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• 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
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The use of PCR in forensic science
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POLYMERASE CHAIN
REACTION
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• 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
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Genomic DNA library & cDNA library
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Production of large amounts of a protein by cloning the protein-coding DNA sequence (gene) in a plasmid expression vector
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DNA Chips
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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
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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?
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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
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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
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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?
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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.