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000820729 245__ $$aA Self-Activated Mechanism for Nucleic Acid Polymerization Catalyzed by DNA/RNA Polymerases
000820729 260__ $$aWashington, DC$$bAmerican Chemical Society$$c2016
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000820729 520__ $$aThe enzymatic polymerization of DNA and RNA is the basis for genetic inheritance for all living organisms. It is catalyzed by the DNA/RNA polymerase (Pol) superfamily. Here, bioinformatics analysis reveals that the incoming nucleotide substrate always forms an H-bond between its 3′-OH and β-phosphate moieties upon formation of the Michaelis complex. This previously unrecognized H-bond implies a novel self-activated mechanism (SAM), which synergistically connects the in situ nucleophile formation with subsequent nucleotide addition and, importantly, nucleic acid translocation. Thus, SAM allows an elegant and efficient closed-loop sequence of chemical and physical steps for Pol catalysis. This is markedly different from previous mechanistic hypotheses. Our proposed mechanism is corroborated via ab initio QM/MM simulations on a specific Pol, the human DNA polymerase-η, an enzyme involved in repairing damaged DNA. The structural conservation of DNA and RNA Pols supports the possible extension of SAM to Pol enzymes from the three domains of life.
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000820729 7001_ $$0P:(DE-HGF)0$$aVidossich, Pietro$$b1
000820729 7001_ $$0P:(DE-Juel1)146009$$aIppoliti, Emiliano$$b2$$ufzj
000820729 7001_ $$0P:(DE-Juel1)145614$$aCarloni, Paolo$$b3$$eCorresponding author
000820729 7001_ $$0P:(DE-HGF)0$$aVivo, Marco De$$b4$$eCorresponding author
000820729 773__ $$0PERI:(DE-600)1472210-0$$a10.1021/jacs.6b05475$$gVol. 138, no. 44, p. 14592 - 14598$$n44$$p14592 - 14598$$tJournal of the American Chemical Society$$v138$$x1520-5126$$y2016
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