DNA fingerprinting

DNA fingerprinting is used to determine paternity

• Look at the DNA of the mother, father and child

• Could these parents produce this child?

DNA fingerprinting

• 2 methods

• Southern Blot and Restriction fragment length polymorphism

• PCR and VNTRs

Different types of DNA• We have talked about plasmid DNA

• In DNA fingerprinting you are looking at genomic chromosomal DNA– You are looking at a persons entire genome which

is very large– We will do some tests to look at smaller pieces– Remember that at each locus, half of your DNA

comes from your mother and half from your father

DNA fingerprinting by Southern Blot

• Southern blot and RFLPs (restriction fragment length polymorphisms)

• RFLPs – variation in length of genomic segment between 2 restriction enzyme sites

• Use probes corresponding to the RFLPs• Some people may not have these restriction

sites

DNA fingerprinting by PCR• DNA is analyzed for specific variable number of

tandem repeats throughout the genome (VNTRs)– Run of repeated nucleotides (4-40)

• Each individual will usually inherit a different variant of each VNTR from their mother and from their father

• 2 unrelated individuals will therefore NOT contain the same pair of sequences

• PCR– primers on either side of the VNTR

Other methods• STR = short tandem repeats, 4-5 repeats, examined

by PCR

• Mitochondrial DNA is maternally inherited– Determine if children have the same mother

• Y chromosome analysis– Determine if male children are related

• These are different approaches but we will not study them in this lab

Uses of DNA fingerprinting

• Identification of a criminal• Exoneration of a person for a crime• Paternity testing• Identification of human remains

Question?

• Why can blood typing only exclude a suspect but DNA fingerprinting can provide positive identification with relatively great accuracy?

Southern Blot

Analysis of RFLPs by Southern Blot

• DNA extraction• Digestion with restriction enzymes• Electrophoresis• Southern Blot and hybridization with

radioactive probe• Detection of RFLPs by autoradiography• Reprobe Southern Blot with additional probes

DNA extraction

• DNA can be obtained from many different sources – Blood– Semen– Hair– Saliva– Tissue from a dead person

How do you determine who committed the crime?

• Get DNA from the crime scene from one of the different sources

• Get DNA from the suspects– Usually from their blood but can use other sources

• Compare the results

Cut DNA with restriction enzymes

• Restriction enzymes will cut out the regions with the repeated segments but their length will be different in different individuals

• These are the regions that are specific to each person

• These are the regions of DNA that will be compared between the crime scene DNA and the suspects DNA

Cut chromosomal DNA with restriction enzymes

• You will get a large number of different size fragments

• You will get a smear on a gel

Electrophoresis and Southern Blot• Electrophoresis separates fragments based on size• DNA in the gel is denatured by soaking in NaOH

– Why do we want to denature the DNA?• Single stranded DNA is transferred to a membrane• Radioactive probe added• Look for regions of hybridization – restriction

fragment length polymorphisms (RFLPs)• Detected by autoradiography

Southern Blot results

Southern Blot results

PCR

Use PCR to do fingerprinting

• need primers to surround the region of the VNTRs

Fingerpinting by PCR• Notice each person has a

different number of repeats at a specific locus or specific VNTR

• These are detected by electrophoresis following PCR

• Which individual could have left forensic sample F?

• The more loci used, the more accurate the analysis

Advantages/Disadvantages of PCR and Southern Blot

PCR Southern Blot

More sensitive – less DNA needed

More DNA needed

Faster – a few hours Slower – at least one day

Use a single primer at a time

Can reprobe with additional probes

Less specific More specific

Results from fingerprinting• 3 possibilities• No match

– Suspect excluded from the group who could have contributed the evidence

• Inconclusive– DNA old, contaminated or not enough sample

• Match between 2 samples– Suspect included in the group who could be the

source of evidence– Not 100% certainty – with more probes, greater

certainty