by Jeffrey Graf

Created on: October 23, 2008

The nucleus of a cell contains the chromosomal DNA for an organism. Since each cell in an organism must have a complete compliment of DNA, all of the DNA in the nucleus must be replicated before a cell divides. Because the organization of chromosomal DNA is complicated, description of the cellular replication process may be unnecessarily complicated. Fortunately, for the purposes of biotechnological applications, the process of DNA replication has has been automated and can be done on a laboratory bench top.

The process of bench top DNA replication is referred to as "Polymerase chain reaction", or PCR. PCR has revolutionized not only the biotechnology industry, but related industries such as forensics. A small amount of DNA, potentially less than a thousandth of a gram, can be duplicated, or amplified, into a quantity that can be used for DNA fingerprinting, or unique identification. Here I will describe some of the basic principles of bench top DNA replication, or PCR.
In broad terms, The DNA will be cycled through multiple series of steps of first breaking segments of double stranded ( helical ) DNA (dsDNA) into to single stranded DNA (ssDNA) chains. The two strands of the DNA double helix are held together by "hydrogen bonds", or bonds that can be easily broken with heat. Hydrogen bonds are what gives motor oil its viscosity, and for example if motor oil is warmed up it becomes less viscous. Likewise, warming of DNA above a given temperature will cause the double stranded DNA to break into two strands of single stranded DNA. At this point, each single strand can be duplicated in a process mediated by an enzyme known as "DNA polymerase", hence the name polymerase in the acronym for PCR. Once polymerization step has taken place, which takes place at low temperature, the mixture can be heated again to separate the newly created double stranded DNA. Thus the cycle of heating and cooling is repeated as many times as is necessary to create the amount of DNA desired. For now obvious reasons, the machine responsible for mediating this process in a bench top is called a "thermo cycler", and is a common piece of equipment in every molecular biology laboratory.
Now I will talk in a little bit more detail about the actual replication step in the PCR cycle. First of all, the DNA polymerase used is from an aquatic microorganism found in hot springs. A unique characteristic of this organism's DNA polymerase is that it has evolved the ability to withstand the high temperatures

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