1. Computation through DNA Jason Meador GST 400 – What is Thought? April 24, 2006

2. How does Computation relate to Biological Systems? DNA Replication, Transcription, Translation and the Turing machine Computing with DNA Computational Biology

3. Turing Machine / DNA Turing machine … –Has an infinite one- dimensional tape divided into cells and operates in a number of finite states. –The tape is read in some consistent manner, left to right –Each cell on the input tape will generate a corresponding output according to the machine’s read-write head –Process continues until a statement results in a halting of the machine DNA/RNA… –Has a infinite one-dimensional tape divided into cells (nucleotides) and operates in a number of finite (4) states. –The tape is read in a consistent manner 5’ – 3’ –Output is determined by the corresponding complimentary base (A-T) and (C-G) (A-U) for RNA –Translation of RNA into protein continues until the STOP codons are encountered (UAA, UAG, UGA)

4. The Genetic Code “Look-up Table”

5. Applications DNA computers have previously been used to perform computational problems with up to 9 variables, selecting the correct answer from 512 possibilities. Currently DNA computers can perform computational problems with up to 20 variables resulting in 2²º or 1,048,576 possible solutions.

6. Computational Biology Molecular Turing machines work as molecular physicians to make diagnoses, prescribe an antibiotic, spot defective DNA/RNA and create replacements. Create algorithms used for diagnosis of similar illnesses

7. Summary DNA works as a molecular Turing machine DNA is not only the “book” about the organism but a “book” about the organism’s environment in which it lives. Computational abilities of DNA and applications.

8. References Adami, C., Ofria, C., Collier, T.C. Evolution of biological complexity. PNAS (Proceedings of the National Academy of Sciences of the United States of America). Vol. 97, Issue 9, pp. 4463-4468. April 25, 2000. Adleman, L. Molecular computation of solutions to combinatorial problems. Science. Vol. 266 1994. pp. 1021-1024. Baum, E. What is Thought? Massachusetts Institute of Technology. 2004. 478 pages. Gershenzon, N. I., Stormo, G. D., Ioshikhes, I.P. Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites. Nucleic Acids Research. Vol. 33, No. 7. April 22, 2005. pp. 2290-2301. Pennicott, K. ‘DNA computer’ cracks code. PhysicsWeb. March 2002. Accessed online March 27, 2006 at http://physicsweb.org/articles/news/6/3/11. Tobin, A., Morel, R. Asking About Cells. Harcourt Brace & Company. 1997. Wong, H. W. Computational Molecular Biology. Journal of the American Statistical Association. Vol. 95, No. 449. March 2000. pp. 322-326.