Regulation of Recombinase Polymerase Amplification by Vibrational Strong Coupling of Water

Abstract

Vibrational strong coupling (VSC) between molecular transitions and photonic structures can be used to tune the reactivity of molecules, and hybrid polariton states have been employed to modify the energy landscape of molecular systems in an optical cavity. To investigate how to modulate life reactions with VSC, herein we selected an in vitro model bioreaction, DNA replication, i.e., recombinase polymerase amplification (RPA), to couple with the typical Fabry–Pérot (FP) cavity mode. Known as an isothermal enzymatic reaction, RPA well satisfies the VSC study within FP cavities. Through tuning the resonance coupling strength between water molecules and FP cavity modes, we can regulate the efficiency of RPA as the cavity modes change from 3100 to 3550 cm–1. The results showed that O–H-based VSC can significantly inhibit the efficiency of RPA by ∼58%. Due to the key role of water in life, O–H stretching vibrational coupling with photonic structures could be a novel tool to regulate life in turn.

Ab Initio Vibro-Polaritonic Spectra in Strongly Coupled Cavity-Molecule Systems

“…Strong light–matter coupling between a molecular system and the electromagnetic field of an optical cavity offers new possibilities to modify chemical reactivity and selectivity, as demonstrated in recent experiments. − A particularly intriguing but not yet fully understood situation occurs when a cavity mode is strongly coupled to molecular vibrations, called vibrational-strong coupling (VSC). − For VSC the rate constants of ground state reactions can be modified even without external driving, i.e., without explicitly adding photons to the cavity. Probably one of the most striking features observed in such experiments is the change of the vibrational spectra due to the formation of molecular vibrational polaritons, hybrid states that involve both cavity modes and vibrational modes of molecules.…”

Cavity Born–Oppenheimer Hartree–Fock Ansatz: Light–Matter Properties of Strongly Coupled Molecular Ensembles

“…In polaritonic chemistry, depending on whether the quantized cavity modes are coupled via their characteristic frequencies to electronic or vibrational degrees of freedom of molecules, the situation is described as electronic-strong coupling (ESC) or vibrational-strong coupling (VSC), respectively. Under ESC, it becomes possible to modify the photochemistry/photophysics of molecules including charge transfer processes and electronic spectroscopy, and photoinduced reactions can be influenced. − Similarly, for VSC, the vibrational spectra of molecules are altered by the formation of light–matter hybrid states, and even the chemical reactivity of the ground state can be modified. ,− ,− The observed effects of molecular ESC and VSC are often discussed phenomenologically, and understanding of the underlying microscopic and macroscopic physical mechanisms, especially with respect to the effects of VSC, is still incomplete. ,− In our recent work we have shown numerically that the interaction between an optical cavity and ensembles of molecules not only leads to cavity detuning and a change of the optical length but also allows for a local molecular polarization mechanism under strong collective vibrational coupling in the thermodynamic limit. The interplay of microscopic and macroscopic polarization is due to cavity-mediated dipole–dipole interaction.…”

Unlimiting ionic conduction: manipulating hydration dynamics through vibrational strong coupling of water

“…This phenomenon is consistent with previous reports on the vibrational strong coupling of water. [32][33][34][35][36][37][38] The anticrossing behavior of the upper and lower polariton branches was evaluated, as shown in Fig. 1b.…”

“…[28][29][30] The modication under vibrational strong coupling can be emphasized especially for the coupling with solvents because of the large number of molecules. 31 Notably, water has been shown to exhibit an ultrastrong coupling regime, [32][33][34][35][36][37][38] allowing for modi-cations in its physicochemical properties. This phenomenon has been demonstrated in various contexts, including the modulation of hydrogen-bonding networks, 32 the manipulation of enzymatic activity, 33,34 the modication of DNA replication 35 and the folding of DNA origami, 36 and the selective crystallization of metal-organic frameworks.…”

“…31 Notably, water has been shown to exhibit an ultrastrong coupling regime, [32][33][34][35][36][37][38] allowing for modi-cations in its physicochemical properties. This phenomenon has been demonstrated in various contexts, including the modulation of hydrogen-bonding networks, 32 the manipulation of enzymatic activity, 33,34 the modication of DNA replication 35 and the folding of DNA origami, 36 and the selective crystallization of metal-organic frameworks. 37 In our previous work, we discovered a more than tenfold enhancement in the H + conductivity of aqueous solutions.…”