Writing Information into DNA

The time is approaching when information can be written into DNA. This tutorial work surveys the methods for designing code words using DNA, and proposes a simple code that avoids unwanted hybridization in the presence of shift and concatenation of DNA words and their complements.

[1]  Solomon W. Golomb,et al.  A New Result on Comma-Free Codes of Even Word-Length , 1987, Canadian Journal of Mathematics.

[2]  F. MacWilliams,et al.  The Theory of Error-Correcting Codes , 1977 .

[3]  D. Fisher The Eighth Day of Creation: Makers of the Revolution in Biology , 1979 .

[4]  Erik Winfree,et al.  Universal computation via self-assembly of DNA: Some theory and experiments , 1996, DNA Based Computers.

[5]  Frank Ruskey,et al.  Fast Algorithms to Generate Necklaces, Unlabeled Necklaces, and Irreducible Polynomials over GF(2) , 2000, J. Algorithms.

[6]  Rusell Deaton,et al.  Encoding Genomes for DNA Computing The Molecular Computing Group , 2001 .

[7]  J. J. Stiffler,et al.  Theory of synchronous communications , 1971 .

[8]  Clifford R. Johnson,et al.  Solution of a 20-Variable 3-SAT Problem on a DNA Computer , 2002, Science.

[9]  A. Condon,et al.  Demonstration of a word design strategy for DNA computing on surfaces. , 1997, Nucleic acids research.

[10]  Michael Zuker,et al.  Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..

[11]  Anne Condon,et al.  Stochastic Local Search Algorithms for DNA Word Design , 2002, DNA.

[12]  Jack J. Stiffler,et al.  Comma-free error-correcting codes , 1965, IEEE Trans. Inf. Theory.

[13]  J. SantaLucia,et al.  Thermodynamics of internal C.T mismatches in DNA. , 1998, Nucleic acids research.

[14]  L F Landweber,et al.  Molecular computation: RNA solutions to chess problems , 2000, Proc. Natl. Acad. Sci. USA.

[15]  H. Blöcker,et al.  Predicting DNA duplex stability from the base sequence. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Richard J. Lipton,et al.  DNA Based Computers , 1996 .

[17]  S. Golomb,et al.  Comma-Free Codes , 1958, Canadian Journal of Mathematics.

[18]  Masami Hagiya,et al.  Successive State Transitions with I/O Interface by Molecules , 2000, DNA Computing.

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

[20]  E. Shapiro,et al.  Programmable and autonomous computing machine made of biomolecules , 2001, Nature.

[21]  David I. Lewin,et al.  DNA computing , 2002, Comput. Sci. Eng..

[22]  R. Corn,et al.  DNA word design strategy for creating sets of non-interacting oligonucleotides for DNA microarrays , 2002 .

[23]  Pak Chung Wong,et al.  Organic data memory using the DNA approach , 2003, CACM.

[24]  E. Vermaas,et al.  In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Max H. Garzon,et al.  Good encodings for DNA-based solutions to combinatorial problems , 1996, DNA Based Computers.

[26]  R. Lerner,et al.  Encoded combinatorial chemistry. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Richard M. Karp,et al.  Universal DNA Tag Systems: A Combinatorial Design Scheme , 2000, J. Comput. Biol..