In 1985 Ronald Cotton was imprisoned for the rape of Jennifer Thompson. She had identified him from pictures and a line-up as the assailant. Circumstantial evidence stacked up against Cotton making it quite clear that Cotton was guilty. He was imprisoned with no flaw in the judicial system to speak of, except one…he was innocent. After 10 years of imprisonment, biochemical technology allowed the comparison of Cotton’s DNA to that of the rapist’s semen, proving his innocence beyond a shadow of a doubt. The same evidence was then used to rightfully convict Robert Poole, a convict who had mentioned the rape to fellow inmates.
Since the early 1980’s DNA "fingerprints" have been used to convict or release possible suspects involved in many crimes. The use of these fingerprints by the FBI’s Forensic Science Systems Unit to form the national DNA registry 
called, Combined DNA Index System (CODIS), is perhaps one of the greatest assets to criminal investigators to date. It is the goal of the FBI to have the Index operating much like the Automated Fingerprint Index System (AFIS). The Standardization Project has insured that all of the genetic information collected across the United States is in a comparable format. All states have authorized the submission of DNA from violent criminals and sexual offenders to CODIS. Almost any type of biological evidence found at a crime scene may be compared to a suspect, including: blood, semen, saliva, bone, tissue, teeth, and even hair follicles.
The methods for obtaining and comparing the genetic samples of evidence and suspects were originally developed to determine the compatibility of Human Leukocyte Antigens (HLA) in individuals for organ and bone marrow transplants. These antigens are highly specific to an individual and are used by the body’s immune system to determine self from non-self. If a transplant is made without first comparing the compatibility of these antigens, there is a very high likelihood that the donated tissue will be rejected and attacked by the recipient’s immune system. The high amount of specificity allows the regions of DNA encoding for the antigens to be extremely useful in identifying one out of several million people. The commonly used methods for isolating and comparing genetic sequences include polymerase chain reactions (PCR) and restriction fragment length polymorphisms (RFLP).
PCR has revolutionized genetic investigations |
The process for PCR is commonly used to analyze genetic information in many genetic investigations. Even a few molecules of DNA can be amplified to produce large quantities. This property makes PCR ideal for analyzing small samples of DNA. The laboratory procedure involves a cycle of denaturing, annealing, and extending DNA. An increase of temperature triggers denaturing. The hydrogen bonds break between the double stranded helix and they separate. In the process of annealing, the temperature is lowered, which enables primers to attach. Primers are segments of DNA having a free OH group on the 3’ carbon of a nucleotide. These primers align with a very specific sequence of amino acids. After the temperature is increased slightly, a DNA polymerase is able to attach nucleotides to the 3’ carbon of the primer and extend the complementary strand. Each temperature-regulated cycle greatly increases the amount of DNA present, which makes more available for amplification in the next cycle.
For analysis, the PCR product is heated once again and washed over a typing strip. These typing strips are composed of different variations of the alleles amplified during the PCR process. HLA DQa was the first type of strip to be used for forensic analysis. The strip is made by fixing Sequence-Specific Oligonucleotide (SSO) probes to a support. The HLA DQa strip tests for the presence of six different kinds of DQa alleles. There are four main types of alleles fixed to the strip. The 1 allele is then subtyped into 1.1,1.2 and 1.3. The SSOs are placed in nine dots along the strip. The first four probes test for alleles 1-4 respectively. The fifth dot is a control that will attach to any DQa type. Any dot lighter than the control probe is considered invalid. The sixth probe is for the subtype 1.1. The seventh probe will indicate a positive response for 1.2, 1.3 or 4. The eighth detects the presence of subtype 1.3. The last probe will respond to every allele except the 1.3 subtype. These SSO probes grab on to complementary PCR-amplified fragments as they are washed over the strip. The strips are then washed to remove any unattached fragments of DNA. The detection of the DNA on the probe goes back to the primers used during PCR. All of these primers were tagged with biotin. The presence of biotin allows streptavidin to bond to the fragments after they attach to the strip. The streptavidin is chemically linked to horseradish peroxidase (HRP). HRP emits the color blue when in the presence of hydrogen peroxide and tetra-methyl-benzidine (TMB). The resulting strip can then be viewed for analysis. Modern forensics uses an HLA DQA1 testing strip. The advantage of the new strip is the detection of the allele 4 subtypes as well as the allele 1 subtypes.
