DNA Sequencing Sean Downes

DNA – Sequencing History Walter Fiers at the University of Ghent (Ghent, Belgium), between 1972 and ,Walter Gilbert and Allan Maxam at Harvard reported the sequence of 24 basepairs. The chain-termination method developed by Frederick Sanger at the University of Cambridge, in England in In 1976–1977, Allan Maxam and Walter Gilbert developed a DNA sequencing method based on chemical modification of DNA and subsequent cleavage at specific bases.

DNA - What is it? (n) deoxyribonucleic acid, desoxyribonucleic acid, DNA (biochemistry) a long linear polymer found in the nucleus of a cell and formed from nucleotides and shaped like a double helix; associated with the transmission of genetic information

DNA – What is it? A DNA chain is basically like a twisted stepladder made from 2 half-ladders, where each step is made of a pair of complimentary halves. The “half-steps” are called bases and they are adenine, guanine, thymine, and cytosine, which are abbreviated as A, G, T, and C. Chemically, A and G are purines, and C and T are pyrimidines. For a good fit, a pyrimidine must pair with a purine; in DNA, A bonds with T, and G bonds with C. These are what are referred to as DNA base pairs.

DNA – What does it do? Chains of DNA bases form the 20 different amino acids which make up all proteins.

DNA – 4 = 20 how...? Since there are only 4 bases there must be combinations of 3 of these, called codons, to make 20 amino acids. Why 3? Because 4 2 only makes 16 whereas 4 3 makes 64 (>20). It turns out that more than one codon may make the same amino acid making the code degenerate, but not ambiguous.

DNA - Sequencing Since DNA forms the amino acids which produce the proteins that (chained together) make up cell structure, finding out how the proteins group to form cells can potentially tell us how it happened, happens, and will happen. This provides us the opportunity to explore the origins of life, find the causes for certain defects and diseases, and hopefully the possibility of finding treatments or even cures.

DNA – Mapping Sequences A complete strand of DNA in a chromosome may contain hundreds of millions of base pairs ( the human genome contains approximately 30,000 genes consisting of roughly 3 billion base pairs) so it is broken up, using various methods, into smaller chains terminated by known “start” and “stop” codons. These chains, or strings, are then analyzed for their protein sequences (→ amino acid sequences → codon sequences).

DNA – Mapping Sequences By looking at protein chains that make up defective cells and comparing them to healthy cells, “defective” genes causes by mutated or missing sequences in the DNA that contribute to certain diseases are being found. So far genetic markers for only a small number of rare conditions have been found.

DNA – and Finite State Automata Hidden Markov Models are used to describe protein sequence families.

DNA – Where to from here? Considering the sheer volume of data generated during DNA sequencing and combinations of

Sources Automata, Computability, and ComplexityTheory and Applications – Elaine Rich