Molecular Computation: RNA Solutions to Chess Problems

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Molecular Computation RNA Solutions to Chess
Problems

• Proceedings of the National Academy of Science
  (PNAS),
• vol. 97, no. 4, pp. 1385-1389, February 15, 2000.
• Cho, Dong-Yeon

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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.

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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).

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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.

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• Synthesis

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Algorithm for Solving the Knight Problem Using
the RNA Library
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Methods of Readout
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RNA Solutions