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Definition
Rediscovering
Biology
Biology is now the study of information stored in DNA - strings
of four letters: A, T, G, and C for the bases adenine, thymine, guanine and cytosine
- and of the transformations that information undergoes in the cell. There were
mathematics here? DNA polymerase is the king of enzymes - the maker of life. Under
appropriate conditions, given a strand of DNA, DNA polymerase produces a second
"Watson-Crick" complementary strand, in which every C is replaced by
a G, every G by a C, every A by a T and every T by an A. For example, given a
molecule with the sequence CATGTC, DNA polymerase will produce a new molecule
with the sequence GTACAG. The polymerase enables DNA to reproduce, which in turn
allows cells to reproduce and ultimately allows you to reproduce. For a strict
reductionist, the replication of DNA polymerase is what life is is all about.
DNA
polymerase is an amazing little nanomachine, a single molecule that "hops"
onto a strand of DNA and slides along it, "reading " each base it passes
and "writing" its complement onto a new, growing DNA strand. This was
in similarity to the Turing machine (toy computer) suitable for mathematical investigation
on the study of the notion of "computability" which preceded the advent
of actual computers by about a decade and led to some of the major mathematical
results of the 20th century. The most striking was that Turing's toy computer
had turned out to be universal and could be programmed to compute anything that
was computable at all. In other words, one could programme a Turing machine to
produce Watson-Crick complementary strings, factor numbers, play chess and so
on.
To build a DNA computer,
tools were essential such as (1) Watson-Crick pairing (2) polymerases (3) Ligases
(4) Nucleases (5)Gel electrophoresis, and (6) DNA synthesis.
To build a computer,
only two things are really necessary - a method of sorting information and a few
simple operations for acting on that information.
DNA
Computer Building
The
Unrestricted model of DNA computing:
To build a DNA computer, the tools
were essentially the following - 1. Watson-Crick
pairing - every strand of DNA has its Watson-Crick complement.
2. Polymerases
- to copy information from one molecule into another.
3. Ligases - to bind
molecules together.
4. Nucleases -to cut nucleic acids.
5. Gel electrophoresis
- a process to separate DNA by length
6. DNA synthesis - to write a DNA sequence
on a piece of paper.
Since Adleman's original experiment, several methods
to reduce error and improve efficiency have been developed. The Restricted model
of DNA computing solves several physical problems with the Unrestricted model.
The Restricted model simplifies the physical obstructions in exchange for some
additional logical considerations. The purpose of this restructuring is to simplify
biochemical operations and reduce the errors due to physical obstructions
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