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PowerPoint Lectures for

Introduction to Biotechnology, Second Edition


William J.Thieman and Michael A.Palladino

Chapter 8
DNA Fingerprinting and Forensic
Analysis

Lectures by Lara Dowland

Copyright © 2009 Pearson Education, Inc.


Chapter Contents

• 8.1 Introduction to DNA Fingerprinting


and Forensics
• 8.2 What Is a DNA Fingerprint?
• 8.3 Preparing a DNA Fingerprint
• 8.4 Putting DNA to Use
• 8.5 DNA and the Rules of Evidence
• 8.6 Familial Relationships and DNA
Profiles
• 8.7 Nonhuman DNA Analysis

Copyright © 2009 Pearson Education, Inc.


8.1 Introduction to DNA Fingerprinting and
Forensics
• Forensic science – intersection of law and science
• Historic examples
– 1800s – photography
– Early 1900s – fingerprints
• DNA Fingerprinting – 1985
– Unique signature found in each person’s genetic makeup

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8.2 What Is a DNA Fingerprint?

• Every individual carries a unique set of genes


– Chemical structure of DNA is same, but the order of the
base pairs differs
• Every cell contains a complete set of DNA that
identifies the organism as a whole
• Only one tenth of 1% of DNA differs from person
to person

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8.2 What Is a DNA Fingerprint?

• Two Main Types of Forensic DNA Testing


– RFLP (restriction fragment length polymorphism)
• Requires larger amounts of DNA
• DNA cannot be degraded
– PCR (polymerase chain reaction)
• Less DNA and DNA can be partially degraded
• Extremely sensitive to contaminating DNA

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8.2 What Is a DNA Fingerprint?

• DNA profiling depends on a small portion of the


genome
– Exons code proteins
– Introns do not code for proteins
• The introns contain repeated sequences of between 1 and
100 base pairs
• Called variable number tandem repeats (VNTR’s)
– Some VNTR’s are inherited from mother and some
from father

Copyright © 2009 Pearson Education, Inc.


8.2 What Is a DNA Fingerprint?

Copyright © 2009 Pearson Education, Inc.


8.2 What Is a DNA Fingerprint?

• DNA fingerprinting is restricted to the detection of


microsatellites
– 1 to 6 nucleotide repeats dispersed throughout the
chromosomes
– Probes used to identify the microsatellite surround the
specific microsatellite being analyzed
– Also called short tandem repeats (STR)
– FBI has chosen 13 unique STRs for testing
• Combined DNA Index System (CODIS)

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8.3 Preparing a DNA Fingerprint

• Specimen Collection
– Search for sources of DNA
– Collection requires scrupulous attention to detail
• Wear disposable gloves; change them frequently
• Use disposable instruments
• Avoid talking, sneezing, and coughing
• Avoid touching any item that might contain DNA
(face, nose, or mouth)
• Air-dry evidence before packaging; mold can
contaminate a sample

Copyright © 2009 Pearson Education, Inc.


8.3 Preparing a DNA Fingerprint

• Enemies of Evidence
– Sunlight and high temperature
– Bacteria
– Moisture
• DNA fingerprinting is a comparative process
– Samples from crime scene must be compared to suspect
DNA
– Best sample from suspect DNA is fresh, whole blood

Copyright © 2009 Pearson Education, Inc.


8.3 Preparing a DNA Fingerprint

• Extraction of DNA
– DNA can be purified
• Chemically (using detergents)
• Mechanically (pressure to force DNA out of cell)

Copyright © 2009 Pearson Education, Inc.


8.3 Preparing a DNA Fingerprint

• RFLP Analysis
– Treat DNA with restriction enzyme
• Restriction enzyme cuts DNA at restriction sites
• Use several restriction enzymes in sequence or combined
– Use agarose gel electrophoresis to separate the pieces
– Gel is chemically treated or heated to denature the DNA
• Allows the binding of a single-stranded probe

Copyright © 2009 Pearson Education, Inc.


8.3 Preparing a DNA Fingerprint

– Southern Blot Technique


• Transfer DNA fragments from gel to nitrocellulose or nylon
membrane
• Membrane incubated with a probe
– Short strand of complementary DNA with a radioactive
or fluorescent tag
– Targeted area on the DNA fragment is called a locus
• Expose X-ray (photo) film to membrane to obtain
permanent record of results

Copyright © 2009 Pearson Education, Inc.


8.3 Preparing a DNA Fingerprint

Copyright © 2009 Pearson Education, Inc.


8.3 Preparing a DNA Fingerprint

• PCR – used to amplify DNA found at crime scene


into an amount that can be analyzed
– DNA produced is identical to the original sample
– Use amplified DNA in a Dot Blot Analysis
• DNA amplified by PCR is blotted onto specially prepared
blot strips
– Each dot on the strip is a different DNA probe from
human DNA

Copyright © 2009 Pearson Education, Inc.


8.3 Preparing a DNA Fingerprint

Copyright © 2009 Pearson Education, Inc.


8.3 Preparing a DNA Fingerprint

– STR Analysis
• Use primers to amplify STR’s in DNA using PCR
• FBI uses 13 STR regions
– Odds that two individuals will have the same 13-loci
DNA profile are more than one in a billion

Copyright © 2009 Pearson Education, Inc.


8.4 Putting DNA to Use

• DNA fingerprinting is a comparative process


– Looking for alignment of bands or dots in the fingerprint
– All tests are based on exclusion
• Testing continues only until a difference is found
• If no difference is found after a statistically acceptable
amount of testing, the probability of a match is high

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8.4 Putting DNA to Use

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8.4 Putting DNA to Use

• The Narborough Village Murders


– 1983 first reported use of genetic fingerprinting in a criminal
case
– Sexual assault and murder of girl in United Kingdom
• The prime suspect’s DNA did not match that found at crime
scene
• Police collected 5500 samples from the area’s population
of likely suspects
• None of the DNA profiles matched the crime scene
• Friend of suspect had given a sample in the name of the
suspect

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8.4 Putting DNA to Use

• Forest Hills Rapist


– DNA first used in United States – 1987
– Victor Lopez tried for the sexual assault of three women
• Reported assailant was a black man; Lopez was not a
black man
– DNA was a match to crime scene

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8.4 Putting DNA to Use

• Terrorism and Natural Disasters Force


Development of New Technologies
– World Trade Center September 11, 2001
• Used DNA techniques to identify the remains of victims
• Tremendous amount of debris, heat, and microbial
decomposition of remains
• Hundreds of thousands of tissue samples from nearly
3,000 individuals

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8.4 Putting DNA to Use

– World Trade Center


• Evident that new strategies would be necessary to quickly
prepare and organize DNA profiles and compare them with
DNA profiles from relatives
• Within 24 hours, collection points had been established
around the city
– Family filed missing person reports and provided cheek
cell swabs for DNA isolation; personal items from the
missing were also collected

Copyright © 2009 Pearson Education, Inc.


8.4 Putting DNA to Use

– World Trade Center


• Several companies were involved in developing new
software programs to help match DNA samples from family
members to DNA profiles of victims
• Used primarily STR, mtDNA, and SNP analysis

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8.4 Putting DNA to Use

– South Asian Tsunami


• December 2004
• Lost over 225,000 lives
• mtDNA, Y-STR’s
• Within 3 months, 800 victims had been identified

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8.5 DNA and the Rules of Evidence

• DNA fingerprinting had to meet legal standards


regarding the admissibility of evidence
• 5 different standards used
– Relevancy test
– The Frye standard
– The Coppolino standard
– The Marx standard
– The Daubert standard

Copyright © 2009 Pearson Education, Inc.


8.5 DNA and the Rules of Evidence

• Simpson/Goldman murders
– Collected 45 samples for DNA analysis, including known blood
samples from the two victims and the suspect; blood drops
found at the crime scene, in the suspect’s home, and in his car
– Pre-trial hearings announced that the DNA collected at the
crime scene matched that of O.J. Simpson
– Defense lawyers attacked the procedures used in collecting,
labeling, and testing the evidence
– Possibility that evidence was tainted became obvious
– DNA evidence not effective

Copyright © 2009 Pearson Education, Inc.


8.5 DNA and the Rules of Evidence

• Human Error and Sources of Contamination


– Chain of custody of samples is compromised
• Collection of evidence must be systematically recorded and
access to evidence must be controlled
– Follow defined standards of laboratory practice and
procedures to prevent DNA damage during the analysis
• DNA and Juries
– Must make sense to the jury
– Statistics can be confusing

Copyright © 2009 Pearson Education, Inc.


8.6 Familial Relationships and DNA
Profiles
• Paternity Testing
– Analyze samples from child and adults involved
• Mitochondrial DNA
– Used to examine samples that cannot be analyzed by
PCR or RFLP
• Older samples that lack nucleated cellular material (hair,
bones, and teeth)
– Inherited from the mother only
– Changes only about 1% every million years due to
random mutation

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8.6 Familial Relationships and DNA
Profiles

Copyright © 2009 Pearson Education, Inc.


8.6 Familial Relationships and DNA
Profiles
• Y-Chromosome Analysis
– Passed directly from father to son
– Useful for tracing relationships among males or analyzing
biological evidence involving multiple male contributors

Copyright © 2009 Pearson Education, Inc.


8.7 Nonhuman DNA Analysis

• Ginseng
– $3 million market in U.S. alone
– Two major herbal products are referred to as ginseng
• One native to North America, the other native to Asia
• Asian ginseng boosts energy; American ginseng calms
nerves
• American variety is rarer and more valuable
• Ancestry of Cabernet Sauvignon Grapes
– Hybrid grapes are considered inferior and are legally excluded
from bearing the prestigious dinstinction appellation d’origine
contrôlée in France
– DNA evidence determined that the ancestors of cabernet
sauvignon grapes are cabernet franc and sauvignon blanc
Copyright © 2009 Pearson Education, Inc.
8.7 Nonhuman DNA Analysis

• Prove a hunter killed a bear illegally in PA


– A law makes it illegal to kill a bear in a den
– Witness reported seeing a hunter discharge gun into den
– Bear’s premolars were removed at registration station to
confirm sex and age of bear
– Collected blood samples from the den and compared with
DNA from bear; were a match
• DNA Tagging to Fight Fraud
– Use DNA as an authentication label hidden in a wide variety of
products
• Footballs in 2003 Super Bowl
• 2000 Sydney Summer Olympics

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