Today the CODIS database is filled with information based on STR analysis.

1. In 1985, Alex Jeffreysused variable regions of DNA called VNTR’s that can be used to create a DNA fingerprint. • Process was called RFLP (restriction fragment length polymorphism). • In RFLP, restriction enzymes are used to isolate VNTR and then are separated using gel electrophoresis • Technique was found to be very costly, time consuming, relied on large amounts of samples

2. PCR, Polymerase Chain Reaction, offered a faster technique that can be used on very small evidence samples. • PCR adapted to utitlize STR (short tandem repeats) • The FBI standardized 13 regions (loci) plus the sex chromosome (AMEL) in DNA profiling. • This led to the formation of the Combined DNA Index System (CODIS).

4. Today the CODIS database is filled with information based on STR analysis. • Short tandem repeats are only 3-5 DNA bases in length and are highly polymorphic. • Database has national, state and municipal indices. • Profiles in the database • Convicted offender index (over 9 million) • Forensic profiles of unkowns (over 300,000) • Arrestee profiles • Unidentified remains & Missing persons • Over 130,000 “hits” in the U.S. • Just under 2,000 in Maryland

5. Population Statistics • 13 different loci + the sex allele that are analyzed in a DNA profile. • Each loci has a variable number of possible short tandem repeats. D3S158 allele • 29 known variations of this one allele! • So any one person could have a 1/29 (0.0344827586) chance of having the same allele size D7S820 allele • 26 known variations • 0.0384615385 Using the Product Rule = .034 x .038 = .0013 In a forensic case involving blood stain evidence, among the 13 loci analyzed there is only a one in 10 billion chance that the DNA from a blood stain would come from another person.

6. PCR Mechanism • Cellular DNA replication is an enzymatic process that copies the entire molecule. • Polymerase Chain Reaction is a “primer mediated” process. • PCR makes millions of copies of a small region of the DNA molecule

7. The PCR Recipe • Template DNA – this is the target sequence to be selected. Can be a gene or a non-coding region. • Primers – short DNA single stranded sequences designed to flank both ends of the target sequence. • Free Nucleotides – dATP, dTTP, dGTP, dCTP. These are the building blocks for the DNA strands. • Taq Polymerase – heat stable enzyme that which builds the DNA strands. • PCR Buffer – provides ideal pH and salts for enzymes to function.

8. The Amazing PCR Bead PCR Beads: Each room-temperature-stable bead contains stabilizers, buffer, dATP, dCTP, dGTP, dTTP, 2 to 2.5 units of puReTaq DNA polymerase, and reaction buffer.

9. The Amazing PCR Bead • To use Ready-To-Go™ beads simply add water, template and primers. The beads are stable at ambient temperature and do not need refrigeration for storage. Ready-To-Go beads minimize pipetting errors eliminate contamination of stock reagents and result in reproducible reactions.

10. PCR Process • Each cycle in the PCR reaction involves three stages • Denature – double stranded molecules are heated up to 95oC causing hydrogen bonds to break and forming single strands • Anneal – primers attach to both sides of target sequence at 55oC • Extension – Taq polymerase adds new bases from primer sequences at 72oC • CLICK HERE FOR PCR MOVIE

11. Transposable Elements • Segments of DNA which have the ability to move to or be copied to other regions of the genome. • One example is Retrotransposons. • Discovered by Barbara McClintock (1940s-50s) while working with maize.

12. Retrotransposons • Move by a “copy & paste” mechanism, but in contrast to transposons, the copy is made of RNA – not DNA. • RNA copies are transcribed back to DNA using the enzyme reverse transcriptase and then inserted into a new location in the genome. 40% of our genome consists of retrotransposons.