Methods Used to Manipulate and Analyze DNA

Forensic DNA typing was made possible not only by advances in knowledge about DNA structure and function but also by advances in the methods and techniques allowing DNA to be manipulated. Different manipulation methods apply to different DNA-typing technologies. For example, nuclear DNA was first typed using the restriction fragment length polymorphism (RFLP) technique. This procedure did not rely on the polymerase chain reaction but on restriction enzymes and Southern blots. (Southern blotting is discussed later in this chapter.) By contrast, the current typing procedure does rely on PCR but does not make use of restriction enzymes.

DNA Analysis Meets Forensic Science

In the 1980s DNA scientists (molecular geneticists) focused on the repeat-sequence polymorphism within DNA. For most researchers these repeat-sequence regions were “road signs” along the sequence of letters (bases) as different laboratories worked on sequencing the entire human DNA. Dr. Alec Jeffreys at the University of Leicester in the United Kingdom realized that these polymorphisms provided excellent tools for human identification in affiliation cases, especially when many regions were examined simultaneously. He called these patterns “DNA fingerprints,” a term that has stuck, especially in the popular media. Most forensic scientists dislike the term because it can create confusion between DNA and conventional fingerprints, and because there are some differences between DNA individuality and fingerprint individuality. Jeffreys published several papers on this subject in the prestigious scientific journal Nature in 1985.

Around this same time, in 1983 and in 1986, two teenage girls had been raped and murdered in the small village of Narborough in Leicestershire, England (see sidebar “The Narborough Murders”). Jeffreys and DNA technology would be drawn into this case, and its outcome became the flash point for the development of DNA-typing methods in forensic science laboratories worldwide.

Within a couple of years forensic science laboratories all over the world had acquired the tools to perform the new DNA-typing technique. Jeffreys’s name will be forever linked with this revolution. In 1998, at its 50th anniversary meeting in San Francisco, the American Academy of Forensic Sciences paid special tribute to Jeffreys in recognition of his contributions.

The DNA Era

Much of the repeated sequence data in the human genome is not functional; it does not specify protein structure. It has been called “junk DNA,” though it may have functions that are not yet clear to scientists. About 20 percent of human DNA is functional, in the sense that it codes for protein. And, within that 20 percent, there is considerable similarity in sequence among different people. This is exactly what would be expected; the structure of functional DNA would be conserved. Any major alterations in the sequence of the functional DNA would lead to problems with the specification of protein structure and would likely cause problems for the individual.

Changes in one or a few bases in DNA are called mutations, and they do occur. Study of variations in functional proteins, such as hemoglobin, makes it clear that some mutations are innocuous. Scientists know this because these mutated versions of hemoglobin are found in living people. In other words, there has been a mutation in DNA, and it has caused a change in the hemoglobin protein, but the person with the mutation is alive and well. The mutation did not therefore affect the functionality of the hemoglobin. But many mutations do cause problems with protein functionality. These problems often lead to serious medical problems. Many mutations probably lead to early death—so early in the development of an embryo that the mother may not yet even realize she is pregnant. Scientists will never see the mutations that prevent such an embryo from surviving.

In the 80 percent or so of DNA that does not specify protein structure, there is enormous sequence and repeat-sequence polymorphism. For the most part it does not seem to have any negative consequences for the individual and can be exploited for purposes of identification, as has been done by forensic scientists.

Analysis and DNA Typing of Blood and Other Physiological Fluids

Once established as human, blood and physiological fluid stains and traces are next DNA typed to find out who may have deposited them. DNA profiling means finding out the DNA types at several different genetic loci.

Genetic loci, or different locations on the DNA, are explained later in the book. The combined set of types at the different locations is the profile. It is the profile that is actually characteristic of an individual.