Definitions. DNA polymorphisms are specific sites in the genome (a specific genome site is sometimes called a "locus") where the precise sequence of DNA tends to differ in unrelated individuals. These polymorphisms are sometimes found in genes-- accounting for the differences in phenotype that we observe between individuals. Within genes, polymorphisms are usually referred to as "mutations" or "variants". There is evolutionary pressure exerted on polymorphisms that occur within genes. In most cases, alteration of DNA sequence will result in the alteration of the function of a particular protein. This alteration, in turn, will frequently make the individual either more or less fit to survive. Evolution thus limits the number of polymorphisms that accumulate within genes.

Evolutionary pressure does not operate in this way on inter-genic ("between the genes") regions of the genome. These regions are vast in most eucaryotic organisms: in the human genome and in most other eucaryotic organisms, more than 50% of the DNA seems not to be associated with any gene. Over time, because there is no selective pressure against them, large numbers of polymorphisms have accumulated in the intergenic regions of most eucaryotic organisms. These polymorphisms have turned out to be valuable tools for genetic mapping and for forensic identification.

Three Types of Polymorphisms. There are three basic types of DNA polymorphisms that tend to be of use in the genetic mapping and forensic analysis applications mentioned above. These are:

1) Simple RFLP's. RFLP is an abbreviation for restriction fragment length polymorphism. Simple RFLP's are single basepair alterations in the DNA sequence at a particular locus on the genome. The alteration in sequence is such that the recognition site for a particular restriction enzyme is either added or eliminated. Thus the pattern of restriction fragments generated by digestion of that DNA with the enzyme in question will be altered. We worked with simple RFLP's in Protocol #3.

2) VNTR's. VNTR is the abbreviation for variable number tandem repeat. VNTR's are polymorphisms where what differs from individual to individual is not the specific sequence at a given locus, but rather, the number of times that a particular block of sequence is repeated at that locus. An example is given below:

The repetitive block of sequence is usually small (less than 20 basepairs) and the number of times it is repeated can vary from just a few, up to 60 or more. VNTR's are detected as variations in fragment length between two fixed points outside of the VNTR region.

VNTR's are hypervariable when compared with simple RFLP's-- many different patterns are possible with VNTR's, whereas with simple RFLP's there are only two possibilities, either a restriction site is there, or its not. VNTR's are thus more useful for forensic applications. We will work with VNTR's in Protocol #5.

3) Interspersed Repetitive DNA. Interspersed repetitive DNA is a class of polymorphism where a particular block of sequence is repeated, not tandemly at a single locus (as was the case with VNTR's), but rather throughout the genome. Only one copy of the sequence block is observed at any given locus, but that same block of sequence is observed at thousands of different loci.

Interspersed repetitive DNA is thought to make up somewhere between 5 and 20% of the human genome. The percentages, specific distribution patterns, and sequences/sizes of the repetitive blocks is generally conserved within species, but varies between species. For this reason, interspersed repetitive DNA sequences have been useful in tracing evolutionary relationships.

We will work with interspersed repetitive DNA in Protocol #4.

Note: Interspersed repetitive DNA elements are also referred to as "satellite DNA", and occasionally as "junk DNA".

Lesley Barber, NHCTC. 2001