I am reading the paper:

Petersheim, M. and Turner, D.H. (1983) Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry, 22, 256-263.

The p at the end of the sequence apparently stands for 3'-terminal phosphate.

What is the difference between RNA sequences with a 3' terminal phosphate and a "normal" RNA sequence? Why would they consider RNA with a 3' terminal phosphate?

  • $\begingroup$ This is just a guess, but maybe it's related to how oligonucleotides are made? That first phosphoramidite would have a 3' phosphorous attached, which would become a 3' phosphate upon cleavage from the support. This could be removed after synthesis, or it could be left attached. $\endgroup$
    – user137
    Oct 12 '20 at 11:41

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