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Biology II Notes
DNA Fingerprinting
       1. Demonstrate an ability to interpret DNA fingerprints 
       2. Carry out a DNA extraction and/or produce a DNA fingerprint using gel electrophoresis 
       3. Describe the importance of DNA analysis in forensics 
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DNA "Fingerprints"
DNA Basics
   - DNA (Deoxyribonucleic acid) is a chemical structure that forms chromosomes. 
   - A piece of a chromosome that dictates a particular trait is called a gene. 
   - DNA has a double helix structure.  (Think of a flexible ladder and twist the top and bottom in different directions.) 
   - Each 'rung' of the 'ladder' contains two bases.
   - A base plus a piece (phosphate & sugar) of the vertical section of the 'ladder' is called a nucleotide.
   - The four bases are adenine (A), guanine (G), cytosine (C), and thymine (T). 
   - A always pairs with T (A-T or T-A) and C always pairs with G (C-G or G-C).
   - DNA strands are read in a particular direction, from the top (called the 5' or "five prime" end) to the bottom (called the 3' or "three prime" end). 
   - In a double helix, the strands go opposite ways: 
                     e.g.  5' T-C-G-A-A-T-G-C 3'
                             3' A-G-C-T-T-A-C-G 5' 
   - Everyone's DNA is composed of a string of these same four bases.
   - The only difference between 2 organisms (people, animals, etc.) is the order of the base pairs. 
   - Every organism's DNA sequence is different and tells exactly how to build and operate their body. 
   - But, because there are so many bases in the sequence, we don't decode the entire DNA molecule when comparing DNA.
   - Scientists use a small number of sequences of DNA that are known to vary among individuals a great deal, and analyze those to get a certain probability of a match. 
   - In forensic science, it is common to have only a small amount of DNA to use for lab work. 
   - PCR (polymerase chain reaction) is performed to increase the amount of DNA.
             1. The double strand of DNA is denatured (by heat or chemicals) into single strands.
             2. The strands are placed in a medium of nucleotides so that the DNA can replicate and you get two complete DNA molecules. 
             3. This process is repeated so that the number of DNA molecules keeps doubling until enough DNA is produced.

VNTRs
   - 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. 
   - Every human being has some VNTRs. 
   - The chances of somebody else having the exact same VNTR results is less than one in a million.
   - To determine if a person has a particular VNTR, a Southern Blot is made and probed through
a hybridization reaction with a radioactive version of the VNTR in question. 
   - The resulting pattern from this process is what we call a DNA fingerprint. 
   - A given person's VNTRs come from the genetic information donated by his or her parents.
   - You can have VNTRs inherited from your mother or father, or a combination, but never a VNTR either of your parents do not have. 
   - Because VNTR patterns are inherited genetically, a given person's VNTR pattern is more or less unique. 
   - The more VNTR probes used to analyze a person's VNTR pattern, the more distinctive and individualized that pattern, or DNA fingerprint, will be. 

DNA Extraction
    This material will be on the DNA Extraction handout. 

Using Gel to Produce a DNA Fingerprint
Make a Southern Blot to analyze the genetic patterns which appear in a person's DNA. 
  Step 1. Isolate the DNA from the rest of the cellular material in the nucleus. This can be done either chemically, by using a detergent to wash the extra material from the DNA,or mechanically, by applying a large amount of pressure in order to "squeeze out" the DNA. 
  Step 2. Cut the DNA into several pieces of different sizes using restriction enzymes. 
  Step 3. Sorting the DNA segments by size using gel electrophoresis. The DNA is 
                a. pour the DNA into a gel (e.g. agarose) 
                b. apply an electrical charge (+ at the bottom, - at the top)
                c. since DNA is slightly negative, they are pulled to the bottom
                d. since the smaller pieces can move more quickly, they travel further down the gel
                e. because of this, the DNA segments will separate according to size (smallest towards the bottom and largest towards the top)
  Step 4. The DNA is separated (denatured) by heat or chemically so that you have 2 single strands of DNA
  Step 5. The gel with the DNA (separated by size) is applied to a sheet of nitrocellulose paper, and baked to permanently attach the DNA to the sheet. 

To analyze the Southern Blot a radioactive genetic probe is created to be is used in a hybridization reaction with the DNA. An X-ray is taken and only the areas where the radioactive probe binds will show up on the film. This allows researchers to identify, in a particular person's DNA, the occurrence and frequency of the particular genetic pattern contained in the probe. 

Why is DNA analysis important in forensics?
   -  VNTR patterns can be obtained from DNA (in blood, hair, skin cells, etc.) left at the scene of a crime and compared with the VNTR patterns in the DNA of a criminal suspect to determine guilt or innocence. 
   - VNTR patterns can also be uses to discover the homicide victim, either from DNA found as evidence or from the body itself.

LINKS:
      - 
      - 
      - DNA Fingerprinting 
           - DNA Fingerprinting in Human Health and Society 
           - An Interview with DNA Forensics Authority Dr. Bruce Weir 
           - Use of DNA in Identification: A talk by Eric Lander 
      - Genetic Science Learning Center
           - How to Extract DNA from Anything Living
           - DNA Extraction from Wheat Germ
     - Access Excellence Activities Exchange
           - Introduction to DNA Extractions
           - DNA Extraction
           - DNA Extraction Lab
           - DNA Sequencing Simulation (Sanger method)
           - Extraction of DNA from onion
      - Extracting DNA
      - Fruitful DNA Extraction
      - Gel Electrophoresis Experiment
      - Basics of DNA Fingerprinting
      - DNA Fingerprinting in Human Health and Society
      - Bode Technology Group [forensic DNA company]
      - Yahoo Forensics Directory
      - Forensic Science
          - DNA
      - DNA in the Courtroom: Innocent or Guilty 
      - DNA Glossary
      - DNA evidence and forensic analysis
      - Nucleotide Sequence Analysis - use for class activity
      - FBI Handbook of Examination Services: DNA Examinations
      - CODIS (Combined DNA Index Service)
      - DNA Testing Kits
      - 
   Forensic Science
      - 
      - Ridges and Furrows
      - Forensic Science Communications (online journal)
      - Procedures for forensic DNA Analysis
      - Reddy's Forensic Home Page
      - 
      - 

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