The Polymerase Chain Reaction • 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
DNA Cloning • 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
Production of large amounts of a protein by cloning the protein -coding DNA sequence (gene) in a plasmid expression vector
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.