biotech - DNA fingerprinting

DNA Fingerprinting

• Developed by Alec Jeffreys in 1984

• identifies an individual based on the patterns formed from the variations in the genetic code

• Also known as DNA profiling, genetic fingerprinting, DNA typing

Human Genome

• 20,000-30,000 genes

• most of the DNA does NOT code for a protein or RNA (is not a gene)

non codng dna splits into

• introns

• Regulatory sequences

• Highly Repetitive DNA

- tandemly repetitive dna

- telomere

- interspaced repetitive dna

Tandemly Repetitive DNA

• Also called VNTRs (Variable Number Tandem Repeats)

• Short DNA sequences repeated in a row

• Types vary by repeat length

• STRs = short repeats (often 4 bases)

• Example: GGAA repeated (4 bp)

Characteristics of VNTRs

• Polymorphic = many forms → many alleles (more than just 2)

• Variation comes from the number of repeat units

• The same DNA sequence (often an STR) is repeated

• The repeat sequence can be repeated many different number of times in the population

Allelic Variation Compared

• In a population, a polymorphic loci has many choices (alleles)

• In an individual, there are only a maximum of two alleles

DNA Fingerprinting Method: STR Analysis

• PCR

  • STR (fragment of interest) is at a specific locus on the chromosome

  • Primers locate and define this fragment

  • PCR amplifies (makes many copies of) the fragment

• Gel Electrophoresis

  • Separates PCR products by size

  • Allows visualization of the DNA fragments

Allelic Variation in an Individual

• Each person will have 2 copies but the copies can be different lengths (heterozygous) or the same length (homozygous)

• A and C homozygous

Allelic Variation

• Only a limited number of alleles exist, but each can be shared by many people (5–20%)

👉 Implication:

• A single allele is not unique to one person

• You need to look at multiple loci to reliably distinguish individuals

Loci

• STR analysis is powerful because it examines multiple loci (specific locations on a chromosome/DNA) at once

• In North America: 13 loci + AMEL (sex marker) used for crime investigations

• Fewer loci are used in paternity testin

Loci answer

• Homozygous locus (location on dna) → 1 band (dna fragment)

• Heterozygous locus → 2 bands
  4 homozygous + 1 heterozygous
  = 4(1) + 1(2) = 6 bands ✅ possible

• 3 homozygous + 2 heterozygous
  = 3(1) + 2(2) = 7 bands ❌ not possible

• 2 homozygous + 2 heterozygous
  = 2(1) + 2(2) = 6 bands ✅ possible

Why use noncoding regions?

Coding regions are too similar between individuals and even species

DNA Fingerprinting Application

• Paternity testing: identifying the father

• Criminal cases: eliminating suspects

• Identifying a corpse

• Immigration disputes

• Food testing (i.e. Champagne, horse meat)

Paternity

• Used to identify a child’s parents

• A child inherits one sent of chromosomes from both parents

• Each band in the child must match a band from either the mother or father

paternity inclusion vs exclusion

• Paternity inclusion: the man could be the father (his DNA matches the child’s at tested loci)

• Paternity exclusion: the man cannot be the father (DNA does not match)

Why inclusion ≠ proof:

• Many people can share the same alleles

• A match at tested loci is not unique to one person

• Only shows he can’t be ruled out, not that he is definitely the father

criminal case

If the blood from the defendant’s clothes:  had one less band, could the victim’s blood still be considered present?  had one more band, could the victim’s blood still be considered present?

If one band was missing, is victim still present?

👉 YES (usually)

• DNA evidence isn’t always perfect

• Bands can be missing due to:

  • degradation

  • experimental errorIf there’s one extra band, is victim still present?

    👉 YES

    • Extra band could mean:

      • contamination

      • mixture of more than one person