• The small sample of DNA serves as template for DNA polymerase

• Make complementary primers • Add primers in more than 1000-fold excess • Heat to make ssDNA, then cool • Run DNA polymerase (usually Taq) • Repeat heating, cooling, polymerase cycle

The Polymerase Chain Reaction

The use of PCR in forensic science

POLYMERASE CHAIN

REACTION

• After cleavage of a plasmid (cloning vector) with a restriction enzyme, a foreign DNA fragment can be inserted

• Ends of the plasmid/fragment are closed to form a "recombinant plasmid"

• Plasmid can replicate when placed in a suitable bacterial host

DNA Cloning

Genomic DNA library & cDNA library

Production of large amounts of a protein by cloning the protein-coding DNA sequence (gene) in a plasmid expression vector

DNA Chips

What are the challenges?

• Error: Molecular operations are not perfect.• Reversible and Irreversible Error• Efficiency: How many molecules

contribute?• Encoding problem in molecules is difficult• Scaling to larger problems

What are the challenges for Computer Science?

• Discover problems DNA Computers are good at– Messy reactions as positive– Evolvable, not programmable

• Characterize complexity for DNA computations with bounded resources

• New notions of what a “computation” is?

What are the challenges for molecular biology?

• Develop computation-specific protocols• Better understanding of basic mechanisms

and properties• Better characterization of processes• Measures of reliability and efficiency• Advanced understanding of biomolecules

other than DNA and RNA

What developments can we expect in the near-term?

• Increased use of molecules other than DNA• Evolutionary approaches• Continued impact by advances in molecular

biology• Some impact on molecular biology by DNA

computation• Increased error avoidance and detection

What are the long-term prospects?

• Cross-fertilization among evolutionary computing, DNA computing, molecular biology, and computation biology

• Niche uses of DNA computers for problems that are difficult for electronic computers

• Increased movement into exploring the connection between life and computation?

Where can I learn more?• Web Sites:

• http://www.wi.leidenuniv.nl/~jdassen/dna.html• http://dope.caltech.edu/winfree/DNA.html• http://www.msci.memphis.edu/~garzonm/bmc.html• (Conrad) http://www.cs.wayne.edu/biolab/index.html

• DIMACS Proceedings: DNA Based Computers I (#27), II (#44), III (#48), IV (Special Issue of Biosystems), V (MIT, June 1999)• Other: Genetic Programming 1 (Stanford, 1997), Genetic Programming 2 (Wisconsin-Madison, 1998), IEEE International Conference on Evolutionary Computation (Indianapolis, 1997)• G. Paun (ed.), Computing with Biomolecules: Theory and Experiment, Springer-Verlag, Singapore 1998.• “DNA Computing: A Review,” Fundamenta Informaticae, 35, 231-245.