DIYbio:Notebook/Open Thermal Cycler/Use Cases

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.