DNA profiling and fingerprint

• What is polymorphic DNA

  When there are multiple forms of a DNA sequence
• Making a DNA fingerprint

  1. Extract DNA

  2. Digest DNA

  3. Run DNA on gel

  4. Southern blot

  5. Probe membrane

  6. Identify bands hybridising to probe
• DNA fingerprinting

  This uses minisatellites.
• Describe the features of minisatellites

  They have a 5 nucleotide identical sequence.

  The core sequence is identical between people but the number of repeats varies.

  They are inherited using mendelian genetics.
• What types of polymorphic DNA are used in genetic identification

  Minisatellites known as Variable number tandem repeats.

  Microsatellites known as Short tandem repeats.

  Single nucleotide polymorphisms.
• What is the number of repeats in a VNTR or STR called

  An allele
• Describe VNTR DNA fingerprinting

  DNA is digested with a restriction endonuclease that cleaves either side of the VNTR core sequence.

  Seperate using gel electrophoresis and visualize using southern blot and a radioactive probe.

  The larger VNTRs migrate more rapidly to the bottom of the gel.

  The size of the bands represents the number of repeats.
• How is multilocus probe used in VNTR fingerprinting

  The probe detects the core sequence and so can detect multiple VNTRs simultaneously
• What can VNTR fingerprinting be used for

  Paternity testing.

  Forensic science.
• What are the limiations of VNTR fingerprinting

  You cannot determine which band represents which locus.
• Disadvantages of southernblot for DNA fingerprinting

  The samples must not be degraded.

  You require a large DNA sample.
• Forensic science techniques


  • Blood typing
  • Fingerprint analysis
  • Hair microscopy
  • Bite mark comparisons
• DNA forensics


  Also referred to as forensic DNA fingerprinting or DNA typing
• DNA profiles


  May be obtained from saliva or bloodspots
• Biological samples that have been degraded can also produce DNA profiles
• Stored DNA profiles allow for matches with those from other crime scene evidence
• Forensic DNA analysis can be used to identify trafficking of endangered species or illegal animals
• Applications of forensic DNA analysis

  • Forensic analysis
  • Paternity analysis
  • Missing person/disaster victims
  • Genealogy and "Deep ancestry"
  • Population migration patterns
• Goals of forensic science

  • Unambiguously match biological specimens to specific individuals
  • Confirm guilty verdict
  • Eliminate innocent suspects
• Types of variable DNA used for genetic identification

  • Minisatellites (VNTRs)
  • Microsatellites (STRs)
  • Single nucleotide polymorphisms (SNPs)
• Minisatellites


  • Short (7-100 nt) identical nucleotide sequences arranged tandemly head to tail
  • Located at a locus on a particular chromosome
  • Inherited in Mendelian fashion
  • Number of repeats at a locus varies between individuals - variants known as alleles
• VNTR-based DNA fingerprinting


  1. Extract DNA

  2. Digest with endonuclease

  3. Separate via gel electrophoresis

  4. Southern blot

  5. Hybridize with radioactive probe

  6. Expose to X-ray to produce banding pattern
• Multilocus probe


  Uses the core sequence of minisatellites to detect multiple VNTRs simultaneously
• Multilocus probe


  • Probed ~25-30 loci
• Multilocus probes used for paternity testing

  Child receives half VNTR alleles from each parent
• Limitations of multilocus fingerprinting

  • Bands cannot be assigned to particular loci
  • DNA fingerprint not amenable to statistical analysis
• Disadvantages of Southern blot method

  • Need sufficient biological material
  • Multistep procedure
  • Requires good quality DNA
• PCR and forensics


  • Requires very little starting material
  • Works with degraded samples
  • Simple, rapid procedure
• Microsatellites (STRs)


  • Repeated sequence of 2-6 nucleotides
  • Present throughout human genome
  • Less hypervariable than VNTRs
• Autosomal STR DNA profiling

  1. Extract DNA

  2. Amplify with fluorescently tagged primers

  3. Separate fragments by capillary electrophoresis

  4. Analyze fragment sizes
• STR profile genotype


  Expressed as number of times STR sequence is repeated
• PCR amplification of VNTRs/STRs

  1. Amplify with flanking primers

  2. Run PCR products on gel
• Multiplex PCR


  1. Amplify DNA containing STRs with up to 10 primer pairs

  2. Label one primer of each pair with different fluorescent dyes
• Ipswich murders


  • Steve Wright convicted based on DNA match
• Croydon murder


  • Mark Dixie convicted based on DNA match
• UK has largest DNA database in the world
• Until recently, all DNA samples taken during criminal inquiries in England and Wales were retained, but Protection of Freedoms Act 2012 outlaws retention of samples from innocent individuals
• Y chromosome analysis


  Useful when male DNA is mixed with female DNA
• 1. chromosome STR profiling


  Cannot differentiate between DNA of males that are fathers, sons or siblings
• Y chromosome does not undergo recombination and has less genetic variation than an autosomal chromosome