Alkyne-Tagged Raman Probes for Local Environmental Sensing by Hydrogen–Deuterium Exchange

Abstract

Alkyne-tagged Raman probes have shown high promise for noninvasive and sensitive visualization of small biomolecules to understand their functional roles in live cells. However, the potential for alkynes to sense cellular environments that goes beyond imaging remains to be further explored. Here, we report a general strategy for Raman imaging-based local environment sensing by hydrogen–deuterium exchange (HDX) of terminal alkynes (termed alkyne-HDX). We first demonstrate, in multiple Raman probes, that deuterations of the alkynyl hydrogens lead to remarkable shifts of alkyne Raman peaks for about 130 cm–1, providing resolvable signals suited for imaging-based analysis with high specificity. Both our analytical derivation and experimental characterizations subsequently establish that HDX kinetics are linearly proportional to both alkyne pK as and environmental pDs. After validating the quantitative nature of this strategy, we apply alkyne-HDX to sensing local chemical and cellular environments. We establish that alkyne-HDX exhibits high sensitivity to various DNA structures and demonstrates the capacity to detect DNA structural changes in situ from UV-induced damage. We further show that this strategy is also applicable to resolve subtle pD variations in live cells. Altogether, our work lays the foundation for utilizing alkyne-HDX strategy to quantitatively sense the local environments for a broad spectrum of applications in complex biological systems.

Bringing Vibrational Imaging to Chemical Biology with Molecular Probes

“…With similar targeted reactions, triple-bond Raman probes with the peak-shift principles have also been rationally designed and developed for sensing pH, fluoride, and metal ions . Recently, the isotope exchange reactions (especially the H/D exchange) have been harnessed on the terminal alkynes for both two-color imaging and cellular environmental sensing applications. , The H/D exchange reaction results in the dramatic alkyne Raman peak shift (>130 cm –1 ) due to both the large mass difference between D and H and the quantum coupling between the alkyne and the adjacent CD. In addition to chemical reactions, Raman peak frequency can also be tuned by the surrounding physical environment.…”

Iridium-catalyzed α-selective deuteration of alcohols

“…High reactivity for alkyne C(sp)-deuteration under neutral conditions would be favourable for the selective deuteration of alkyne-tagged probes for Raman imaging. 30,31…”

Raman Spectroscopy for Chemical Biology Research

“…The development of new Raman probes and analytical methods should further expand the potential of Raman spectroscopy for chemical biology research. For example, recently, Wei et al reported a new method for Raman imaging-based local environment sensing via hydrogen–deuterium exchange (HDX) of the terminal alkyne tag . This work demonstrates that UV-induced thymidine dimer formation can be detected by alkyne-HDX from EdU-labeled cells.…”