Molecular Computation RNA solutions to chess problems国际象棋问题的分子计算方法.pptVIP

Molecular Computation : RNA solutions to chess problems Dirk Faulhammer, Anthony R. Cukras, Richard J. Lipton, and Laura F. Landweber PNAS 2000; vol. 97: no. 4: 1385-1389  2004.11.20 Summarized by Seong Hwan Kim Table of Contents “Knight Problem” Key features Preparation before experiment Experiment Result Discussion Knight Problem in Chess Game(1/2) ‘Knight ’ in chess game ? A piece in the game, depicted as a horse’s head Plays and captures alternatively on white and black square “Jumping” available ? ignore any pieces in its moving path Powerful at the center position rather than edge Knight Problem in Chess Game(2/2) ‘Knight Problem ’ ? Knight tour problem Hamiltonian path problem in graph theory a variant of knight problem Asking a configuration of knights on a n x n chess board such as ‘no knight is attacking any other knight on the board ’ Key features Applying molecular computation algorithm To a 3x3 chessboard problem Using RNA library Searching RNA strands that fit the constraints Destructive algorithm with RNase H Instead of conventional hybridization extraction Hydrolyze RNA strands inappropriate for the solution constraints Using hybridization of RNA and complementary bit DNA oligonucleotides as a hydrolysis marking Preparation(1/6) : problem expression Knight problem expression 9 positions of 3x3 chessboard ‘no knight is attacking any other knight on the board ’ Preparation(2/6) : solution expression RNA library Made through synthesis of DNA “Half Libraries” A RNA strand means 10-bit solution Contain 1024 different strands 10-bit library for a instance of a 9-bit problem Ignore any position that computes less reliably Preparation(3/6) : Sequence Design 3 criteria 1) different bit encodings Maximizing Hamming Distances between different strands as well as between different parts of individual strand = 5 matches over a 20-nt window, both within and between all 210 possible strands Average melting temperat