CRISPR-Cas Mechanism Deep Dives: Kinetics, Intermediates, and Conformational Control

This Research Topic is part of a set of companion collections. Authors are welcome to submit to either this collection or Multiplex and Combinatorial Genome Editing: Mechanisms, Kinetics, and Structural Basis of CRISPR-Cas Systems, depending on which best aligns with their expertise and the focus of their work.CRISPR-Cas systems have transformed genome engineering and molecular diagnostics, yet many of the most consequential determinants of performance—specificity, speed, and outcome control—are governed by mechanism. From target search and R-loop formation to catalytic activation, cleavage, and product release, CRISPR effectors operate through multi-step pathways shaped by transient intermediates, conformational checkpoints, and competing kinetic routes. Understanding these processes at the level of rate constants, structural transitions, and energy landscapes is increasingly essential for rationally improving editing efficiency, minimizing off-target activity, and engineering next-generation CRISPR tools.This Research Topic will bring together mechanistic studies that dissect CRISPR-Cas function through the lens of kinetics, intermediates, and conformational control. We welcome contributions spanning single-molecule and ensemble biophysics, time-resolved structural methods, computational modeling, and quantitative biochemistry that reveal how CRISPR effectors make decisions—when they bind, when they cut, when they stall, and when they disengage. Particular interest includes work that links measurable kinetic parameters to functional outcomes in cells and applications, such as editing precision, PAM and seed recognition, mismatch discrimination, target search strategies, and activation of collateral cleavage in diagnostic platforms.We encourage submissions that address, but are not limited to, the following themes:1. Kinetic frameworks for CRISPR reactions: target search, binding, R-loop propagation, activation, cleavage, and turnover2. Transient intermediates and checkpoints that govern mismatch discrimination and off-target outcomes3. Conformational transitions and allostery in Cas enzymes (e.g., HNH/RuvC coordination, domain rearrangements, guide/target-induced activation)4. Single-molecule and time-resolved approaches (smFRET, optical/magnetic tweezers, rapid quench/flow, stopped-flow, cryo-EM heterogeneity analysis)5. Thermodynamic and energy-landscape models connecting structure, dynamics, and catalytic probability6. Mechanisms across CRISPR classes and types, including Cas9, Cas12, Cas13, and emerging or engineered variants7. Guide RNA and target design principles derived from mechanistic insights (mismatch position effects, bulges, modifications, length/chemistry)8. Engineering via mechanistic control, including fidelity- or activity-enhanced variants, nickases, base/prime editors, anti-CRISPR regulation, and switchable systems9. Mechanistic determinants of diagnostic performance, including collateral cleavage kinetics and signal amplification strategiesArticle types may include Original Research, Methods, Reviews, and Mini-Reviews that provide quantitative and mechanistically gro Topic editors: Jhuma Bhadra, Debmalya Bhunia, Tianzi Wei Source: https://www.frontiersin.org/research-topics/78371/crispr-cas-mechanism-deep-dives-kinetics-intermediates-and-conformational-control