DNA fingerprinting (also known as DNA profiling or DNA typing) refers to any technique for identifying individuals based on the unique features of their genomes. Many eukaryotic genomes have thousands of sites (loci) that contain short DNA sequences that are repeated one after another along part of a chromosome and that vary in repeat number between individuals. These repetitive sequences, called tandem repeat sequences, are at the core of modern DNA fingerprinting.
Short Tandem Repeats and Minisatellites
Tandem repetitive DNA sequences fall into two major classes:
1. Repeating units that are just 2 to about 6 bases long. These are short tandem repeats (STRs), also known as microsatellites or simple sequence repeats (SSRs). For example, one of the STRs used in the FBI DNA profiling system is GATA, which is repeated between 5 and 16 times.
2. Repeating units that are from about 8 to 100 bases long. These are minisatellites, or variable number tandem repeats (VNTRs).
In current forms of DNA fingerprinting, STRs are used almost exclusively because their shorter size makes them easier to amplify by PCR. STRs are thought to originate when DNA polymerase skips or mistakenly adds extra bases during replication. Soon after these sequences were first identified, STRs were found to be “hypervariable,” meaning that they vary among individuals far more than other types of sequences. This makes them ideal for DNA fingerprinting. Each repeat number variant of an STR, known as an STR allele, is transmitted from parent to offspring just like any other DNA sequence. How can STRs and minisatellites be used for DNA fingerprinting?
DNA Fingerprinting Using PCR
Investigators obtain a DNA sample and then perform PCR using primers that flank a region containing an STR or minisatellite (Figure a). PCR allows minute amounts of DNA to be analyzed, something that’s critical in most criminal investigations. Once an STR is amplified, gel elecrotrophoresis is used to determine the number of repeats. Primers are available that allow the analysis of many different STRs in a single polymerase chain reaction.
For example, today’s FBI fingerprinting method amplifies 13 different STRs found at various sites in the human genome. Figure b shows the principle of using DNA fingerprinting in paternity tests. Besides paternity analysis, DNA fingerprinting has been used to convict criminals, to exonerate the falsely accused or imprisoned, and to identify remains, including victims of terrorism and politically motivated killings. DNA fingerprinting has enormous impacts on society, and it raises important issues about the balance between privacy and public protection.