Projects Andy thought might yield results quickly.
1.) Design oligonucleotide sequences (pick length, composition, sequence).
- How do these variables affect the answers you're likely to get?
2.) Order the same oligonucleotide as both DNA and PNA (peptide nucleic acid), with a biotin moiety.
- What are PNAs, what do they look like, where would you get them from?
3.) Immobilize on streptavidin-coated beads.
- What is the basis for streptavidin-biotin interactions?
- Where would you get these beads from?
4.) Select RNA binding sequences based on a centrifugation partition.
- What are possible artefacts?
- What controls or simultaneous experiments could you run to prevent these?
5.) After multiple rounds, clone and sequence binding species. Compare binding motifs for DNA versus PNA.
- How will you identify binding motifs?
6.) Determine how many binding motifs you obtained; compare with how many binding motifs you expected.
- How will you calculate how many binding motifs were expected?
Further questions and issues:
- Has anyone done this before? What does the primary literature look like?
- PNAs can potentially be used as antisense drugs. How might your findings influence the design of these drugs?
- If you used a library that could be introduced into real-time PCR reactions, you could actually quantify the progress of the selection. What is real-time PCR? How does it work? How can it be used to quantitate amplicons?
- How could your data be used for calculating the delta G of binding of a given PNA base-pair?