A Many-Body Dispersion Approach to the Pre-Reaction DNA-EcoRI Catalytic Complex

Long-range electronic dispersion correlations are critical in the synchronized cleavage of double-strand DNA by type II restriction endonucleases. Such enzymes–including EcoRI­–bind catalytically to spatially separated nucleotides via sequence-specific enzymatic subunits observed to activate through assistance from the DNA. It has been proposed that many-body electronic correlations across the complex mediate the synchronized catalysis with EcoRI creating a decoherence-free subspace during cleavage. A model remains to be developed for the complex’s entangled electrons, where two distant phosphodiester bonds are cleaved in concert by coordination with divalent metal cations. The role of quantum electronic fluctuations of these ions, the aqueous solution, enzyme residues, & DNA bases have yet to be considered in the current model for DNA-EcoRI catalysis. To support the analysis of collective many-body dispersion eigenmodes associated with the complex, realistic pre-reaction state complex configurations with Mg2+ were constructed to examine ligand-dependent electronic fluctuations. A theoretical computational model was developed to perform accurate quantum chemical analysis to gain an understanding of the multipartite entanglement contributing to the correlations in double-strand catalysis.