Select double-stranded DNA binding sites for transcription factors.

Projects Andy thought might yield results quickly.

1.) Identify and order commercially available transcription factors.
  • Where and how will you look for these (hint: you have to buy them, so why not Google 'transcription factor' and 'price' or 'catalog')?
  • How will you figure out which transcription factors are interesting?
2.) Carry out filter-based selections using a double-stranded DNA library.
3.) After multiple rounds clone and sequence binding species.
4.) Identify binding motifs.
  • How will you identify binding motifs?
5.) Compare binding motifs with those in the human genome.
  • How will you do these comparisons?
Further questions and issues:
  • Has anyone done this before? What does the primary literature look like?
  • Can double-stranded DNA 'decoys' of transcription factors be used as drugs? How might this work? Has anyone done this?
  • How could your data be used to find otherwise unknown transcription factor binding sites in a genome?
  • How could your data be used to map transcriptional networks in a newly sequenced genome?
  • How could you get data on multiple transcription factors simultaneously or in parallel?

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