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DNA Electrophoresis

Mark Bergland and Karen Klyczek (University of Wisconsin-River Falls)
Screen Shots | What's New | System Requirements

DNA Electrophoresis is an open-ended simulation which cuts any DNA sequence with any combination of restriction enzymes, runs realistic gels and Southern blots of the resulting DNA fragments, and converts DNA fragments to mapping fragments for restriction mapping. Eight wells are available for loading, with up to 40 fragments per well visible on the screen. There are four main screens: Data Screen, Genbank Filter, Gel Photos, and Lab Bench.

Use the Data Screen to quickly digest DNA, load it into wells, and run gels. Southern blots can then be run after selecting an appropriate probe. The Genbank Filter will remove everything from a standard Genbank file except for the DNA sequence. From this screen you can also open a web browser and access the Genbank Query Form directly. The Gel Photos screen is used to compare photos taken of current gels andalso to view photos taken of previous gels which have been saved as PICT files. Gels can also be set up and run on the Lab Bench using simulated laboratory equipment.

After running a gel, mapping of restriction fragments can be done from either the Data Screen or the Lab Bench. Mapping fragments can be moved to solve the map after conducting a series of single and double digestions.

A new Resource Manual describes several case studies that were developed using DNA sequences obtained from GenBank via the internet. Among the cases that have been developed are several in human genetics (sickle cell anemia, Duchenne’s muscular dystrophy, Alzheimer’s disease, breast cancer susceptibility, cystic fibrosis, fragile X syndrome), forensics (a murder case), and phylogenetic studies (primate relationships and squirrel taxonomy).

 

Screen Shots

The gel electrophoresis simulation screen after running gels.

What's New?

New Features in Version 2.06

  • Resource Manual with case studies requiring DNA analysis in areas such as human genetics, forensics, infectious disease, and ecology.
  • Animated tutorials demonstrating program features.

Additional new features:

  • The simulation can now separate larger fragments .
  • “Quick Instructions” have been added to each screen
  • The Note Pad now is resizable, and can be printed directly.
  • The Well Data window is resizable and contents can be saved and printed.
  • An optional “genomic smear” feature has been added.

System Requirements

Macintosh or Power Macintosh

  • System 6.07 or later; System 7.1 for Power Macintosh. System 7.5+ recommended.
  • At least 8 MB of RAM, 16 MB recommended for best performance.
  • 68030 processor or greater; 68040 or Power Mac is recommended
Windows 3.1 or Windows 95
  • Windows 3.1 or later, or Windows 95.
  • 80486 processor; Pentium recommended.
  • At least 8 megabytes of RAM.
Both platforms require at least an 8-bit, 256 13" color monitor


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