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DNA Fingerprinting

Dateline: 07/06/98

By Alan Bruzel

Deoxyribonucleic acid (DNA) is a linear, polymeric molecule composed of four repeating units, or bases: adenine (A), cytosine (C), guanine (G), and thymine (T). A gene is a specific sequence of these bases that directs the cellular synthesis of a particular protein. There are an estimated 100,000 genes in human DNA. However, this represents only 3% to 10% of a human's entire DNA complement; the remaining 90% or more of the DNA does not code for protein, but controls gene expression, orders the three-dimensional structure of the DNA, or has yet undiscovered properties.

This non-gene DNA harbors areas where the base sequences vary between individuals. Most of the time, these variances are without apparent ill effect. Therefore, I (and 10,000 other people) may have an A at one DNA site, whereas you (and 10,000 other people) may have a G in the same location. By contrast, such differences manifesting themselves in genes can have powerful consequences, and are the underpinnings of inherited diseases.

There are three types of DNA variability that are commonly used in DNA fingerprinting: restriction fragment length polymorphism, variable number of tandem repeats, and short tandem repeats (STRs). STR analysis is a popular method of DNA fingerprinting, and will be the technique discussed in this article.

STRs, also known as microsatellite repeats, consist of repeated sequences of two to seven bases. For example, the [GT]₄ repeat is GTGTGTGT and [CAG]₆ is CAGCAGCAGCAGCAGCAG.

The human genome contains hundreds of thousands of these STRs evenly distributed on all chromosomes. Consequently, there are thousands of each kind of repeat; that is, thousands of [GT]_n, [CAG]_n, [CTG]_n, [GATA]_n, etc. As a result, unequivocal DNA fingerprinting depends upon the unique DNA flanking sequences on each side of a repeat. These unique flanking sequences allow the analyst to zero in on a defined area of a hundred or so bases in a human genome that contains three billion bases.

Let's look at the STR designated D7S820 (GenBank number G08616) located on human chromosome 7. D7S820 contains a [GATA]_n repeat, where n can range from 6 to 14. The next paragraph shows the DNA sequence of a D7S820 STR with twelve GATA repeats. (DNA is an unbroken, continuous polymer; the example displayed here shows gaps for the sake of readability. The [GATA]₁₂ region is capitalized, and the unique flanking regions are underlined.)

aatttttgta ttttttttag agacggggtt tcaccatgtt ggtcaggctg actatggagt tattttaagg ttaatatata taaagggtat gatagaacac ttgtcatagt ttagaacgaa ctaacGATAG ATAGATAGAT AGATAGATAG ATAGATAGAT AGATAGATAG ATAgacagat tgatagtttt tttttatctc actaaatagt ctatagtaaa catttaatta ccaatatttg gtgcaattct gtcaatgagg ataaatgtgg aatcgttata attcttaaga atatatattc cctctgagtt tttgatacct cagattttaa ggcc

It is these unique, flanking sequences that are used to amplify the region between them. The amplification procedure, known as the polymerase chain reaction (PCR), enzymatically synthesizes thousands of copies of the intervening DNA region. This amplification enables forensic laboratories to generate enough DNA for analysis from hair roots and blood samples. Only one nanogram of DNA, a billionth of a gram, is required for a successful PCR. In a separate reaction, the PCR products have their DNA sequence determined. This sequence reveals the number of repetitive units in the sample.

A person inherits an equal amount of nuclear DNA from each parent. Therefore, among all the other DNA passed down from one's father and mother, one inherits one maternal copy of D7S820, and one paternal copy of D7S820. The chromosome diagram below tracks STR variability in D7S820 from grandparents to parents to children. For ease in following the example, each copy of D7S820 has a different number of [GATA] repeat units. For example, the maternal grandfather has one chromosome 7 with [GATA]₇ in its D7S820 STR, and another chromosome 7 with [GATA]₈ in its D7S820 STR. His daughter inherited his [GATA]₇ STR and his wife's [GATA]₉ STR. The relationship of child to parent can be followed using this one marker.

In real life situations, more than one STR is analyzed. A hair found at the scene of a crime with [GATA]₉ and [GATA]₁₄ in its D7S820 STR does not automatically single out child D as a suspect. There are thousands of unrelated people with this one STR pattern. However, a match in three STRs (D7S820, D13S317, and D16S539, for example) gives more than a 2000 to 1 probability that the DNAs are from the same person. Using nine STRs gives more than a one billion to 1 probability. This degree of certainty in matching a DNA sample to an individual is behind the US military's use of DNA typing for its members. This may eliminate interment of remains as "unknowns."

The same DNA fingerprinting techniques are also being investigated for use in establishing animal pedigrees, as well as matching illegally harvested timber in the possession of a logger to the stumps left in the forest.

Recommended Web resource for additional information:

DNA Molecules
An article from this Web site examining genetic complexity.

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