Many-body dispersion effects and plasmonic correlations in the catalytic synchronization of a DNA-enzyme complex

Long-range van der Waals dispersion forces could play a significant role in explaining the action of certain restriction enzymes inducing DNA double-strand breaks [J. Theor. Biol. 2016, 391, 102-112]. In particular, dipolar interactions among spatially separated nucleotides and enzymatic molecular subunits may be responsible for long-range synchronization of quantum electronic density fluctuations. Zero-point modes of such plasmon-like oscillations may promote double-strand breakage, in lieu of external chemical energy from ATP. Our analysis of Many-Body Dispersion (MBD) effects in the catalytic behavior of EcoRI, a sequence-specific DNA-targeting enzyme used widely in genomic science, offers clues for more refined investigations of the collective electron fluctuations (plasmon) in complex (bio)molecular systems [Chem. Soc. Rev. 2019, 48, 4118]. We present analysis of these MBD eigenmodes applied to EcoRI at different steps along the catalytic trajectory, including entropic measures of the degree of collectivity of each mode (i.e., its vectorial distribution in the atomic site basis) and other quantum information metrics, to understand the delocalization properties in Hilbert space and their implications for distant “plasmonic allostery” in 3+1-dimensional physical space.