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Focus: Then & Now

DNA Fingerprinting
The New Sherlock Holmes
By Amrita Goyal

O n a clear night, anyone with a good


telescope can see that the sky is
strewn with thousands of satellites
critical evidence in thousands of crimi-
nal cases and exonerations (3). In a more
familiar example, it was also used to
ranging from two to six base pairs long.
On the other hand, in a minisatellite,
the repeating units range from ten to
some are manmade satellites, launched identify another killer, the lethal tainted 100 base pairs. These are also known
into orbit for communications and de- spinach in the recent E. coli outbreaks, as variable number tandem repeats, or
fense, and some are natural ones, such and helped trace the outbreak back to VNTRs (8).
as our beloved Moon. However, there its source in California (4). The characteristic of micro and
is another type of satellite that is much Amazingly enough, DNA fingerprint- minisatellites that makes them useful
closer to home: the human genome is ing technology will soon enable doctors for identification purposes is that they
also littered with satellites. to detect as few as 10 cancerous cells in are highly polymorphic they can vary
Genetic satellites are entirely different an entire lymph node (5), and will allow significantly in length from person to
from the ones overhead. A DNA satel- person. The length of each satellite in
lite is a region that consists of a short se- DNA fingerprinting has your DNA is inherited. Just as with any
quence of DNA repeated over and over not only transformed other gene on an autosomal chromo-
againlike an extended genetic stutter, some, you have two alleles: one inherited
hundreds to thousands of nucleotides
criminal forensics and from your mother and one from your
long (1). Satellite regions in DNA are judicial systems around father (2). (see fig. 1)
apparently functionless and have long the world, but has also Variations in satellite length are the
been dismissed as junk DNA. revolutionized fields of result of fortuitous mistakes in the
Although nature has no readily appar- biology ranging from process of crossing-over during meiosis.
ent purpose for satellite DNA, humans Because of the repetitive nature of mi-
evolutionary studies to
have been happy to put these regions to cro- and minisatellite regions, occasion-
good use: variation between individuals cancer detection and ally when the chromosomes undergo
in the lengths of their DNA satellites treatment. crossing over, they do not align properly.
is the basis for one of the most revolu- When the strands of DNA pair, instead
tionary techniques in molecular biology: them to determine whether a woman of lining up so the crossover occurs at
DNA fingerprinting. who had breast cancer is at risk for re- the same place in the satellite on both
Astoundingly, despite its ubiquity in lapse (6). In evolutionary studies, DNA chromosomes, they can slip and cross
todays courts and on shows like Law fingerprinting has even traced the origin over at the wrong tandem repeat. This
and Order and CSI, DNA fingerprinting of all of mankind to Africa! (7). leads to a deletion of a repeat on one
was only developed two decades ago (2). chromosome and an insertion of a
In the short time since its invention, this Micro and minisatellites galore! repeat on the other. This generates two
technology has not only transformed DNA satellites were first identified by new alleles of the satellite, one longer
criminal forensics and judicial systems biologists in the 1960s, and come in than either of the original alleles, and
around the world, but has also revolu- two typesmicrosatellites and minis- one shorter (1).
tionized fields of biology ranging from atellites (1). Thus, the lengths of satellite regions
evolutionary studies to cancer detection Microsatellites, also known as simple are highly variable between people. This
and treatment. sequence repeats (SSRs), are made of re- wealth of variation across the population
DNA fingerprinting has provided peating units of nucleotides, each repeat makes satellites invaluable for identifica-
14 Harvard Science Review fall 2006
Focus: Then & Now
tion purposes. The probability that two DNA after primer is then copied by a examined in PCR-based fingerprinting
random people have the same number molecule of DNA polymerase in a third are significantly shorter than the minis-
of repeats at each and every one of step called extension. Multiple cycles of atellites used in restriction enzyme based
multiple satellites is infinitesimally small, these three steps allow for exponential analysis, they are much less likely to be
nearing one in 5 x 1019 (2). This prob- amplification of the region copied by degraded. Most of the time, the DNA
ability is so low that in forensic analysis, the primers (9). in blood or semen from a crime scene
a DNA fingerprint allows near certain Primers can be designed to amplify has been significantly degraded by time
positive identification of the source of regions of DNA containing satellites. If and exposure to the elements and would
a sample. The heritability of satellite al- the PCR products are then separated by be nearly impossible to fingerprint with
leles has also allowed the development gel electrophoresis and a Southern Blot restriction analysis (12).
of DNA fingerprinting-based paternity performed to image the DNA bands,
and maternity testing (2). Breast cancer detection
Every year, the lives of hundreds of
Restriction enzyme-based women are destroyed by rapists and
fingerprinting murderers. DNA fingerprinting has
Jeffreys original procedure, restriction helped identify and imprison untold
fragment length based DNA finger- numbers of such violent offenders.
printing (RFLP analysis), is relatively But, there is another serial killer of
straightforward: a restriction enzyme is women, far more insidious than any
used to cut the DNA at specific points, of these criminals. It is one who has
yielding fragments of varying lengths. taken hundreds of thousands of lives,
These cleaved pieces of DNA are then and who nearly every woman lives in
subjected to gel electrophoresis to fear ofbreast cancer. But soon, DNA
separate them based on size, and finally fingerprinting will help put a stop to this
visualized by Southern blotting (2). killer too. DNA fingerprinting will be
When genomic DNA is cleaved with used to identify renegade cancerous cells
particular restriction enzymes, the result- (5), and has been shown to be useful in
ing fragments can contain a minisatellite assessing a cancer survivors likelihood
(VNTR) region. Since the number of of relapse (6).
repeats in the satellite determines its All of the hallmarks of malignancy
length, and gel electrophoresis separates in a cancer cell, such as uncontrolled cell
the digested DNA into bands based on division, secretion of angiogenic factors,
the length of the fragments, the pattern the resulting banding pattern reflects and the ability to infiltrate other tissues
of bands reflects the number of repeats the lengths of the satellite regions. The and metastasize are the result of genetic
in a minisatellite. When enough loci are fingerprint created is just like the finger- mutations. Such genetic mutations also
examined, each persons DNA will yield print generated by restriction enzyme result in changes in the DNA fingerprint
a unique banding patternhis or her analysis (10). of that cella cancerous cell has a dif-
unique DNA fingerprint (2). While the first DNA fingerprints ferent DNA fingerprint than the rest of
were made using the restriction enzyme the healthy cells in the body.
PCR-based fingerprinting method, the PCR-based method became Because of the amplification of DNA
In 1983, Kary Mullis developed a tech- dominant soon after its development during PCR-based DNA fingerprinting,
nique that would revolutionize molecu- in 1988. The important advantage to it is possible to detect the presence of
lar biology: the polymerase chain reac- PCR-based DNA fingerprinting is that less than 10 cancerous cells in an entire
tion, better known as PCR. This gave by virtue of the amplification process, lymph node. This incredible sensitivity
scientists an in vitro way to exponentially it is possible to begin with only a tiny will allow doctors to determine whether
amplify DNA (9). amount of DNA. While RFLP analysis tissue is cancerous long before a tumor
The general procedure and concept requires a sample of blood at least the would be visible by simply fingerprinting
behind PCR is a simple one. First, the size of a quarter, it is possible to fin- a sample of it. Such early detection will
genomic DNA is denatured, its strands gerprint the DNA of a single cell using undoubtedly save countless lives.
separated by heating. Then a primer--a PCR-based DNA fingerprinting (10). Doctors will also be able to see if
synthetic single of stranded piece DNA- It is also possible to analyze old or a cancer has metastasized, or check
-binds to the complementary portion of degraded samples using PCR-based fin- whether or not they have removed all
the genomic DNA. The portion of the gerprinting. Because the microsatellites of a tumor by fingerprinting biopsy

fall 2006 Harvard Science Review 15


Focus: Then & Now
These applications range was eventually used to trace the source
a) b) from monitoring endangered of the infection back to a handful of
species to tracking down the farms in California (4). Fingerprinting
source of tainted food. has also been used to identify viruses of
For example, DNA fin- all types that infect humans, including
gerprinting of samples of DNA viruses, RNA viruses, and even
tissue left behind by animals retroviruses (14).
has allowed scientists to track As is evidenced by this multitude
the size and genetic diversity of applications, although DNA finger-
within populations of endan- printing is only two decades old, in the
gered species. Fingerprinting short time since its birth it has revolu-
is used to help them deter- tionized nearly every facet of biology
mine the number of unique (not to mention the justice system).
individuals in an area and Fingerprinting has given us a method
ascertain how closely related to establish paternity, and a method to
Figure 1. a) A DNA fingerprint from a paternity test, using they are (8). identify nearly any living thing. DNA
several satellites. Lane 1 is the mother, 2 is the child, and 3 As DNA fingerprinting fingerprinting has already saved untold
is the father (Varsha). b) DNA fingerprint for each member of
a family, using a single satellite. Each person has two copies
can be used in humans to numbers of lives by both putting away
of the satellite. Larger DNA fragments with more repeats are match a DNA sample with its violent criminals and by helping identify
closer to the top of the gel. In both a) and b), each of the source, it can also be used to deadly bacteria and viruses. Soon it will
childrens bands is inherited from their parents.
trace the source of finished save even more lives by helping to cure
samples. Although the majority of re- meat products back to spe- cancer.
search in cancer cell detection has been cific animals. This can be very useful in
done with breast cancer, it is possible to outbreaks of diseases such as mad cow Crime and punishment
adapt this technology for the detection disease, since other animals that could In 1990, the FBI created a national
of other types of cancer (5). be infected need to be destroyed, and DNA databank known as CODIS. This
In tumors, cancerous cells divide at contaminated meat products need to extremely valuable database contains
an astounding rate. However, in many be recalled to prevent further spread of the DNA fingerprints of convicted sex
cases they also die rapidly. When they the disease. Similarly, fingerprinting can offenders and violent criminals, as well
die they often release their contents, also be used to trace plants and plant as DNA profiles from evidence taken
including their DNA, into the sur- products back to their sources (8). from crime scenes. CODIS is respon-
rounding tissue. Studies have shown DNA fingerprinting has also made sible for having helped bring thousands
that with many breast cancers, there significant contributions to the study of criminals to justice. In fact, in over
is a large amount of free DNA float- of human evolution and migration. In 30,000 cases, matching of crime scene
ing in the blood plasma that probably 2003, scientists conducted an analysis evidence to DNA profiles of known
comes from the cancerous cells. Sci- of 377 satellites in each of over a thou- criminals and inmates has led the police
entists have shown that the higher the sand people, hailing from every corner to a suspect. To take these fingerprints,
concentration of tumor DNA in the of the globe. The amount of diversity the FBI uses a standard panel of 13
blood, the more likely the patient is to between and within populations was microsatellites, which together yield a
relapse. Such a measuring stick for the then analyzed, and this statistical analy- remarkably miniscule 1 in 575 trillion
probability of relapse will undoubtedly sis was used to establish definitive sup- chance of a random match (12).
help oncologists save lives, by alerting port for the out-of-Africa theory of The most common use of DNA
them that a patient is likely to become human evolution and migration (7). evidence in courts is to help positively
sick again (6). It is also possible to fingerprint identify a rapist or murderer. This is
bacteria and viruses. Such analyses done by comparing the DNA finger-
Other biological applications are extremely important, and have print of a sample of blood or semen
Humans are not the only creatures who widespread applications. For example, left at the crime scene to that of the
can be fingerprintedanything with a during the spinach recalls of this past suspect. Fingerprints can also be made
DNA or RNA genome, including ani- fall, DNA fingerprinting of the bacteria using DNA in urine, saliva, and any
mals, plants, bacteria, and viruses can on spinach leaves was used to deter- number of other bodily sources. In pa-
be fingerprinted the same way. DNA mine which packages of spinach were ternity testing, the DNA fingerprints of
fingerprinting thus has an incredible contaminated with the deadly E. Coli the child, the mother, and the father are
number of biological applications. O157:H7 bacteria. This information compared. Paternity is the determined

16 Harvard Science Review fall 2006


Focus: Then & Now
by assessing whether it would be pos- post-9/11
Sequence to 5 3
sible for the child to have inherited the world. Amplify 3 5
combination of bands in their DNA Even five
fingerprint from the alleged father and years later, Heat DNA

mother. efforts are


5 3 3
With DNA fingerprinting, inves- still under- 5
tigators have been able to re-examine way to re- Primers Anneal
Polymerase is added and
evidence from old cases, leading to cover the complimentary strand is
synthesized.
the arrests of violent killers and rapists remains 5 5
3 3
who would have otherwise gone free. of all 2749 3 5 5 3
However, re-examination of evidence victims of Repeat 60 cycles

has also exonerated dozens of unjustly the terrorist Figure 2. PCR-based DNA fingerprinting uses PCR to amplify satellite regions of
imprisoned people, and even saved attacks of DNA. DNA strands are separated byLOTS heating,
OF DNA!!!!!and complementary primers then
bind to the DNA. DNA polymerase replicates the satellite. Multiple cycles of this
innocent people from being executed. September lead to exponential amplification of the satellite. The PCR products are then
Project Innocence, a non-profit legal 11th, 40% run out on a gel to yield the DNA fingerprint.
clinic, has freed 153 innocent men on the of whose far above us, beaming information back
basis of post-conviction DNA testing remains have not been identified. Sadly, and forth to us on Earth. Next time
(3). In Illinois in 2003, thirteen men on in most cases, these remains come in you look up at the stars, and Earths
death-row were exonerated on the basis the form of tiny fragments of shattered satellite, the moon, be glad that we re-
of DNA evidence. DNA fingerprinting bone; it is often impossible to separate alized the importance of the immense
saved thirteen innocent men who would the remains of one person from those amount of information contained in
have otherwise been executed for crimes of another. DNA fingerprinting has our DNA satellites.
they did not commit (12). been the most important tool in this
effort, and has been used to reunite Amrita Goyal 09 is a Chemistry concen-
Genetic discrimination families with the remains of their loved trator in Lowell House.
While the 13 markers used by the FBI ones (13).
are useful for matching a DNA sample In one case, remains determined
References:
to its source, these loci are otherwise to belong to at least two people were
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(1985): 577-579.
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Questions and Answers. US Food and Drug Ad-
or genetic diseases (13). However, there if any of the intermingled unidentified min. <http://www.cfsan.fda.gov/~dms/spinacqa.
are many loci that could be used to remains might belong to a terrorist. html#collect >. Sept 25, 2006. Accessed Sept 29,
2006.
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strike a balance between using all infor- we are now faced with is should we minisatellites. Nucleic Acids Research. 23 (1988):
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