 10-12, 1996
and the DIMACS Special Focus on DNA Computing.
Paper Available at: ftp://dimacs.rutgers.edu/pub/dimacs/TechnicalReports/TechReports/1997/97-83.ps.gz