Computation through DNAComputation through DNA

Jason MeadorJason Meador

GST 400 – What is Thought?GST 400 – What is Thought?

April 24, 2006April 24, 2006

How does Computation relate to How does Computation relate to Biological Systems?Biological Systems?

DNA Replication, DNA Replication, Transcription, Transcription, Translation and the Translation and the Turing machineTuring machine

Computing with DNAComputing with DNA

Computational Computational BiologyBiology

Turing Machine / DNATuring Machine / DNA

Turing machine …Turing machine …– Has an infinite one-Has an infinite one-

dimensional tape divided into dimensional tape divided into cells and operates in a cells and operates in a number of finite states.number of finite states.

– The tape is read in some The tape is read in some consistent manner, left to rightconsistent manner, left to right

– Each cell on the input tape will Each cell on the input tape will generate a corresponding generate a corresponding output according to the output according to the machine’s read-write headmachine’s read-write head

– Process continues until a Process continues until a statement results in a halting statement results in a halting of the machineof the machine

DNA/RNA…DNA/RNA…– Has a infinite one-dimensional Has a infinite one-dimensional

tape divided into cells tape divided into cells (nucleotides) and operates in (nucleotides) and operates in a number of finite (4) states.a number of finite (4) states.

– The tape is read in a The tape is read in a consistent manner 5’ – 3’ consistent manner 5’ – 3’

– Output is determined by the Output is determined by the corresponding complimentary corresponding complimentary base (A-T) and (C-G) (A-U) for base (A-T) and (C-G) (A-U) for RNARNA

– Translation of RNA into Translation of RNA into protein continues until the protein continues until the STOP codons are STOP codons are encountered (UAA, UAG, encountered (UAA, UAG, UGA)UGA)

The Genetic Code “Look-up Table”The Genetic Code “Look-up Table”

ApplicationsApplications

DNA computers have previously been DNA computers have previously been used to perform computational problems used to perform computational problems with up to 9 variables, selecting the correct with up to 9 variables, selecting the correct answer from 512 possibilities.answer from 512 possibilities.

Currently DNA computers can perform Currently DNA computers can perform computational problems with up to 20 computational problems with up to 20 variables resulting in 2²º or 1,048,576 variables resulting in 2²º or 1,048,576 possible solutions. possible solutions.

Computational BiologyComputational Biology

Molecular Turing Molecular Turing machines work as machines work as molecular physicians to molecular physicians to make diagnoses, make diagnoses, prescribe an antibiotic, prescribe an antibiotic, spot defective DNA/RNA spot defective DNA/RNA and create replacements.and create replacements.

Create algorithms used Create algorithms used for diagnosis of similar for diagnosis of similar illnessesillnesses

SummarySummary

DNA works as a molecular Turing machineDNA works as a molecular Turing machine

DNA is not only the “book” about the DNA is not only the “book” about the organism but a “book” about the organism but a “book” about the organism’s environment in which it lives.organism’s environment in which it lives.

Computational abilities of DNA and Computational abilities of DNA and applications.applications.

ReferencesReferences

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