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Comparing DNA Using Gel Electrophoresis - Part 1

written by: Robyn Broyles•edited by: Paul Arnold•updated: 6/25/2009

Experts in genetics, forensics, and many other fields compare DNA sequences on a routine basis. A DNA strand is a chain of single molecules, too tiny to visualize or analyze directly. So how can DNA sequences be compared?

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    DNA Comparison

    Genetics researchers have developed a multitude of methods of comparing DNA sequences. One ingenious approach is gel electrophoresis, a stand-by in the field of DNA sequencing. Gel electrophoresis takes advantage of certain properties of DNA, including its natural electrical charge and its high molecular weight.

    Electrophoresis is a general term for the phenomenon of charged particles traveling in the direction of the opposite charge when placed in an electrical field. Electrophoresis can be used as an analysis tool, as it is in gel electrophoresis, if other factors influence the rate of travel.

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    Preparing the DNA Sample

    There are several methods available for preparing the DNA sample for analysis via electrophoresis. In the past, the DNA strands were cut up using restriction enzymes, which sever DNA strands at specific sequences. The resulting segments would have highly specific lengths because the restriction enzymes work at precise locations. Different DNA strands would yield different combinations of segment sizes. This procedure, called restriction fragment length polymorphism (RFLP), has significant drawbacks. In particular, it requires large amounts of DNA, which makes it unusable for comparing trace amounts of the genetic material.

    The most commonly used preparation technique today is polymerase chain reaction (PCR). PCR creates many copies of its DNA source, making it useful for analyzing trace samples. Each sample is prepared separately.

    • In PCR, small fragments of DNA called primers are mixed with the sample DNA, a number of free bases (A, C, T, and G) for raw material, and an enzyme called Taq DNA polymerase. The primers are chosen to match (complement) the beginning and end of the DNA sample. The primers are necessary to start the copying of DNA.
    • The end result of PCR is a large amount of DNA sequences identical to the original sample. Their length is determined by the specific primers that were chosen, because the polymerase enzyme starts copying only at the section matching the primer.
    • Whether through PCR or another technique, the prepared DNA samples now consist of a large number of segments of a very specific length. Each DNA sample's segments have a unique length or combination of lengths.

Gel Electrophoresis: How Does It Work?

Gel electrophoresis is one of the many tools used to compare and analyze DNA samples. Discover the amazing science behind this clever DNA fingerprinting technology.
  1. Comparing DNA Using Gel Electrophoresis - Part 1
  2. The Gel Electrophoresis Procedure: Part 2