Select and compare aptamers under different conditions

Projects Andy thought might yield results quickly.

1.) Identify different buffer conditions you might use for selection.
  • What are your variables? Ionic strength, pH, metal ions, temperature, what else? Which variables are most interesting or important to a successful selection?
2.) Select anti-lysozyme aptamers.
3.) Clone and sequence aptamers.
4.) Compare binding across different sets of conditions.
  • Do aptamers that bind at one ionic strength or pH still bind at another? How specific is evolution for a given condition? Are some variables more important than others?
Further questions and issues:
  • Has anyone done this before? What does the primary literature look like?
  • Do the aptamers from a given pool or different pools bind at the same or different sites on lysozyme? How would you determine this? How might you do an ELISA? What is an ELISA?
  • Do your experiments have any bearing on the origin of life? It is thought that modern life was preceded by a 'RNA world.' What is the RNA world hypothesis? Is a robust RNA world more likely under some environmental conditions than others? Did your experiments delimit the conditions under which RNA was more or less functional?



2 comments:

Gwen said...

I did this! I looked at R0 background binding to lysozyme in 96 different buffers. I then selected 3 buffers that provided either high, normal (used the lysozyme buffer used in Colin Cox's previous selection), & low R0 background binding. I then performed 3 parallel anti-lysozyme aptamer selections. I can tell you more about this work, if you're interested.
-Gwen

Brad Hall said...

Do you have any of the data? A paper? Post it up here and maybe someone can work off it. I remember you did the selection but did you test the binding of one aptamer in the other conditions? Ow specific was the aptamer to it's selection environment?