Local rather than global folding enables the lead-dependent activity of the 8-17 deoxyribozyme: evidence from contact photo-crosslinking

Journal of Molecular Biology
Yong Liu, D Sen

Abstract

The 8-17 deoxyribozyme is an in vitro selected enzyme capable of sequence-specific cleavage of RNA. While selected to be a magnesium and zinc-utilizing enzyme, the 8-17 DNAzyme has been shown to utilize lead for its catalysis. Fluorescence-based experiments have indicated that the magnesium- and zinc-utilizing versions of the DNAzyme-substrate complex need to form a defined tertiary structure to be active, but no such global folding is required for the lead-mediated activity. Here, we have investigated this phenomenon, including the use of contact photo-crosslinking to map the tertiary fold of the lead-dependent DNAzyme. While our results recapitulate that global folding is not required for the lead activity, they reveal strikingly distinct lead-mediated modes of activity under conditions of low versus moderate solution ionic strength. Even in very low salt buffers, where no global folding of the 8-17 DNAzyme occurs, the active site of the enzyme appears to form a distinct local fold, one that cannot be modelled easily by DNA/RNA constructs that preserve key sequence and secondary structure features of the active site.

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Citations

Oct 4, 2016·Inorganica Chimica Acta·Kevin HwangYi Lu
Jun 10, 2017·Chemical Reviews·Wenhu ZhouJuewen Liu
Mar 10, 2010·Chembiochem : a European Journal of Chemical Biology·Kenny Schlosser, Yingfu Li
Jan 18, 2012·Chembiochem : a European Journal of Chemical Biology·Kevin E NelsonYi Lu
Dec 14, 2017·Quarterly Reviews of Biophysics·Falk WachowiusPhilipp Holliger
Aug 10, 2017·Organic & Biomolecular Chemistry·Wenhu ZhouJuewen Liu
Oct 13, 2017·Organic & Biomolecular Chemistry·Alessio PeracchiAlfredo Credali
Oct 11, 2020·Bioorganic & Medicinal Chemistry·Yang LiJunlin He
Feb 2, 2018·Biochemistry·Marjorie Cepeda-PlazaYi Lu
Jun 18, 2010·Methods : a Companion to Methods in Enzymology·Edward K Y Leung, Dipankar Sen

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