DNA as a vehicle for the self-assembly model of computing.

A DNA version of the self-assembly model of computing, feasible using currently available laboratory techniques, is proposed. Input signals are coded into unmethylated and methylated oligonucleotides which then hybridize with a backbone that contains complementary sequences. Different input signal patterns are thus represented as DNA duplexes with distinctly different conformational dynamics, in particular different equilibria of B and Z DNA. The pattern classification activity of the system is mediated by the interactions that lead to the secondary structural organization. Circular dichroism may be used for readout.

[1]  Liberman Ea,et al.  [Letter: Molecular computer. II. Formal description (system of operators)]. , 1973 .

[2]  Michael Conrad,et al.  On design principles for a molecular computer , 1985, CACM.

[3]  Klaus-Peter Zauner,et al.  Molecular computing: steps towards integration , 1995 .

[4]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[5]  Klaus-Peter Zauner,et al.  Parallel Computing with DNA: Toward the Anti-Universal Machine , 1996, PPSN.

[6]  V Sasisekharan Left-handed DNA duplexes. , 1983, Cold Spring Harbor symposia on quantitative biology.

[7]  Adrian J. Harwood,et al.  Basic DNA and RNA protocols , 1996 .

[8]  Gerald F. Joyce,et al.  Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA , 1990, Nature.

[9]  G. F. Joyce RNA evolution and the origins of life , 1989, Nature.

[10]  Michael Conrad Molecular computing: the lock-key paradigm , 1992, Computer.

[11]  W Zacharias,et al.  Methylation of cytosine influences the DNA structure. , 1993, EXS.

[12]  John M. Walker,et al.  Molecular Biology and Biotechnology , 1988 .

[13]  Erik Winfree,et al.  A sticker based model for DNA computation , 1996, DNA Based Computers.

[14]  Michael Conrad,et al.  Molecular computing as a link between biological and physical theory , 1982 .

[15]  Hans-Paul Schwefel,et al.  Parallel Problem Solving from Nature — PPSN IV , 1996, Lecture Notes in Computer Science.

[16]  J. P. Jost,et al.  DNA Methylation: Molecular Biology and Biological Significance , 1993 .

[17]  Rolf Herken,et al.  The Universal Turing Machine: A Half-Century Survey , 1992 .

[18]  Michael Conrad,et al.  The price of programmability , 1988 .

[19]  Alfred Nordheim,et al.  THE CHEMISTRY AND BIOLOGY OF LEFT-HANDED Z-DNA , 1984 .