Background Information

Activities

General Outline

  1. Reintroduce the structure of DNA and its constituent nucleobases (Structure & Function, Information Flow)
  2. Walk through the set-up of pouring an agarose gel while describing the concept of molecular sieving
    1. Prepare the gel as a demonstration
      1. Place gaskets at end of casting tray
      2. Place comb in center of the casting tray
      3. Add 60 ml TBE buffer to a flask with 0.6 g agarose
      4. Microwave solution for 1 minute while watching to avoid boil-over
      5. Stop from boil-over and swirl solution with gloved or mitted hand
      6. Continue microwaving if not completely molten
      7. Place casting tray in refrigerator and pour the solution into tray
    2. Have student groups assemble casting trays and prepare gels
      • Caution students about the temperature of the molten agarose and warn them not to move trays after pouring
    3. While gels are solidifying, inform students of the % of gel effect on firmness and pore size with an emphasis on migration retardation of objects being pulled through the pores
    4. Inquire about the charge of DNA molecules and the direction in which the molecules should move and fractionate
  3. When gels are cooled and firm, gently wiggle the gaskets off ends to avoid tearing gel
  4. Place casting tray with gel into electrophoresis tank and ensure gel is covered with buffer (or add additional buffer)
  5. Demonstrate the use of fixed volume pipettors and load samples in order into instructor gel
  6. Have students load gels and assist when needed
  7. Cover electrophoresis tanks with lids and run at 110V for at least 30 minutes (Systems)
    1. Ensure that all groups are ready to run if sharing power supplies or an error will occur
    2. Observe the bubbles as an indicator of proper current
  8. During the running, you may describe the concepts of restriction enzymes
  9. Describe the concept of forensics using RFLPs and molecular sieving
    (Structure & Function, Evolution, Interdisciplinary Nature of Science, Science & Society, Process of Science, Visual Communication)
    • This is an introduction to Lab 13
  10. Review the results of the gels and have students document the migration of the dyes
    1. Review the migration patterns of dyes and illustrate the differences in colors
    2. Students often do not have any inkling that multiple bands indicate a mixture of dyes
    3. Review the blue dyes that migrated in opposite directions
    4. Inquire which dye molecules were largest, smallest, and their charges

Curricular Notes

This unit covers the NSF Vision & Change Core Competencies:

  1. Quantitative Reasoning: doubling and exponential nature of replication
  2. Integration of Systems: electrophoresis and genome diversity
  3. Science & Society: forensics
  4. Interdisciplinary Nature of Science: RFLPs/VNTRs and forensics, electrophoresis
  5. (Visual) Communication: review of gels

This unit covers the NSF Vision & Change Core Concepts:

  1. Structure & Function: DNA base complementarity
  2. Information Flow: DNA replication
  3. Systems: integration of genome diversity
  4. Evolution: diversity of genomes

This unit covers additional General Education competency:

  1. Life-long Learning
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