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What is DNA Fingerprinting?

Each of us has the same chemical structure of DNA. But there are millions
of differences in the DNA sequence of base pairs symbolized as A, T, C, G.
This makes the uniqueness among us so that each of us except twins is
different from each other
genetically. DNA sequence
thus can be just like a
fingerprint to identify every
person entirely. But there are
so many base pairs in DNA
sequences that it is hard and
time-consuming to read out all
the sequences. Scientists
have developed many
techniques in order to quicken
the identification process.
Restriction Fragment Length Polymorphism (RFLP)
Restriction Fragment Length Polymorphism (RFLP) is a difference in
homologous DNA sequences that can be detected by the presence of
fragments of different lengths after digestion of the DNA samples in
question with specific restriction endonucleases. RFLP, as a molecular
marker, is specific to a single clone/restriction enzyme combination. Most
RFLP markers are co-dominant (both alleles in heterozygous sample will
be detected) and highly locus-specific.
Every strand of DNA has pieces that
contain genetic information which
informs an organism's development
(exons) and pieces that, apparently,
supply no relevant genetic
information at all (introns). Although
the introns may seem useless, it has
been found that they contain
repeated sequences of base pairs.
These sequences, called Variable
Number Tandem Repeats (VNTRs),
can contain anywhere from twenty to
one hundred base pairs.

An example of Variable Number
Tandem Repeats (VNTRs) on
three chromosome pairs.

Every human being has
some VNTRs. To
determine if a person has
a particular VNTR, a
Southern Blot is
performed, and then the
Southern Blot is probed,
with an RFLP probe
through a hybridization
reaction, with a
radioactive version of the
VNTR in question. The pattern which results from this process is what is
often referred to as a DNA fingerprint.
An RFLP probe is a labeled DNA PCR primer sequence that hybridizes
with one or more
fragments of the digested
DNA sample after they
were separated by gel
electrophoresis, thus
revealing a unique blotting
pattern characteristic to a
specific genotype at a
specific locus. Short, single
- or low-copy genomic
DNA or cDNA clones are
typically used as RFLP
probes.
Isolation of sufficient DNA
for RFLP analysis is time-consuming and labor intensive. However, PCR
can be used to amplify very small amounts of DNA, usually in 2-3 hours, to
the levels required for RFLP analysis. Therefore, more samples can be
analyzed in a shorter time.
A given person's VNTRs come from the genetic information donated by his
or her parents; he or she could have VNTRs inherited from his or her
mother or father, or a combination, but never a VNTR either of his or her
parents do not have.

through VNTR patterns. the more distinctive and individualized that pattern. National DNA Databank: CODIS The COmbined DNA Index System. will be.Because VNTR patterns are inherited genetically. Law enforcement agencies at federal. state. the database contained over 5 million DNA profiles in its Convicted Offender Index and about 188.g. The more VNTR probes used to analyze a person's VNTR pattern. or other genetic evidence left at the scene of a crime can be compared. In March 2003 President Bush proposed $1 billion in funding over 5 years to reduce the DNA testing . All DNA profiles stored in CODIS are generated using STR (short tandem repeat) analysis.000 DNA profiles collected from crime scenes but not connected to a particular offender. If a match is made between a sample and a stored profile. The current version of CODIS uses two indexes to generate investigative leads in crimes where biological evidence is recovered from the crime scene. As of August 2007. The Forensic Index contains DNA profiles developed from crime scene evidence. CODIS. a given person's VNTR pattern is more or less unique. All 50 states have laws requiring that DNA profiles of certain offenders be sent to CODIS. CODIS can identify the perpetrator. either from DNA found as evidence or from the body itself. This technology is authorized by the DNA Identification Act of 1994. CODIS utilizes computer software to automatically search its two indexes for matching DNA profiles. with the DNA of a criminal suspect to determine guilt or innocence. blood and saliva) gathered in crimes that have no suspect and compare it to the DNA in the profiles stored in the CODIS systems. hair. As more offender DNA samples are collected and law enforcement officers become better trained and equipped to collect DNA samples at crime scenes. or DNA fingerprint. and local levels take DNA from biological evidence (e. the backlog of samples awaiting testing throughout the criminal justice system is increasing dramatically. VNTR patterns are also useful in establishing the identity of a homicide victim.. Criminal Identification and Forensics DNA isolated from blood. skin cells. blends computer and DNA technologies into a tool for fighting violent crime. The Convicted Offender Index contains DNA profiles of individuals convicted of felony sex offenses (and other violent crimes).

build crime lab capacity. unsolved crime scene evidence. protect the innocent. CODIS is a computer software program that operates local. . thereby linking serial crimes to each other and identifying suspects by matching DNA profiles from crime scenes with profiles from convicted offenders. State. and identify missing persons. support training. stimulate research and development. CODIS software enables State.backlog. The success of CODIS is demonstrated by the thousands of matches that have linked serial cases to each other and cases that have been solved by matching crime scene evidence to known convicted offenders. local. and national databases of DNA profiles from convicted offenders. Every State in the Nation has a statutory provision for the establishment of a DNA database that allows for the collection of DNA profiles from offenders convicted of particular crimes. and national law enforcement crime laboratories to compare DNA profiles electronically. and missing persons.

in fact. One common technology used in DNA fingerprinting is the RFLP (restriction fragment length polymorphism) analysis. The sequence of rungs is different for different persons and it is just like paragraphs of alphabets. They are then treated with buffer. So this variability can be used to identify each person. T respectively. They are in turn symbolized as A. This can be done by using one's hairs or blood. have no specific function but with high variability among people. Each rung contains a pair of nitrogenous bases which are distinguished into four different types: adenine. The DNA molecules are enclosed in the nucleus of the cells. The pure DNA molecules can then be separated from the destroyed proteins by centrifugation. cytosine and thymine. guanine. The rest of the sequence. The DNA molecules are now still packed in the form of chromatin by proteins. enzymes and chloroform so as to destroy the proteins. Most of the sequence can function to regulate protein synthesis and to regulate cell activities. .How to perform DNA Fingerprinting? DNA contains two strands which are joined together by the forces between the two nitrogenous bases on both strands. We can imagine that DNA is a long ladder with many rungs. The first step is to extract genomic DNA (entire DNA pool of a person) from a person. C. G. so the extract of cells needs to be lysed by breaking the cell membrane and the nucleus envelope to release the DNA molecules.

This pattern is different for different persons and hence can be used for distinguishing people. The mixture of fragments is then allowed to run in the gel electrophoresis. . The DNA long chains are cut by restriction enzymes. For example. The electrophoresis can separate the fragments by electrical charges and a pattern of the fragment can be obtained eventually. A specific restriction enzyme can cut a specific locus on the DNA chain. The probe is a small radioactive fragment of DNA which is complementary to and can match with the sequence of the DNA on the nylon membrane. The separated DNA molecules are now still colorless and so it is hard to see them for identification. The DNA fragments are then transferred from the gel to a nylon membrane which is called a Southern Blot. Probes have to be added to make them visible on a photographic film. which is the DNA fingerprint of a person. This results in the appearance of a pattern of dark bars on the film. This matching is called hybridization. EcoR1 will only cut the chain at the sequence of GAATTC.The extracted DNA molecules are now in a very long chain and need to be cut into many fragments which are easier to be recognized. The radiation from the probes can cause darkening on the photographic films.

If somebody's DNA fingerprint matches with that from the scene this will be a strong evidence showing that he has committed the crime. the semen left in the victims' vagina can also be extracted and be used to reveal the DNA sequence which is later compared with the criminal suspects' DNA fingerprints so as to find out who did the rape. Paternity A child can inherit most of the DNA fragment pattern from his parents. The DNA fingerprint of these cells from the scene can be revealed and are compared with the DNA fingerprint obtained from criminal suspects. . By comparing the DNA fingerprints between the child and the suspect parents. it is possible to identify who the parent of the child is.Applications Forensic Uses Blood or fragments of tissues such as hair and skin cells may be left in the scene of crime. Also in the case of rapes.

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Southern blotting combines agarose gel electrophoresis for size separation of DNA with methods to transfer the sizeseparated DNA to a filter membrane for probe hybridization. depending on the direction of the transfer) the gel. or by placing a stack of paper towels and a weight on top of the membrane and gel). The method is named after its inventor. have later been named in reference to Southern's name. ion exchange interactions bind the DNA to the membrane due to the negative charge of the DNA and positive charge of the membrane. northern blot.e. A sheet of nitrocellulose (or.Southern Blot A Southern blot is a method routinely used in molecular biology to check for the presence of a DNA sequence in a DNA sample. Other blotting methods (i. . The DNA fragments are then electrophoresed on an agarose gel to separate them by size. whereas northern and western blots should not. but using RNA or protein. Southern.. alternatively. western blot. Buffer transfer by capillary action from a region of high water potential to a region of low water potential (usually filter paper and paper tissues) is then used to move the DNA from the gel on to the membrane. As the technique was eponymously named. Pressure is applied evenly to the gel (either using suction. Southern blot should be capitalized. the British biologist Edwin M. to ensure good and even contact between gel and membrane. nylon) membrane is placed on top of (or below. southwestern blot) that employ similar principles. Method Restriction endonucleases are used to cut high-molecular-weight DNA strands into smaller fragments.

The transfer step of the DNA from the electrophoresis gel to a membrane permits easy binding of the labeled hybridization probe to the sizefractionated DNA. required for analysis by autoradiography or other detection methods. In some cases. usually by incorporating radioactivity or tagging the molecule with a fluorescent or chromogenic dye. To ensure the specificity of the binding of the probe to the sample DNA. The membrane is then exposed to a hybridization probe. After hybridization. excess probe is washed from the membrane. and the pattern of hybridization is visualized on X-ray film by autoradiography in the case of a radioactive or fluorescent probe. . most common hybridization methods use salmon testes (sperm) DNA for blocking of the membrane . or by development of color on the membrane if a chromogenic detection method is used. rather than DNA. The probe DNA is labelled so that it can be detected. Result Hybridization of the probe to a specific DNA fragment on the filter membrane indicates that this fragment contains DNA sequence that is complementary to the probe.The membrane is then exposed to high temperature (60 to 100 °C) (in the case of nitrocellulose) or exposed to ultraviolet radiation (nylon) to permanently and covalently crosslink the DNA to the membrane. the hybridization probe may be made from RNA. It also allows for the fixation of the target-probe hybrids.

Fl . 2008 A maid. . Ms.The High Rise Killer DNA Fingerprint Tampa. dead in her bathtub. Jones. Some of the blood was matched to the victim. found Sarah Elizabeth Jones.June 13. The numerous areas of blood were analyzed by crime scene technicians and were found to have come from two different people. had been on vacation at the time her body was found. The victim appeared to have been killed after a struggle at her condo near the beach. who worked for an import company in St. Police speculate that the killer was injured in the struggle with the victim leaving his or her blood at the condo. The maid said that the doors were locked when she arrived. Police found items strewn about the condo as well as blood in three different places including the bathroom where the body was found. 35. but other samples came from an individual other than the victim. She was not known to have a boyfriend but one man had been by seen by neighbors entering her condo on at least two occasions. doing her daily cleaning at a posh condo. Petersburg.

The samples were then compared using Restriction Fragment Length Polymorphism (RFLP) technology. IAFIS returned a match on two different men. From these samples police hoped to determine which man’s blood matched the blood found at the scene that would identify the killer. 25. 45. Lane 1 was used for the DNA length reference markers. including the victim. The samples were run on an electrophoretic gel for comparison. The first set of fingerprints belonged to Gerald Goss.Police also found fingerprints belonging to at least three persons. 3) the blood of John Kennedy and 4) the blood of Gerald Goss were treated with the restriction enzyme HindIII and placed in an electrophoresis gel in lanes 2 thru 5 respectively. who listed his occupation as writer. The DNA from four blood samples 1) the unknown blood found at the site. The second set belonged to John Kennedy. 2) the blood of the victim. The fingerprints were sent to the Integrated Automated Fingerprint Identification System (IAFIS) run by the FBI. . of Denver. from New Jersey. Search warrants were obtained for blood samples from each man. who listed his occupation as librarian.

Put the gel back into its container and plastic bag. Empty the plastic tray. Remove the nylon membrane with forceps using the end with the label. 5. Place the nylon membrane face up on a paper towel.Teacher Southern Blot Instructions Prior to the experiment the teacher needs to fill the “Gel Buffer”. Smooth out bubbles with a gloved finger. 19. 6. 13. 18. The “Fluor Tag” tube can be filled with water with a small amount (1-5 drops per gallon) of blue food coloring (VERY light blue) if you wish. Handle the nylon with forceps using the end with the label. Let the DNA transfer proceed for 10-20 minutes. 16. 10. 23. Pour 50 milliliters of buffer (Gel Buffer) into the tray. 7. Place the sponge into the plastic tray. --------------------------------------------------------------------------------------------------------------------The Students Should Always Wear Gloves 1. 25. carefully remove the gel from its plastic bag and place it on the sponge. Pour the tube of fluorescent probes (Fluor Tag) into the plastic tray. Place the nylon membrane face down in the plastic tray. With your fingers. 8. Examine the nylon membrane with a fluorescent light and fill in the Southern Blot data . 24. Place the nylon membrane face down in the plastic tray. Wait 5 minutes. 22. 17. “Fluor Tag” and “Wash” tubes with water. 12. 20. Pour the tube of wash buffer (Wash) into the plastic tray. 4. Place the nylon membrane face up on a paper towel. Place a two inch stack of paper towels on top of the membrane. 21. 15. Place the wetted nylon membrane face-down onto the gel with the printed part at the bottom of the gel (the wells are at the top of the gel). Remove the nylon membrane with forceps using the end with the label. Remove the nylon membrane from its plastic bag. 9. Remove the nylon membrane with forceps using the end with the label. Place the nylon membrane face up on a paper towel. Remove the sponge and empty the plastic tray. 11. 14. 2. 3. Remove the paper towels. Wait 5 minutes. Wet the sponge with water from the sink faucet.

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19. 13. 8. Place the nylon membrane face down in the plastic tray. Place the nylon membrane face down in the plastic tray. 15. Remove the nylon membrane from its plastic bag. Pour the tube of wash buffer (Wash) into the plastic tray. 3. Place the nylon membrane face up on a paper towel. 11. Remove the paper towels. Empty the plastic tray. Wait 5 minutes. 6. 10. 4. 24. Smooth out bubbles with a gloved finger. Wait 5 minutes. Pour 50 milliliters of buffer (Gel Buffer) into the tray. 9. 18. 23. Pour the tube of fluorescent probes (Fluor Tag) into the plastic tray. Place the nylon membrane face up on a paper towel. 2. 7. 20. 12. Remove the nylon membrane with forceps using the end with the label. 5. 16. Let the DNA transfer proceed for 10-20 minutes. Place the sponge into the plastic tray. 25. Wet the sponge with water from the sink faucet. Place the nylon membrane face up on a paper towel. 21. Place the wetted nylon membrane face-down onto the gel with the printed part at the bottom of the gel (the wells are at the top of the gel). Remove the nylon membrane with forceps using the end with the label. 22. Place a two inch stack of paper towels on top of the membrane. 17.Student Southern Blot Instructions Wear Gloves 1. Remove the nylon membrane with forceps using the end with the label. With your fingers. Remove the sponge and empty the plastic tray. 14. Examine the nylon membrane with a fluorescent light and fill in the Southern Blot data sheet. Handle the nylon with forceps using the end with the label. Put the gel back into its container and plastic bag. carefully remove the gel from its plastic bag and place it on the sponge. .

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Teacher Key “The High Rise Killer” DNA Marker Unknown 1 115 bp 109 bp 103 bp 95 bp 84 bp 75 bp 62 bp 54 bp 43 bp 30 bp 2 Victim 3 Suspect #1 4 Suspect #2 5 .

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Student Worksheet “The High Rise Killer” DNA Marker Unknown 1 115 bp 109 bp 103 bp 95 bp 84 bp 75 bp 62 bp 54 bp 43 bp 30 bp 2 Victim 3 Suspect #1 4 Suspect #2 5 .

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