Linkage between proton binding and folding in RNA: Implications for RNA catalysis

P. C. Bevilacqua; T. S. Brown; D. Chadalavada; J. Lecomte; E. Moody; S. I. Nakano

doi:10.1042/BST0330466

Linkage between proton binding and folding in RNA: Implications for RNA catalysis

P. C. Bevilacqua, T. S. Brown, D. Chadalavada, J. Lecomte, E. Moody, S. I. Nakano

Research output: Contribution to journal › Article › peer-review

13 Scopus citations

Abstract

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 pK_a towards neutrality. Simulations and thermodynamic experiments implicate linkage between folding and protonation in nucleobase pK_a shifting. Even small oligonucleotides are shown to fold in a highly co-operative manner, although they do so in a context-specific fashion. Linkage between protonation and co-operativity of folding may drive pK_a shifting and provide for enhanced function in RNA.

Original language	English (US)
Pages (from-to)	466-470
Number of pages	5
Journal	Biochemical Society transactions
Volume	33
Issue number	3
DOIs	https://doi.org/10.1042/BST0330466
State	Published - Jun 2005

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Biochemistry

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abstract = "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 context-specific fashion. Linkage between protonation and co-operativity of folding may drive pKa shifting and provide for enhanced function in RNA.",

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T2 - Implications for RNA catalysis

AU - Bevilacqua, P. C.

AU - Brown, T. S.

AU - Chadalavada, D.

AU - Lecomte, J.

AU - Moody, E.

AU - Nakano, S. I.

PY - 2005/6

Y1 - 2005/6

N2 - 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 context-specific fashion. Linkage between protonation and co-operativity of folding may drive pKa shifting and provide for enhanced function in RNA.

AB - 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 context-specific fashion. Linkage between protonation and co-operativity of folding may drive pKa shifting and provide for enhanced function in RNA.

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Linkage between proton binding and folding in RNA: Implications for RNA catalysis

Abstract

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