1. DNA basics DNA is a molecule located in the nucleus of a cell Every cell in an organism contains the same DNA Characteristics of DNA varies between individuals within a species and between species

2. What is DNA?

3. DNA is contained in chromosomes Chromosomes contain DNA and associated proteins (which allow the DNA to condense/wind up tightly)

4. What is a chromosome? Tightly packed DNA wrapped around histone proteins

5. Chromosomes, DNA, genes, and nucleotidesgenegenegene Chromosomes contain DNA Genes are sequences of DNA nucleotides Genes are located on chromosomes Chromosomal regions in between genes contain variable nucleotide sequences

6. Forensic DNA analysis seeks nucleotide variation in DNA Point mutations from errors in DNA replication –RFLP (Restriction Fragment Length Polymorphism) analysis Variable number tandem repeats (VNTRs) –STR (Short tandem repeat) analysis

7. Why is there nucleotide variation between the DNA of individuals of the same species? All the DNA nucleotides in a cell must be copied (replicated) prior to cell division Random copying errors are made during DNA replication

8. Every human cell contains 3.4 billion nucleotide pairs DNA replication copies DNA nucleotides

9. DNA replication

10. DNA polymerase & point mutations 1 mistake made every 10,000 replicated nucleotides

11. Repair enzymes limit mutations to 1 in a billion replicated nucleotides

12. Point mutations are a source of genetic diversity

13. Point mutations & genetic variation Point mutations in the wild type gene result in new alleles

14. Genetic variation Alleles are differences (variation) in a gene within a population of a species Genes determine phenotype (physical characteristic) of a structure, molecule, etc.

15. Forensic DNA analysis and nucleotide variation Restriction endonucleases (enzymes) cut DNA at specific short palindromic nucleotide sequencesRestriction endonucleases

16. Forensic DNA analysis & nucleotide variation RFLP (Restriction Fragment Length Polymorphism) analysis –Began in 1985

17. Gel electrophoresis Gel electrophoresis separates DNA fragments by size

18. RFLPs are DNA “fingerprints”

19. RFLP analysis and DNA probes

20. Forensic RFLP analysis uses multiple DNA probes If each probe identifies an RFLP with a frequency of 1 in 100 persons, then 5 probes yields 1 in 10 billion

21. Case Study - OJ Simpson

22. Modern forensic DNA analysis Based on the Polymerase Chain Reaction (PCR)PCR

23. Polymerase chain reaction (PCR) 25-30 PCR cycles yield ~1 million copies of the DNA sample Can be used on trace quantities of DNA –Saliva, hair follicle, trace dried blood

24. PCR conducted in a thermal cycler

25. Forensic PCR & VNTRs VNTR – variable number tandem repeat –Individuals vary in the number of repeats

26. PCR, VNTRs and Paternity

27. PCR and STRs (Short Tandem Repeats) STRs are short VNTRs

28. STRs Repeats of 3-7 nucleotides –5-20 repeats –5-20 alleles per STR PCR amplifies fragments ~200-500 nucleotides in length

29. STR primers flank the repeat region Penta D

30. Many STRs have been identified STR database

31. Analyzing STRs Capillary electrophoresis

32. STR data Each peak identifies a different STR allele

33. Multiplexing Using several VNTR/STR primer sets simultaneously

35. Gender identity in DNA typing Amelogenin gene (tooth pulp) –Located on both X and Y chromosomes –X chromosome amelogenin gene is shorter by 6 nucleotides

37. Y chromosome specific STRs

38. Mitochondrial DNA

39. Mitochondrial DNA & forensics Part of the mitochondrial genome is highly polymorphic, making it useful for human identification. –The two most variable regions known as HV1 and HV2 are usually amplified and sequenced to compare the difference between the evidence and reference samples –Mt DNA varies ~1-2% between unrelated individuals (two individuals differ by an average of 87 nucleotides in the approx 800bp region commonly sequenced by forensic labs) Because mtDNA presents technical and interpretational challenges, mtDNA is reserved for cases where nuclear DNA analysis failed due to minimal quality or quantity. –1000s of copies of the mtDNA genome maybe present in a single cell. Because of its abundance and small size compared to nuclear chromosomes, mtDNA is often the last typable DNA present in a small, old and badly degraded sample. If no results obtained with other systems, often mtDNA can be typed. –MtDNA is used to type the dead cells in hair shafts, bones and teeth.

40. CODISCODIS – Combined DNA Index System 13 standardized STRs (p. 379) –Available commercially Each STR has a specific frequency within a population –Multiple STRs used to unambiguously identify a person