Linkage between proton binding and folding in RNA: implications for RNA catalysis.

@article{Bevilacqua2005LinkageBP,
  title={Linkage between proton binding and folding in RNA: implications for RNA catalysis.},
  author={Philip C. Bevilacqua and Trevor S. Brown and Durga M. Chadalavada and J L Lecomte and Eddie W. Moody and S-I Nakano},
  journal={Biochemical Society transactions},
  year={2005},
  volume={33 Pt 3},
  pages={466-70}
}
Small ribozymes use their nucleobases to catalyse phosphodiester bond cleavage. The hepatitis delta virus ribozyme employs C75 as a general acid to protonate the 5'-bridging oxygen leaving group, and to accomplish this task efficiently, it shifts its pKa towards neutrality. Simulations and thermodynamic experiments implicate linkage between folding and protonation in nucleobase pKa shifting. Even small oligonucleotides are shown to fold in a highly co-operative manner, although they do so in a… CONTINUE READING
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