What makes DNA Computing possible?

1. What makes DNA Computing possible? • Great advances in molecular biology • PCR (Polymerase Chain Reaction) • DNA Selection by affinity • DNA Filtering • DNA Gel Electroforesis • DNA Denaturation Renaturation • DNA Restriction Enzymes • DNA Sequencing • Ability to produce massive numbers of DNA molecules with specified sequence and size

2. What is a typical methodology of DNA Computing? • Encoding: Map problem instance onto set of biological molecules and molecular biology protocols • Molecular Operations: Let molecules react to form potential solutions • Extraction/Detection: Use protocols to extract result in molecular form

3. What are the basics from molecular biology that I need to know to understand DNA computing?

4. PHYSICAL STRUCTURE OF DNA

5. 3’ OH 5’ C Minor Groove 34 Å 5’ 3’ Sugar-Phosphate Backbone Major Groove 5’ 3’ Nitrogenous Base C 5’ 3’ 0H Central Axis 20 Å

7. (-) (+) (+) (-) to Sugar-Phosphate Backbone (+) (-) to Sugar-Phosphate Backbone Guanine Cytosine Hydrogen Bond INTER-STRAND HYDROGEN BONDING (+) (-) (-) (+) to Sugar-Phosphate Backbone to Sugar-Phosphate Backbone Adenine Thymine

10. STRAND HYBRIDIZATION

14. Enzymes of Molecular Biology • DNA Polymerase • DNA Ligase, Helicase, Topoisomerase • DNA Repair Ezymes • DNA Recombinase • Reverse Transcriptase • Restriction Enzymes • Nuclease

15. DNA Replication • DNA is a double-helical molecule • Each strand of the helix must be copied in complementary fashion by DNA polymerase • Each strand is a template for copying • DNA polymerase requires template and primer • Primer: an oligonucleotide that pairs with the end of the template molecule to form dsDNA • DNA polymerases add nucleotides in 5'-3' direction

17. DNA Polymerase

18. DNA Ligase   ’ ’   ’ ’ ’ ’ Ligase Joins 5' phosphate to 3' hydroxyl

20. DNA Helicase

21. DNA Topoisomerase

22. DNA Damage Repair Enzymes

23. DNA Recombination Enzymes

24. Integrase

25. Reverse Transcriptase

26. Restriction Enzymes • Bacteria have learned to "restrict" the possibility of attack from foreign DNA by means of "restriction enzymes" • Type II and III restriction enzymes cleave DNA chains at selected sites • Enzymes may recognize 4, 6 or more bases in selecting sites for cleavage • An enzyme that recognizes a 6-base sequence is a "six-cutter"

27. 5’ P - - OH 3’ EcoRI - P 5’ 3’ OH - HindIII AluI HaeIII RESTRICTION ENDONUCLEASES

28. Exo-Nuclease

29. Recombinant DNA Technology • Cleavage DNA at specific sites by restriction enzymes,which greatly • facilitates the isolation and manipulation of individual DNA. • Rapidsequencing of all the nucleotides in a purified DNA fragment, • which makes it possible to determine the boundaries of a gene and the • amino acid sequence it encodes. • Nucleic acid hybridization, which makes it possible to find a specific • sequence of DNA or RNA. • DNA cloning, whereby a single DNA molecule can be copied to • generate billions of identical molecules. • DNA engineering, by which DNA sequences are altered to make • Modified versions of genes, which are reinserted back into cell.

30. 5’ P - - OH 3’ EcoRI - P 5’ 3’ OH - HindIII AluI HaeIII RESTRICTION ENDONUCLEASES

31. Electrode Samples Slower Gel Buffer Electrode Faster GEL ELECTROPHORESIS – Separation of DNA fragments

32. DNA molecules can be radioactively labeled

33. DNA Sequencing