DNA

The capacity to blunder slightly is the real marvel of DNA.

Without this special attribute, we would still be anaerobic bacteria
and there would be not music.
--Lewis Thomas

Objectives
At the end of this powerpoint and discussion, you should be
able to:

Define new terms related to DNA

Identify forensic experts and their field of expertise
Summarize significant cases involving DNA
Describe general structure and parts of a DNA molecule
Identify the uses, types of DNA typing and summarize each technique
Explain CODIS and whose DNA is contained and how many loci are
used in the US for identification by CODIS
Explain the case of the Romanovs family both from this lecture and the
website
Give class and individual characteristics of blood
Compare and contrast nuclear v mitochondrial DNA
Describe uses for mitochondrial and Y-chromosome typing
Introduction

Saint Louis University

2

Historical Information
James Watson and Francis Crick------1953 discovered
the configuration of the DNA molecule
Ray White--1980 describes first polymorphic RFLP
marker
Alec Jeffreys------1985 isolated DNA markers and called
them DNA fingerprints
Karry Mullis-------1985 developed PCR testing
1988--FBI starts DNA casework
1991--first STR paper
1997-1998---------FBI launches CODIS database.
2003--Completion of the Human Genome Project
Saint Louis University

People of Historical
Significance
James Watson, Francis Crick, and Maurice Wilkins
jointly received the Nobel Prize in 1962 for their
determination of the structure of DNA. What is
interesting about this fact is that Rosalind Franklin
had as much to do with the discovery as the other
three gentlemen with her work with X-ray
crystallography. She died of cancer and could not
be honored for her work. Find out more at
Chemical Achievers:
www.chemheritage.org/EducationalServices/chemach/ppb/cwwf.html

DNA

Saint Louis University

Colin Pitchfork
1983-86 England

1983, a 15-year-old schoolgirl raped and murdered

semen sample with type A blood group and enzyme profile, matched 10
% of the adult male population.
1986, 15-year-old girl strangled and sexually assaulted in the same town.
semen samples had same blood type
adult males in three villages a total of 5,000 men - were asked to
volunteer and provide blood or saliva samples.
blood typing done and DNA profiling done on the 10 per cent of men
who had the same blood type as the killer.
got a friend to give blood in his name
Colin Pitchfork was arrested and his DNA profile matched with the
semen from both murders. In 1988 he was sentenced to life for the two
murders.
Saint Louis University

Tommy Lee Andrews

1986- first trial to admit DNA in the U.S.
24 rapes in Orlando, Florida between May, 1986 and
Dec, 1986.
All connected to a serial rapist, but he was unidentified.
He was caught in 1987, by fingerprint match.
But his blood type matched- and a semen sample was
requested.
They all matched--now a Court had to be convinced.
Ultimately he was convicted and sentenced to 115
years.
Saint Louis University

Jesse James
Historians say James died rather
unromantically in April 1882 at the age
of 34, shot in the back by a member of
his own outlaw gang while straightening
a picture on the wall of his home.
He was apparently buried on the family
homestead near Kearney, Mo. The
remains were moved in 1902 and
reburied next to his wife at Mount Olivet
Cemetery in Kearney, 20 miles northeast
of Kansas City, Mo
DNA

Saint Louis University

Jesse James
A team of crime-lab specialists conducted a
study and concluded that the remains in the
Missouri grave marked "Jess W. James" do
belong to the outlaw.
Also, DNA evidence taken from the grave site
was compared in 1996 to two descendants of
James' sister Susan, and found to match almost
exactly - genetic proof that the James family
line extended from the outlaw's mother, Zerelda
James, to living descendants.
Saint Louis University

Jesse James

Saint Louis University

Animal DNA to the Rescue

In 1994, Shirley Duguay, a 32-year-old mother of
five, disappeared. Her body was found in a shallow
grave a few months later. Among the chief suspects
in the murder was the womans estranged commonlaw husband, Douglas Beamish, who was living
nearby in his parents home. Royal Canadian
Mounted Police had no evidence linking Beamish
to the crime. During the search for the victims
body, however, the Mounties discovered a plastic
bag containing a leather jacket with blood stains
that matched the victims blood. The jacket also
contained 27 strands of white hair, which forensic
investigators determined were from a cat.
Saint Louis University

10

Snowball
The Mounties remembered a
white cat named
Snowball
Your text
here
living in Beamishs
parents home. The trick
was to prove the cat hair
found in the jacket was
Snowballs and that it was
unique in comparison to
other cats.
DNA

Saint Louis University

11

The Romanovs
Anastasia Romanov was the youngest daughter of Tsar
Nicholas of Russia and his wife Tsarina Alexandra.
Anastasia had three older sisters. Olga, Maria, and
Tatiana, and a younger brother Alexei. In 1917, the
Bolsheveks led by Vladimir Lenin overthrew the
Romanovs. Anastasia and her family were imprisoned
in Siberia and, in July of 1918. they were brutally
murdered by the Boshevik soldiers. In order to prevent
those remaining loyal to the Tsar from finding his
remains, the bodies were buried in a secret location.
Saint Louis University

12

Was She Really Dead??

In the 1920s an unknown woman in a mental hospital in
Germany claimed to be Anastasia Romanov. While in
the hospital she adopted the name Anna Anderson.
Since the 1918 massacre of the Romanov family rumors
have persisted that some members of the imperial family
may have survived. Could this unknown woman be
Anastasia Romanov the youngest daughter of Tsar
Nicholas? Anna Anderson had the same hair color, eye
color, height and distinctive body markings including a
deformed foot, that the Romanov princess had. Could
Anastasia have escaped the brutality of the Bolshevik
soldiers? Anna Anderson claimed to be Anastasia until
her death in 1984.
Saint Louis University

13

Skeletal Remains
In 1991 the remains of the royal Romanov family
were exhumed in Yekaterinburg, Siberia. Portions
of nine skeletons were found. Scientists used
various techniques to identify the skeletal remains.
They were able to identify the bodies of the Tsar
and Tsarina as well as three of their children. Two
skeletons were missingAnastasia and the
youngest son Alexei.

Saint Louis University

14

What happened to Anastasia Romanov?

For most of the 20th century, this question persisted
without a conclusive answer. Could she have
survived the massacre that took the lives of her
entire family? Or did she escape and live out her life
without ever being recognized for whom she truly
was? In 1994, scientists were able to use modern
DNA technology to analyze the evidence and
determine whether Anna Anderson was really
Anastasia.
Saint Louis University

15

DNA Interactive--The Romanovs

Go to the:

Click on: Applications and then on Recovering

the Romanov.
Watch, read and answer the questions given to you
on the Romanov family, the mystery of Anna
Anderson, and the section of science solves a
mystery.
Saint Louis University

16

Plant DNA Tells the Story

In May 1992 the body of a woman was
found in the brush near some paloverde
trees in Maricopa County, Arizona.
The suspect admitted that he had picked
up the victim, who had been
hitchhiking, and had sexual relations
with her in the pickup. But he said he
had made her get out of the truck after
they had argued. He denied being at the
crime scene, and he denied killing her.

17

PLANT DNA

Police obtained the assistance of a plant molecular genetics

specialist from the University of Arizona, who could
compare the DNA profile of the seed pods recovered from
the suspects pickup with those of the trees in the vicinity of
the crime scene. The geneticist conducted blind tests on a
number of palo verde trees, and the tests showed that each
exhibited a different profile. The seed pods from the pickup
truck showed identical profiles (indicating that they fell
from the same tree), and their profile matched that of one
particular tree at the scene.
The court allowed the evidence because the expert did a
good job of running his tests blind and of establishing that
there was much detectable variation in the trees.

18

Recent Developments
As late Dec 2006, more body parts (bones)
were being found at the 9/11 site in under
ground areas of New York City.
As of September 2014
________ killed
________ identified
________ % unidentified

DNA

Saint Louis University

19

General DNA Information

Double helix--two coiled DNA strands
Composed of nucleotides--unit containing a sugar
molecule (deoxyribose), phosphate group and a
nitrogen-containing base
In humans, the order of these bases is 99.9% the same.
Four bases

1. adenine
2. cytosine
3. guanine
4. thymine

Bases always pair A to T and G to C.

DNA
Each cell contains all of the organism's
genetic instructions stored as DNA.
Each very long DNA molecule is tightly
wound and packaged as a chromosome.
Each DNA molecule that forms a
chromosome can be viewed as a set of
shorter DNA sequences. These are the
units of DNA function, called genes. A
set of human chromosomes contains one
copy of each of the roughly 30,000
genes in the human "genome.

DNA

Saint Louis University

21

DNA Body Locations

Can be found in all body cellsblood, semen, saliva,
urine, hair, teeth, bone, tissue
Most abundant in our buccal (cheek) cells
35.000 genes in the human body which are portions of
DNA that code for specific proteins
Blood is mainly composed of red blood cells that have no
nuclei; and therefore, no nuclear DNA
DNA obtained from blood comes from white blood cells

DNA

Saint Louis University

22

Human Genome Contains 23

Pairs of Chromosomes
http://www.ncbi.nlm.nih.gov/genome/guide/

Butler, J.M. (2001) Forensic DNA Typing, Figure 2.2, Academic Press

10 11 12

13 14 15 16 17 18 19 20 21 22 X
Saint Louis University

Sex-chromosomes

23

Karyotype

Humans have 23 of
chromosomes with one set
coming from mom and one
set coming from dad. The
first 22 pair are called
autosomes. The last pair
are our sex chromosomes.
What is the sex of the
individual represented by
this karyotype?
female

Saint Louis University

24

DNA TYPING
DNA typing is a in which DNA is converted
into a series of bands that ultimately
distinguishes each individual. Only onetenth of a single percent of DNA (about 3
million bases) differs from one person to the
next. Scientists use these regions to
generate a DNA profile of an individual.

Non-Coding Regions
3 percent of the human DNA sequences
code for proteins
97 percent is non-coding and is repetitive;
repeating the same sequence over and
over
50 percent of the human genome has
interspersed repetitive sequences
Saint Louis University

26

Uses of DNA profiling

To identify: potential suspects

To exonerate: individuals
To identify: crime and casualty victims
To establish: paternity
To match: organ donors

Saint Louis University

27

Understanding DNA Typing

DNA typing methods create PATTERNS that
ultimately distinguish each individual.
The key to understanding DNA typing lies in the
knowledge that within the worlds population
numerous possibilities exist for the number of
times a particular sequence of base letters can
repeat itself on a DNA strand.

Saint Louis University

28

DNA TYPING
Fingerprinting
RFLP Restriction Fragment Length
Polymorphism
PCR Polymerase Chain Reaction
STRShort Tandem Repeats
Mitochondrial--use of maternal DNA in the
mitochondria
Y-chromosomes with use of male inheritances

RFLP--Summarized Steps
Isolation--separate DNA from the cell
Cutting --using a restriction enzyme to make
shorter base strands
sorting-by size using electrophoresis
analyzing--the specific alleles for identification

Saint Louis University

30

PCR--Polymerase Chain
Reaction
PCR is a technique for making many copies of
a defined segment of a DNA molecule.
Every gene has at least two alternative forms
called alleles. An individual receives one
allele from mother and one from father.
If the alleles are the same, the individual is
said to be homozygous for the trait; if the
two alleles are different, the individual is
heterozygous.
Saint Louis University

31

PCR
Three steps:
Animation**********
Denaturation 1 minute 94C
******************* Separating the stranfs of
DNA
********
Annealing 45 seconds 54C
Add forward and reverse
primers

Extention 2 minutes 72C

Adding the dNTPs
(nucleotides) and
duplicating the DNA

Electrophoresis
An electrical current moves through a
substance causing molecules to sort by
size.
Smaller, lighter molecules will move the
furthest on the gel.

Saint Louis University

33

Electrophoresis (cont.)
Run the gel.

Observe and compare

bands of DNA.

DNA

Saint Louis University

34

HOMEWORK--DNA
INTERACTIVE
Go to the website below to see a STR animation
demonstration. Click on human identification , profiling
and then on the third circle called Todays DNA
Profiling.

http://www.dnai.org/d/index.html

35

Short Tandem Repeats (STR)

STR is the latest method of DNA typing.
STRs are locations (loci) on the
chromosome that contain short sequences of
3 to 7 bases that repeat themselves with the
DNA molecule. This methods advantages
include a higher discrimination than RFLP,
less time, smaller sample size, and less
susceptible to degradation.
Saint Louis University

36

Short Tandem Repeats (STR)

Extract the gene from the sample. Amplify
the sample by means of PCR
Separate by electrophoresis
Examine the distance the STR migrates to
determine the number of repeats

Saint Louis University

38

Short Tandem Repeats (STR)

Each person has two STR types each gene--one inherited
from each parent.
Continue the process with additional STRs from other
genes
Imagine how the probability of a match DECREASES by
using an INCREASING number of STRs.

Saint Louis University

39

Separation of STR Fragments

Electrophoresis
Fragments separated on basis of mass/charge

Two types:
1. Gel
2. Capillary

Saint Louis University

40

STR Detection Methods

Silver staining (gel only)
Fluorescence detection
Fluorescent dye attached to a PCR primer
Labeled dye incorporated in amplified STR product
Fluorescent dye-labeled products are analyzed as they pass
by a detection window on gel or capillary platform
Dyes can separate alleles of similar sizes from different loci

STR genotypes visualized on electropherogram*

********************

Saint Louis University

41

Why STRs are Preferred

Genetic Markers

Rapid processing is attainable

Abundant throughout the genome
Highly variable within various populations
Small size range allows multiplex development
Discrete alleles allow digital record of data
PCR allows use of small amounts of DNA material
Small product size compatible with degraded DNA
STRs in forensic are: inherited independently**** are
inherited independently
Saint Louis University

42

Profiler Plus Allelic Ladders

VWA

D3S1358

AMEL

D8S1179

D5S818

FGA

D21S11

D13S317

D18S51

D7S820

COfiler Allelic Ladders

D3S1358

AMEL

D16S539

TH01

TPOX

CSF1PO

D7S820

Identifiler

D8S1179

D7S820

CSF1PO

D21S11
D3S1358

TH01

D13S317

D16S539

D2S1338

D19S433

VWA
AMEL

DNA

D5S818

TPOX

D18S51
FGA

PowerPlex 16 Ladders
D3S1358

TH01

D5S818

AMEL

VWA

DNA

D21S11

D13S317 D7S820

D8S1179

Penta E

D18S51

D16S539

TPOX

Penta D

CSF1PO

FGA

Three Possible Outcomes

Inclusion--The DNA profile appears the same.
Lab will determine the frequency.
Exclusion--The genotype comparison shows
profile differences that can only be explained by
the two samples originating from different sources.
Inconclusive--The data does not support a
conclusion as to whether the profiles match.
DNA

Saint Louis University

47

Determining Probability
Databases are established by which one has
determined how often a particular allele on a
loci appears in a given population. By
increasing the number of alleles on different
loci the probability of having two people with
the exact combination becomes astronomical.

Saint Louis University

48

FBIs CODIS DNA Database

Combined DNA Index
System
Used for linking serial
crimes and unsolved
cases with repeat
offenders
Launched October 1998
Links all 50 states
Requires >4 RFLP
markers and/or 13 core
STR markers
DNA

Saint Louis University

49

People in the News

Sir Alec Jeffreys is credited with the DNA profiling
using RFLP. It was September of 1984 after years
of work that he saw his first series of blots on an Xray. The technique was first used in forensics,
when in 1985 he was asked by police to confirm the
rape confession of a 17 year old boy, Richard
Buckland who was denying a rape of another
young woman. The DNA from the boy and that
taken from the victims eliminated him as a suspect,
but helped to later convict Colin Pitchfork whose
DNA did match.
DNA

Saint Louis University

50

People In The News

Kary Mullis received a Nobel Prize
in chemistry in 1993, for his
invention of the polymerase chain
reaction (PCR). The process,
which Kary conceptualized in
1983, is hailed as one of the
monumental scientific techniques
of the twentieth century.

People in the News

John M. Butler is THE leading expert on DNA
typing. He is currently a fellow at the National
Institute of Standards and Technology.
Butler received his bachelors degree from
Brigham Young University . He earned his Ph.D.
from the University of Virginia.
Butler has written a textbook on DNA Typing.

DNA

52

Types of DNA
Nuclear
found in the nucleus
constitutes 23 pair of
chromosomes inherited
from both parents
each cell contains only
one nuclei

Mitochondrial
found in the cytoplasm
is inherited only from
mother
each cell contains hundreds to
thousands of mitochondria
can be found in skeletal
remains

NuclearDNAispresentintheheadofthesperm.MitochondrialDNAispresentinthetailAt
conception,theheadofthespermenterstheegganduniteswiththenucleus.Thetailfallsoff,losing
thefathersmitochondrialDNA.
Saint Louis University

53

Mitochondrial DNA
Analysis of mtDNA is more:
rigorous
time consuming
costly than nucleic testing of DNA

mtDNA is constructed in a circular or loop

37 genes are involved in mitochondrial energy
generation
Is best used when nuclear DNA typing is not
possible
Saint Louis University

54

Mitochondria DNA

Saint Louis University

55

The Unknown Soldier

The remains of the Vietnam
unknown soldier in Arlington
cemetary were exhumed and tested
using mtDNA.
Forensic anthropologists took the
aged and damaged samples of bone
for mitochondrial DNA (mtDNA)
testing. Because mtDNA is passed
along the maternal line, scientists
compared the Unknown Soldier's
DNA against two samples
submitted by First Lieutenant
Blassie's mother and sister and
found a match.
DNA

Saint Louis University

56

Lt. Michael Blassie

Air Force Reserve Capt. Pat Blassie, Lt. Blassie's sister,
said "For 26 years my mother wondered where her son
was," Blassie said. "DNA testing was very important.
No one has questioned the results."
On May 11, 1972, North Vietnamese anti-aircraft guns
sliced apart Air Force 1st Lt. Michael Joseph Blassies
A-37 attack jet while it made a low-level bombing run
near An Loc, 60 miles north of Saigon.
On July 11, 1998, 1st Lt. Michael Blassie was buried
with full military honors in Jefferson National
Cemetery, Missouri in the same cemetery as his father.

DNA

Saint Louis University

57

Y-chromosome Analysis
There are two sex chromosomes in mammals, the X
and the Y. Females have two X chromosomes
while males have an X and a Y. The Y
chromosome has the genes for making a
mammal a male (and little else). It is the
smallest chromosome and has around 75 genes.
Why is the Y chromosome so useful for these
studies?
The main reason is that the Y chromosome is
the only chromosome without a partner.
Because the Y chromosome is all alone, it only
recombines with itself. Most of the Y
chromosome, therefore, passes almost
unchanged from generation to generation.

DNA

Saint Louis University

58

The Y chromosome
A core set of Y chromosome short tandem repeat (Y-STR) loci
have been selected for use in human identification
applications. The core Y-STR loci were recommended and
include the following: DYS19, DYS389I, DYS389II,
DYS390, DYS391, DYS392, DYS393, DYS438, DYS439,
and the multi-copy locus DYS385 a/b.

DNA

Saint Louis University

59

Y Chromosome Analysis Example

Saint Louis University

60

Thomas Jefferson and

Sally Hemings
Sally Hemings, whose given name was probably Sarah,
was the daughter of Elizabeth (Betty) Hemings and,
allegedly, John Wayles, Thomas Jefferson's father-inlaw. She became Thomas Jefferson's property as part
of his inheritance from the Wayles estate in 1774 and
came with her mother to Monticello by 1776.
There were many rumors even before he became
President that Jefferson had fathered a child or
children with Sally.
Saint Louis University

61

Thomas Jefferson
Thomas Jefferson did not have surviving sons from his legal
wife. But his paternal uncle's male lineage is in tact to
present time.
The study - which tested Y-chromosomal DNA samples from
male-line descendants of Field Jefferson (Thomas Jefferson's
uncle), John Carr (grandfather of two of Jefferson's nephews
and whose descendants believed fathered Hemings
children), Eston Hemings, and Thomas C. Woodson (whose
descendents believed he was the first born son of Jefferson
and Hemings)- indicated a genetic link between the Jefferson
and Hemings descendants.
The results of the study established that an individual carrying
the male Jefferson Y chromosome fathered Eston Hemings
(born 1808), the last known child born to Sally Hemings.
There was no connection between Jefferson and Woodson.

Saint Louis University

62

FamilyPedigree Results
Member
Jefferson

Microsatellite STRMini
15,12,4,11,3,9,11,10,15,13,7
15,12,4,11,3,9,11,10,15,13,7
15,12,4,11,3,9,11,10,15,13,7
15,12,4,11,3,9,11,10,15,13,7
15,12,4,11,3,9,11,10,16,13,7

Satellite MSY1
(3)5, (1)14, (3)32, (4)16
(3)5, (1)14, (3)32, (4)16
(3)5, (1)14, (3)32, (4)16
(3)5, (1)14, (3)32, (4)16
(3)5, (1)14, (3)32, (4)16

Hemings
(Easton)
Carr

15,12,4,11,3,9,11,10,15,13,7

(3)5, (1)14, (3)32, (4)16

14,12,5,12,3,10,11,10,13,13,7
14,12,5,11,3,10,11,10,13,13,7
14,12,5,12,3,10,11,10,13,13,7

(1)17, (3)36, (4)21

(1)17, (3)37, (4)21
(1)17, (3)36, (4)21

Woodson
(Thomas)

14,12,5,11,3,10,11,13,13,13,7
14,12,5,11,3,10,11,13,13,13,7
14,12,5,11,3,10,11,13,13,13,7

(1)16, (3)27, (4)21

(1)16, (3)27, (4)21
(1)16, (3)27, (4)21

Present Work in DNA

CODIS--Combined DNA Information System.
A data base of DNA profiles of individuals convicted of sex
crimes and other violent crime

TWGDAM--The Working Group for DNA

Analytical Methods
Wrote the standards for DNA analysis that are part of a national
crime laboratory accreditation program

Innocence Project
Group of college law students work on cases where DNA may
prove innocence (or guilt)

Saint Louis University

64

DNA--The Search for Innocence

DNA implicates the guilty and exonerates the innocent--R.
Saferstein

TheInnocenceProjectattheBenjaminN.CardozoSchoolofLawat
YeshivaUniversity,foundedbyBarryC.ScheckandPeterJ.Neufeld
in1992,isanonprofitlegalclinicandcriminaljusticeresourcecenter.
Weworktoexoneratethewrongfullyconvictedthroughpostconviction
DNAtesting;anddevelopandimplementreformstopreventwrongful
convictions.ThisProjectonlyhandlescaseswherepostconviction
DNAtestingcanyieldconclusiveproofofinnocence.
Overtheyearsmanyinnocentpeoplehavebeenwronglyconvicted
withnowayofprovingtheirinnocence.Sincethelate1980s,DNA
technologyhasbeenavailable.People,asaresult,havebeenreopening
casesandtestingtheevidenceforDNA.Somehavebeenexonerated
becausetheirDNAdidnotmatch.

318 exonerated as of 10/2/14.

The Future
Greater automation of the DNA typing process
Use of SNPs--single nucleotide polymorphism
which measures a one nucleotide change or
difference from one individual to another. More
sites are needed to differentiate between
individuals (30 to 50 SNPs to attain the
frequencies of the 13 STR loci), but it can be
done with robots and automation.

Saint Louis University

66

Touch DNA
Touch DNArefers to the DNA left behind from skin cells
when a person touches or comes in contact with an item
Cases
Danielle Van Dam
Jon Benet Ramsey
Anthony Case
DNA in the trunk?
mtDNA from the hair
DNA on the duct tape
Touch DNA

A Interesting DNA
Dilemma
A human chimera--when two separate embryos
merge into one.
Begin as two or more eggs fertilized by different
sperm. These usually become fraternal twins, but
in a few cases they merge while in utero,
becoming one single individual with a different
cells carrying distinct genetic codes.

68

Internet Assigned Readings

DNA Evidence--7 pages
http://science.howstuffworks.com/genetic-science/dnaevidence.htm
DNA Profiling--3 pages
http://science.howstuffworks.com/dna-profiling.htm
DNA in the Courtroom--6 pages
Romanov (8 pages)
http://www.plosone.org/article/info:doi/10.1371/journal.pone.000
4838
24 pages total

Saint Louis University

69

Class Videos
DNA Structure http://www.youtube.com/watch?v=qy8dk5iS1f0
DNA Song http://www.youtube.com/watch?v=x5yPkxCLads
DNA Rap http://www.youtube.com/watch?
v=oCRJ4r0RDC4&feature
DNA Evidence http://www.youtube.com/watch?
v=dXYztbkMXwU

Saint Louis University

70