Molecular Computation: RNA Solutions to Chess Problems Proceedings of the National Academy of Science (PNAS), vol. 97, no. 4, pp , February 15, Cho, Dong-Yeon

Abstract We introduce RNA as a molecule for computation to present a general approach for the solution of the famous SAT problems.  Using a combination of a binary RNA library and ribonuclease (RNase) H digestion, we developed a destructive algorithm that would hydrolyze RNA strands that did not fit the constraints of a chosen problem.

Knight Problem Definition  What configurations of knights can one place on an n  n chess board such that no knights is attacking any other knight on the board.  ((  h  f)  a)  ((  g  i)  b)  ((  d  h)  c)  ((  c  i)  d)  ((  a  g)   f)  ((  b  f)  g)  ((  a  c)  h)  ((  d  b)  i)  This is simplifies to ((  h  f)  a)  ((  g  i)  b)  ((  d  h)  c)  ((  c  i)  d)  ((  a  g)   f).

Design and Synthesis of a 10-Bit DNA Library Template Important criteria to design of the combinatorial pool  Each of the bit encodings must be fundamentally different. (Maximize the Hamming Distances)  The strands were biased to avoid secondary structure so that each bit position would be equally accessible to the enzymes and oligonucleotides that operate on the pool molecules.  The strands were controlled to avoid hybridization to themselves or to any other library strands by more than seven consecutive base pairs.

Synthesis

Algorithm for Solving the Knight Problem Using the RNA Library

Methods of “ Readout ”

RNA Solutions