How is DNA used to solve crimes?
CRIMINAL CASES ARE BUILT ON THREE
TYPES OF EVIDENCE:



Identification evidence – a witness coming
into the court and saying, “That’s him, that’s the
man.”
Physical evidence – the victim’s property or a
weapon found in the defendant’s pocket.
Confessions – admissions from the defendant’s
own mouth
JURIES CONVICT WHEN ALL THREE KINDS OF
EVIDENCE ARE PRESENT AND WHEN EACH KIND
CORROBORATES THE OTHERS.
WHEN THERE IS ONLY ONE KIND OF EVIDENCE, A
JURY MAY CONVICT OR THEY MAY NOT, DEPENDING
ON THE WEIGHT AND QUALITY OF THE SINGLE LEG OF
THE TRIAD OF CRIMINAL PROOF.
DNA USE IN FORENSIC CASES
Most are rape cases (>2 out of 3).
 Looking for match between evidence and suspect.
 Must compare victim’s DNA profile.

Challenges
•Mixtures must be resolved.
•DNA is often degraded.
HUMAN IDENTITY TESTING
Forensic cases -- matching suspect with
evidence
 Paternity testing -- identifying father
 Historical investigations
 Missing persons investigations
 Mass disasters -- putting pieces back
together
 Military DNA “dog tag”
 Convicted felon DNA databases

How is DNA used as evidence?
• DNA collected from a crime scene can either link a suspect to the evidence or
eliminate a suspect, similar to the use of fingerprints.
• DNA can identify a victim through DNA from relatives, even when no body can
be found.
• DNA can link crime scenes together by linking the same perpetrator to different
scenes locally, statewide, and across the nation.
• DNA can place an individual at a crime scene, in a home,
or in a room where the suspect claimed not to have been.
• DNA can refute a claim of self-defense and put a weapon in
the suspect's hand.
• It can change a story from an alibi to one of consent.
What factors affect DNA evidence?
Several factors can affect the DNA left at a crime scene, such as environmental
factors (e.g., heat, sunlight, moisture, bacteria, and mold). Therefore, not all DNA
evidence will result in a usable DNA profile. Further, DNA testing cannot identify
when the suspect was at the crime scene or for how long.
What is CODIS?
CODIS stands for COmbined DNA Index System, which
is an electronic database of DNA profiles that can identify
suspects. DNA profiles from individuals convicted of
certain crimes, such as rape, murder, and child abuse, are
entered into CODIS and help officers identify possible
suspects when no prior suspect existed.
Sources of Biological Evidence
 Blood
 Semen
 Saliva
 Urine
 Hair
 Teeth
 Bone
 Tissue
True or False?
Which three statements below are true?
1. The DNA in a man's blood is the same as the DNA in his skin cells and saliva.
2. Each person's DNA is different from every other individual's.
3. DNA can be found in all parts of our body except hair.
4. DNA can have forensic value even if it is decades old.
5. DNA evidence was first used to get a conviction in a trial in 1987.
Watch the video segment from NOVA: "The
Killer's Trail" and be ready to answer the
questions on the next slide.
Video Quiz
Choose the best answer for each.
1. Who was the victim?
A. Marilyn Sheppard
B. Sam Sheppard
C. Sam Sheppard, Jr.
2. What are the keys to DNA fingerprinting?
A. Chromosomes
B. Alleles
C. Nitrogen bases
3. Where did the scientist get the sample of DNA for Marilyn Sheppard?
A. Hair
B. Skin
C. Fingernail
4. Whose blood was found in the blood trail?
A. Marilyn Sheppard
B. Sam Sheppard
C. Neither
DNA AND CODIS
Combined DNA Index System CODIS
 CODIS began as a pilot project in 1990 serving 14 state
and local laboratories.
 The DNA Identification Act of 1994 (Public Law 103 322) formalized the FBI's authority to establish a
national DNA index for law enforcement purposes
 October 1998, the FBI's National DNA Index System
(NDIS) became operational.

NDIS (NATIONAL DNA INDEX SYSTEM)

NDIS is the highest level in the CODIS hierarchy, and
enables the laboratories participating in the CODIS
Program to exchange and compare DNA profiles on a
national level
HOW NDIS WORKS
CODIS generates investigative leads in crimes where
biological evidence is recovered from the crime scene
using two indexes: the forensic and offender indexes.
 The Forensic Index contains DNA profiles from crime
scene evidence.
 The Offender Index contains DNA profiles of
individuals convicted of sex offenses (and other violent
crimes) with many states now expanding legislation to
include other felonies.

Matches made among profiles in the Forensic Index
can link crime scenes together; possibly identifying
serial offenders.
 Based on a match, police in multiple jurisdictions can
coordinate their respective investigations, and share
the leads they developed independently.
 Matches made between the Forensic and Offender
indexes provide investigators with the identity of the
perpetrator(s).
 After CODIS identifies a potential match, qualified
DNA analysts in the laboratories contact each other to
validate or refute the match.

PARTICIPATING STATES
April 2004 - 49 States, US Army, the FBI, and Puerto
Rico
 All states currently participate in NDIS except for
Mississippi

STATISTICS:
As of April 2004 the
profile composition of
the National DNA
Index System (NDIS)
is as follows:
 Total number of
profiles: 1,762,005



Total Forensic
profiles: 80,302
Total Convicted
Offender
Profiles: 1,681,703
MEASURING SUCCESS
Ultimately, the success of the CODIS program will be
measured by the crimes it helps to solve.
 CODIS's primary metric, the "Investigation Aided,"
is defined as a case that CODIS assisted through a
hit (a match produced by CODIS that would not
otherwise have been developed).
 As of April 2004, CODIS has produced over 13,600
hits assisting in more than 16,600 investigations.

1/18/2006
DNA FINGERPRINTING
BRIEF HISTORY OF FORENSIC DNA
TYPING
1980 - Ray White describes first polymorphic
RFLP marker
 1985 - Alec Jeffreys discovers multilocus VNTR
probes
 1985 - first paper on PCR
 1988 - FBI starts DNA casework
 1991 - first STR paper
 1995 - FSS starts UK DNA database
 1998 - FBI launches CODIS database



1984 Dr. Alec Jefferys
Leicester University in England
Gave the name to this identification – genetic
fingerprinting
Jefferys also discovered particular locations of
the DNA ladder where repetitive patterns show
the greatest variability in the number of times
they repeat.
EXAMPLE OF GEL
FROM 1984
1/18/2006
The DNA
fingerprinting
technique is
developed.
ANOTHER
EXAMPLE FROM
1985
Genetic
fingerprinting
enters the
courtroom.
1/18/2006
• The first practical test of DNA fingerprinting
involved a two year struggle by Christiana Sarbah
and her son, Andrew, to prove to the Home Office
in England that they were, indeed, mother and
son.
• The ordeal began in 1983 when Andrew, then 13,
arrived in England after a long stay in Ghana with
Christiana's estranged husband.
• Immigration officials held him at Heathrow
Airport, claiming his passport was forged, or that
a substitution had been made.
• Only after intervention by a Member of
Parliament was Andrew allowed to stay at his
family's home in London.
• Hammersmith Law Centre, which provides
legal aid to the under-privileged, amassed
huge amounts of evidence, including
photographs & statements by family
members. Various tests to determine genetic
characteristics showed that Christiana and
Andrew were almost certainly related.
• However, the tests could not determine
whether Christiana was his mother or merely
an aunt.
• After reading in the local newspaper about a
scientific discovery that could prove
maternity, Centre workers contacted Alec
Jeffreys at Leicester University, and asked
him to take on the case. Jeffreys accepted,
believing it would be an ideal test of the DNA
fingerprint technology he had recently
developed.
• Jeffreys used DNA extracted from blood
samples from Christiana, Andrew, an
unrelated individual, and Christiana's three
undisputed children. Jeffreys produced the
DNA fingerprints seen at the right.
• He compared the banding patterns of all the
individuals. Alec Jeffreys showed that Andrew's
DNA fingerprint contained about 25 bands that
were inherited from his mother. The possibility that
Christiana is the "true" mother's sister is one in
600,000.
• Although Andrew's father's DNA was not available,
Jeffreys reconstructed the father's DNA fingerprint
from bands present in Christiana's three other
children, but absent in Christiana.
• About half of Andrew's bands match bands in the
father's compilation and the remaining bands were
all present in Christiana's fingerprint.
• The possibility of this happening by chance is less
than one in a trillion.
• The Home Office accepted the DNA fingerprint
evidence, and allowed Andrew to stay in England
with his mother and siblings. The Home Office also
announced that it would not contest future
immigration cases if similar DNA evidence were
available.
FIRST PRACTICAL TEST OF DNA FINGERPRINTING
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1/18/2006
• In July 1987, Randall Scott Jones and Chris
Reesh, both teenagers, were shooting with a 30/30
hunting rifle at Rodman Dam recreation area in
Florida. While they were shooting, Jones' pickup
truck became stuck in a sandpit.
• A fisherman suggested they ask a couple in a
pickup parked nearby for help. Jones and Reesh
approached the truck, where Kelly Lynn Perry and
her fianc’e, Matthew Brock, were sleeping. The
two men debated whether or not to wake them to
ask for assistance.
• The following morning, fishermen found the bodies
of Perry and Brock in the woods adjacent to the
recreation area.
• Police investigated and revealed that each had
been shot in the head with a 30-caliber bullet and
that Perry had been sexually assaulted. Their
pickup was reported stolen.
• In August, Jones was arrested in Mississippi
found driving Brock's pickup. Reesh was arrested
the next day in Palakta, Florida, after Jones told
police that they were together that night in July.
Both were indicted on counts of first-degree
murder and sexual battery.
• A semen sample, retrieved from Perry's body, and blood samples from
Reesh, and Jones, were compared at a laboratory that specializes in DNA
fingerprint testing.
• Using the results of the DNA fingerprint and other evidence, officials were
able to piece together the events of the crime:
• Without waking the couple in the pickup, Jones shot both Perry and
Brock in the head at close range. He and Reesh then dragged the
bodies into the woods nearby. They towed Jones' truck from the sand
with Brock's pickup and left with both trucks.
• Later Jones returned to the crime scene, moved the bodies further into
the woods, and raped Perry.
• A representative from the DNA fingerprinting laboratory tested that the
chance of another person having the same DNA fingerprint as Jones was
one in 9,390,000,000 about twice the earth's population (at the time).
• After deliberating only 15 minutes, the jury convicted Jones of murder and
rape.
• The judge sentenced him to a double death sentence, making the first case
involving DNA fingerprint evidence in U.S. legal history in which the death
sentence was handed down.
• Reesh was sentenced to six years in prison and twenty years probation
(because he didn’t pull the trigger or rape the woman).
MURDER AT RODMAN DAM
1988
First Case using DNA
fingerprinting (in the
USA) to hand down
death penalty.
DNA SOURCES
1/18/2006
Blood
 Semen
 Body
 tissues

2
1
4
3
GENE
1/18/2006
EUKARYOTIC GENE
1/18/2006
 Introns
 Noncoding
sequence
 80 -10,000 nucleotides
 Exons
 Coding sequence
 shorter
RESTRICTION ENZYMES
Evolved by bacteria to protect against viral DNA infection.
 Endonucleases- Cleave (or cut) DNA Strands.
 3,000 + restriction enzymes known.
 Search for a specific sequence of bases in the DNA, then
they cut the DNA within that sequence.



Sticky Ends: have a short segment of single
stranded DNA on each end of the fragments
produced.
Blunt Ends: have no single strands on their ends
after they are cut.
1/18/2006
1/18/2006
RESTRICTION
ENZYMES
RESTRICTION ENZYME EXAMPLE
1/18/2006
TaqI
T CGA
AGC T
Cuts between T and C
Leaves sticky end CG
STICKY END OF ECOR1
1/18/2006

EcoR1
GAATTC
 AATT

PREPARING AND RUNNING STANDARD AGAROSE
DNA GELS
The equipment and supplies necessary for
conducting agarose gel electrophoresis are:
 An electrophoresis chamber and power supply
 Gel casting trays, which are available in a variety of
sizes and composed of UV-transparent plastic. The open
ends of the trays are closed with tape while the gel is being
cast, then removed prior to electrophoresis.
 Sample combs, around which molten agarose is poured to
form sample wells in the gel.

Electrophoresis buffer, usually Tris-acetate-EDTA
(TAE) or Tris-borate-EDTA (TBE).
 Loading dye, which contains something dense (e.g.
glycerol) to allow the sample to "fall" into the sample
wells, and one or two tracking dyes, which migrate in the
gel and allow visual monitoring or how far the
electrophoresis has proceeded.


Ethidium bromide, a fluorescent
dye used for staining nucleic
acids. NOTE: Ethidium bromide is
a known mutagen and should be
handled as a hazardous chemical wear gloves while handling.


Methylene Blue can be used as a
dye to visualize the DNA as well.
This is what we will use in class.
Transilluminator (an ultraviolet
lightbox), which is used to
visualize ethidium bromidestained DNA in gels. NOTE:
always wear protective eyewear
when observing DNA on a
transilluminator to prevent
damage to the eyes from UV light.
TO POUR A GEL:




Agarose powder is mixed with electrophoresis buffer to the
desired concentration, then heated until completely melted.
Ethidium bromide may be added to the gel at this point to
facilitate visualization of DNA after electrophoresis.
After cooling the solution to about 60C, it is poured into a
casting tray containing a sample comb and allowed to solidify
at room temperature or.
After the gel has solidified, the comb is removed. The gel is
inserted into the electrophoresis chamber and just covered
with buffer.
Samples containing DNA mixed with loading dye are then
pipetted into the sample wells, the lid and power leads are
placed on the apparatus, and a current is applied. DNA will
migrate towards the positive electrode, which is
usually colored red.
When adequate migration has occurred (usually 30 min.
at 100 volts), DNA fragments are visualized by
staining.
 Be aware that DNA will diffuse within the gel over time,
and examination or photography should take place
shortly after cessation of electrophoresis.

ELECTROPHORESIS
1/18/2006
MIGRATION OF DNA FRAGMENTS IN AGAROSE
Fragments of linear DNA migrate through agarose
gels with a mobility that is inversely proportional
to their molecular weight. In other words, longer
fragments move slower than shorter ones.
 So fragments are separated by size in the gel. Long ones
stay close to the wells, short one move farther away.

FRAGMENT SIZE VS. DISTANCE
TRAVELED
1/18/2006
DEMONSTRATION OF DNA
ELECTROPHORESIS:
1/18/2006
SAMPLE DNA FINGERPRINT
EXAMPLE 1
1/18/2006
GCATGCATGCATGCATG
CAT
EXAMPLE 1
1/18/2006
EXAMPLE 2
1/18/2006
Andrew 1:
-GAATTC---(8.2 kb)--GCATGCATGCATGCATGCAT---(4.2
kb)---GAATTCPolly 1:
-GAATTC---(8.2 kb)--GCATGCATGCATGCATGCAT---(4.2
kb)---GAATTC-
EXAMPLE 2
Polly 2:
-GAATTC--(1.8 kb)-GAATTC--(1.2 kb)-GCATGCATGCATGCATGCAT--(1.3
kb)-GAATTC-
1/18/2006
Andrew 2:
-GAATTC--(1.8 kb)-CCCTTT--(1.2 kb)-GCATGCATGCATGCATGCAT--(1.3
kb)-GAATTC-
EXAMPLE 2
1/18/2006
PATERNITY CASE
1/18/2006
DNA TECHNOLOGY AS IDENTIFICATION EVIDENCE

“DNA analysis can promote a more just society, both by
making punishment of the guilty more likely and by
assuring exoneration of the innocent”
- Harlan Levy - Assistant District Attorney, Manhattan
WHY IS DNA EXCELLENT EVIDENCE FOR
CONVICTION?


Less than 1 percent of any individual’s DNA is
different from that of other people
The pieces of DNA that do not code for our arms,
legs, heads…. Those pieces that have no function
are very different in each individual.

Generally, courts have
accepted the reliability of DNA
testing and admitted DNA test
results into evidence. However,
DNA fingerprinting is
controversial in a number of
areas:



the accuracy of the results,
the cost of testing, and
the possible misuse of the
technique.
olymerase
hain
eaction
ABOUT KARY B. MULLIS
He is an American
biochemist who won the
Nobel Prize in 1993 for his
discovery of PCR. He
shared the prize with
Michael Smith, who is
also a biochemist.
DNA NUMBERS ARE MERELY A MEANS OF
STATING THE CHANCES OF PARTICULAR MATCHES
TO OCCUR.
TAQ POLYMERASE
THERMUS AQUATICUS
THERMAL CYCLER
MATERIALS OF PCR
target
DNA
Taq DNA polymerase
2 Primers


~20 nucleotides in length
Forward and reverse
the
four DNTP’S
 Adenine
 Thymine
 Cytosine
 Guanine
cofactor
MgCl2.
PRIMERS:

Two different primers are used because:
The backbones run in opposite directions.
 The beginning and the end of the target sequence need
to be marked.
 Taq Polymerase must have a beginning point to build
the rest of the DNA onto.

DNTPS:

DNTPs are the
nucleotides that the
new DNA is built
from.
LOCATE THE TARGET SEQUENCE
Scientists determine which GENE they are interested
in replicating.
 Determine where primers would bond upstream and
downstream of at each end of the gene.

STEPS IN 1 CYCLE OF PCR:
STEP 1 - DENATURING
• 60 seconds
• @ 94°C
• Backbones separate.
STEP 2 - ANNEALING
• 60 seconds
• @ 60°C
• Forward and Reverse Primers
bond to the template.
TAQ POLYMERASE BINDS
TO THE PRIMERS
STEP 3 - EXTENSION
•
•
•
2 minutes
@ 72°C
Taq Polymerase uses DNTP’s to build
the rest of the new backbones.
Multiplex PCR




Over 10 Markers Can Be
Copied at Once
Sensitivities to levels less
than 1 ng of DNA
Ability to Handle Mixtures
and Degraded Samples
Different Fluorescent Dyes
Used to Distinguish STR
Alleles with Overlapping
Size Ranges
AVAILABLE KITS FOR STR ANALYSIS
Kits make it easy for labs to just add DNA samples
to a pre-made mix
 13 CODIS core loci

Profiler Plus and COfiler (PE Applied Biosystems)
 PowerPlex 1.1 and 2.1 (Promega Corporation)


Increased power of discrimination
CTT (1994): 1 in 410
 SGM Plus™ (1999): 1 in 3 trillion
 PowerPlex ™ 16 (2000): 1 in 2 x 1017

Human Identity Testing with Multiplex STRs
Two different individuals
AmpFlSTR® SGM Plus™ kit
DNA Size (base pairs)
D3
amelogenin
D8 TH0
1 VWA D21
D19
D16
D18
FGA
probability of a random
match: ~1 in 3 trillion
amelogenin D3
D19
D8
VWA
TH0
1
D2
Results obtained in less than 5
hours with a spot of blood the
size of a pinhead
D16
D21
FGA
D18
Simultaneous Analysis of 10 STRs and Gender ID
D2
THE POWER AND SIGNIFICANCE OF A MATCH GROWS AS
MORE LOCATIONS ON THE DNA LADDER ARE ANALYZED
AND AS MATCHES ARE FOUND ON MORE PIECES AT
ANOTHER CHROMOSOME.

1 DNA fragment match could happen in 1/100 people.

2 DNA fragment matches = happen in 1/10,000.

numbers grow exponentially (100 x 100).

3 DNA fragment matches = 1/1,000,000 (1 million)
(10,000 x 10,000).

4 DNA fragment matches = 1/100 million.

5 DNA fragment matches = 1/10 billion.

(There are only a little over 7 billion people living on the face of the earth).