title: Molecular computation: RNA solutions to chess problems.
abstract: We have expanded the field of "DNA computers" to RNA and present a general approach for the solution of satisfiability problems. As an example, we consider a variant of the "Knight problem," which asks generally what configurations of knights can one place on an n x n chess board such that no knight is attacking any other knight on the board. Using specific ribonuclease digestion to manipulate strands of a 10-bit binary RNA library, we developed a molecular algorithm and applied it to a 3 x 3 chessboard as a 9-bit instance of this problem. Here, the nine spaces on the board correspond to nine "bits" or placeholders in a combinatorial RNA library. We recovered a set of "winning" molecules that describe solutions to this problem.
authors.affiliation: Department of Ecology, Princeton University, Princeton, NJ 08544, USA.
authors.forename: D
authors.initials: D
authors.lastname: Faulhammer
authors.forename: A R
authors.initials: AR
authors.lastname: Cukras
authors.forename: R J
authors.initials: RJ
authors.lastname: Lipton
authors.forename: L F
authors.initials: LF
authors.lastname: Landweber
mesh_terms: D000465:Algorithms; D020650:Combinatorial Chemistry Techniques; D019295:Computational Biology; D004247:DNA / Q000737:chemistry*; D005717:Games, Experimental; D009838:Oligodeoxyribonucleotides; D016133:Polymerase Chain Reaction; D012313:RNA / Q000737:chemistry*; D012260:Ribonucleases
chemical_list: D009838:Oligodeoxyribonucleotides; D012313:RNA; D004247:DNA; D012260:Ribonucleases