DIYbio:Notebook/Open Thermal Cycler/Use Cases

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Use cases of a thermal cycler:

  1. A user has X DNA and wants to increase the quantity of X, or quantity of Y (a subsequence of X) in order to:
    1. Sequence the DNA -- more quantity is needed
    2. Send DNA to a friend
    3. Transform cells -- more quantity is needed
    4. Archive DNA
  2. A user wants to study their genome
    1. Small SNP-sensitive sets of primers are used to amplify DNA. Electrophoresis is used to image PCR product, where short bands indicate SNP match/mismatch (Kay Aull)
  3. A user wants to extract DNA sequence Z from organism O. The user knows short sequences surrounding the region (primers) -- unknown sequence is needed
  4. A user has DNA and wants to create copies that are each a little bit different
    1. Error prone PCR
  5. A user wants a sequence of DNA but doesn't want to synthesize it
    1. Use primers + sequence X to create more of sequence X
  6. A user wants to determine what tree is in their backyard using a simple test (~1 species/sample)
    1. Amplify species-specific DNA + digestion + gel electrophoresis + imaging ==> Webpage showing species
  7. A user wants to determine what bacteria are on a crosswalk button (100+ species/sample) (Jason Bobe)
    1. Amplify species-specific DNA + sequencing
  8. A user wants to combine a sequence onto a known sequence (tailing - per Jake)
    1. i.e. take a sequence and make add biobrick ends onto it
  9. A user wants to synthesize a gene (Alec Nielsen)
    1. Assemble shorter (~60bp), overlapping oligos into a large, contiguous strand of DNA
  10. A user wants to screen for successfully transformed cells (Alec Nielsen)
    1. Colony PCR: screen successful transformants from "background" colonies by PCRing many colonies with primers for the desired vector
  11. A user wants to incubate/heat inactivate/chill a culture/reaction (Alec Nielsen)
    1. I.e., non-PCR activities: For example, incubate a restriction digest at 37 C for a few hours, heat inactivate reaction at 80 C for ten minutes, then hold at 4 C indefinitely. Convenience!

Advanced use cases:

  1. The user wants to observe gene expression in cells over a time period (Josh Perfetto)
    1. User is presented with a graph showing the change in expression over time, or other desired result (RT PCR)

The Pain of Current Thermal Cyclers: Price - thermal cyclers Interface - current models are Application -

The Open Thermal Cycler: Design something a great number of current non-thermocycler users will use.