DNA fingerprinting takes advantage of the natural presence of repetitive regions of DNA sequence within the genome. These regions of DNA do not contain genes, that is, they are non-coding. Some of these repetitive regions are believed to play a role in maintaining chromosome structure, recombination, and/or regulatory control. Because these regions are non-coding, they accumulate mutations faster than coding regions, where mutations are much more likely to affect the individual's survival, and thus tend not be transmitted to the next generation. Since mutations occur randomly, each individual carries a unique set of these repetitive sequences.

DNA fingerprinting is performed either by probing DNA with markers that contain the repetitive sequences, or by using PCR to amplify specific repeat regions within the genome. Two types of DNA fingerprinting techniques are described below:

• Variable Number Tandem Repeat (VNTR) analysis relies on regions of DNA that contain different numbers of short, repeating sequences in different individuals, and at different positions in the genome (called loci). Genomic DNA is fragmented at restriction sites that flank the VNTRs. Analysis of the digested DNA by Southern blot reveals a unique pattern of bands based on the number of repeats in the individual. Whereas one person may have two repeats at each of three loci, another may have one copy at one locus and two at both of the others, thus the pattern will vary at the third location. Depending on the length of the repeat, VNTRs are classified as microsatellite (12 - 200 bases) or minisatellite (2 - 4 bases).
  
  
• PCR-based methods of fingerprinting identify unique profiles of DNA fragments by varying the nature of PCR primer and the conditions under which the primer anneals. The conditions can be varied so that only sequences with exact complementarity to the primer sequence will bind; or at the other extreme, so that all sequences that are somewhat similar will bind. A profile of different sizes of bands is generated that reflects the various loci targeted by the primer. PCR-based fingerprinting is typically used to screen whole genomes, producing a large number of individual-specific bands. PCR-based methods include, randomly amplified polymorphic DNA (RAPD), arbitrarily primed PCR (AP-PCR), and amplified length fragment polymorphism (AFLP).

*DNA Fingerprinting is actually a patented process, but the term has been adopted to describe the analysis of repetitive sequences.