How to Build Plasmon-Driven Molecular Jackhammers that Disassemble Cell Membranes and Cytoskeletons in Cancer.

Plasmon-driven molecular machines with ultrafast motion at the femtosecond scale are effective for the treatment of cancer and other diseases. It is recently shown that cyanine dyes act as molecular jackhammers (MJH) through vibronic (vibrational and electronic mode coupling) driven activation that causes the molecule to stretch longitudinally and axially through concerted whole molecule vibrations. However, the theoretical and experimental underpinnings of these plasmon-driven motions in molecules are difficult to assess. Here the use of near-infrared (NIR) light-activated plasmons in a broad array of MJH that mechanically disassemble membranes and cytoskeletons in human melanoma A375 cells is described. The characteristics of plasmon-driven molecular mechanical disassembly of supramolecular biological structures are observed and recorded using real-time fluorescence confocal microscopy. Molecular plasmon resonances in MJH are quantified through a new experimental plasmonicity index method. This is done through the measurement of the UV-vis-NIR spectra in various solvents, and quantification of the optical response as a function of the solvent polarity. Structure-activity relationships are used to optimize the synthesis of plasmon-driven MJH, applying them to eradicate human melanoma A375 cells at low lethal concentrations of 75 nm and 80 mW cm-2 of 730 nm NIR-light for 10 min.

Dynamics of single-base editing: Theoretical analysis.

Recent experimental advances led to the development of DNA base editors (BEs) with single-nucleotide precision, which is critical for future progress in various scientific and technological fields. The molecular mechanisms of single-base discrimination, however, remain poorly understood. Using a recently developed stochastic approach, we theoretically investigated the dynamics of single-base editing. More specifically, transient and mean times to edit "TC" motifs by cytosine BEs are explicitly evaluated for correct (target) and incorrect (bystander) locations on DNA. In addition, the effect of mutations on the dynamics of the single-base edition is also analyzed. It is found that for most ranges of parameters, it is possible to temporarily separate target and bystander products of base editing, supporting the idea of dynamic selectivity as a method of improving the precision of single-base editing. We conclude that to improve the efficiency of single-base editing, selecting the probability or selecting the time requires different strategies. Physical-chemical arguments to explain the observed dynamic properties are presented. The theoretical analysis clarifies some important aspects of the molecular mechanisms of selective base editing.

Dynamics of Single-Base Editing: Theoretical Analysis.

Recent experimental advances led to the development of DNA base editors (BEs) with a single-nucleotide precision that is critical for future progress in various scientific and technological fields. The molecular mechanisms of single-base discrimination, however, remain not well understood. Using a recently developed stochastic approach, we theoretically investigated the dynamics of single-base editing. More specifically, transient and mean times to edit "TC" motifs by cytosine BEs are explicitly evaluated for correct (target) and incorrect (bystander) locations on DNA. In addition, the effect of mutations on the dynamics of the single-base edition is also analyzed. It is found that for most ranges of parameters, it is possible to temporarily separate target and bystander products of base editing, supporting the idea of dynamic selectivity as a method of improving the precision of single-base editing. We conclude that to improve the efficiency of single-base editing, selecting the probability or selecting the time requires different strategies. Physical-chemical arguments to explain the observed dynamic properties are presented. The theoretical analysis clarifies some important aspects of molecular mechanisms of selective base editing.

Strength of Graphene-Coated Ni Bi-Crystals: A Molecular Dynamics Nano-Indentation Study.

Nanoindentation simulations are performed for a Ni(111) bi-crystal, in which the grain boundary is coated by a graphene layer. We study both a weak and a strong interface, realized by a 30 ∘ and a 60 ∘ twist boundary, respectively, and compare our results for the composite also with those of an elemental Ni bi-crystal. We find hardening of the elemental Ni when a strong, i.e., low-energy, grain boundary is introduced, and softening for a weak grain boundary. For the strong grain boundary, the interface barrier strength felt by dislocations upon passing the interface is responsible for the hardening; for the weak grain boundary, confinement of the dislocations results in the weakening. For the Ni-graphene composite, we find in all cases a weakening influence that is caused by the graphene blocking the passage of dislocations and absorbing them. In addition, interface failure occurs when the indenter reaches the graphene, again weakening the composite structure.