DNA Analysis and Genomics

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DNA Analysis and Genomics
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Genomics

• Genomics studying whole sets of genes and their
  interactions.
  
• We can separate molecules on the basis of charge,
  size, and other physical properties.
  
• For DNA, size is the basis for the separation.

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Restriction Fragment Analysis

• Analysis of restriction fragments shows certain
  differences in the nucleotide sequences of DNA.
  
• We can use gel electrophoresis to sort the DNA
  fragments by size.
  
• Two different alleles for a trait will have
  slightly different nucleotide sequences.
  
• Thus they will have slightly different
  restriction sites and produce different
  restriction fragments.

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Gel Electrophoresis

• Samples of DNA molecules are put into wells or
  cuts in a gel material called agarose.
  
• These samples have been cut with restriction
  enzymes and therefore are of various lengths.
  
• The DNA molecules are negatively charged.
• The gel chamber has a positive and negative end
  based on the current flow through the devise.
  
• The molecules migrate toward the positive end.
• This produces bands of DNA down the length of the
  gel.

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RFLPs

• Restriction fragment length polymorphisms are
  differences in the DNA sequence on homologous
  chromosomes that can result in different banding
  patterns.
• RFLPs served as a basis for starting point for
  mapping the genome.
  

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The Procedure

• Here is a gel.
• The wells are empty.
• We will use a micropipet to pipet DNA into the
  wells.

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The DNA

• Here are examples of microtubes which contain
  DNA,
  
• Always keep the lid closed when not in use and
  never lay them down on the counter you will
  contaminate the counter and the DNA.

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Loading the Gels

• The micropipet contains a small amount of DNA
  which is carefully loaded into each well.
  
• Always number the DNA samples so that you know
  which sample is in which well.

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Wells are Loaded

• Blue dye has been added to the DNA to make it
  visible.
  
• Here is an example of wells that contain DNA
  samples.

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Running the Gels

• The loaded agarose is put into the chamber and
  the power source is turned on.
  
• The DNA will begin to migrate down the gel.

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DNA Migration

• After some time, the bands of DNA can be seen
  moving away from the wells.

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Staining

• Once the DNA has migrated a sufficient amount to
  see different banding patterns, the gel must be
  stained for easier viewing.

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Viewing

• A light box makes viewing the band much easier.
• Never place the gel directly on the box. Use
  plastic wrap to protect the light box.

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Results

• Here is an example of what a stained gel looks
  like.
  
• Notice the darker blue bands at different places
  on the gel.
  
• Each band represents a fragment of a particular
  size.

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Analysis

• The distance the DNA migrates can be measured and
  used to determine the size of the fragment.
  
• The size of the fragment will be measured in base
  pairs or bps.