Simultaneous dual-channel imaging to quantify interdependent protein recruitment to laser-induced DNA damage sites

New Methodologies to Study DNA Repair Processes in Space and Time Within Living Cells

DNA repair requires a coordinated effort from an array of factors that play different roles in the DNA damage response from recognizing and signaling the presence of a break, creating a repair competent environment, and physically repairing the lesion. Due to the rapid nature of many of these events, live-cell microscopy has become an invaluable method to study this process. In this review we outline commonly used tools to induce DNA damage under the microscope and discuss spatio-temporal analysis tools that can bring added information regarding protein dynamics at sites of damage. In particular, we show how to go beyond the classical analysis of protein recruitment curves to be able to assess the dynamic association of the repair factors with the DNA lesions as well as the target-search strategies used to efficiently find these lesions. Finally, we discuss how the use of mathematical models, combined with experimental evidence, can be used to better interpret the complex dynamics of repair proteins at DNA lesions.

Direct measurement of protein-protein interactions by FLIM-FRET at UV laser-induced DNA damage sites in living cells

Protein-protein interactions are essential to ensure timely and precise recruitment of chromatin remodellers and repair factors to DNA damage sites. Conventional analyses of protein-protein interactions at a population level may mask the complexity of interaction dynamics, highlighting the need for a method that enables quantification of DNA damage-dependent interactions at a single-cell level. To this end, we integrated a pulsed UV laser on a confocal fluorescence lifetime imaging (FLIM) microscope to induce localized DNA damage. To quantify protein-protein interactions in live cells, we measured Förster resonance energy transfer (FRET) between mEGFP- and mCherry-tagged proteins, based on the fluorescence lifetime reduction of the mEGFP donor protein. The UV-FLIM-FRET system offers a unique combination of real-time and single-cell quantification of DNA damage-dependent interactions, and can distinguish between direct protein-protein interactions, as opposed to those mediated by chromatin proximity. Using the UV-FLIM-FRET system, we show the dynamic changes in the interaction between poly(ADP-ribose) polymerase 1, amplified in liver cancer 1, X-ray repair cross-complementing protein 1 and tripartite motif containing 33 after DNA damage. This new set-up complements the toolset for studying DNA damage response by providing single-cell quantitative and dynamic information about protein-protein interactions at DNA damage sites.

In Situ Analysis of DNA-Protein Complex Formation upon Radiation-Induced DNA Damage

The importance of determining at the cellular level the formation of DNA–protein complexes after radiation-induced lesions to DNA is outlined by the evidence that such interactions represent one of the first steps of the cellular response to DNA damage. These complexes are formed through recruitment at the sites of the lesion, of proteins deputed to signal the presence of DNA damage, and of DNA repair factors necessary to remove it. Investigating the formation of such complexes has provided, and will probably continue to, relevant information about molecular mechanisms and spatiotemporal dynamics of the processes that constitute the first barrier of cell defense against genome instability and related diseases. In this review, we will summarize and discuss the use of in situ procedures to detect the formation of DNA-protein complexes after radiation-induced DNA damage. This type of analysis provides important information on the spatial localization and temporal resolution of the formation of such complexes, at the single-cell level, allowing the study of heterogeneous cell populations.

Nonlinear Brillouin spectroscopy: what makes it a better tool for biological viscoelastic measurements

Brillouin spectroscopy is an emerging tool in biomedical imaging and sensing. It is capable of assessing the high-frequency viscoelastic longitudinal modulus with microscopic spatial resolution. Nonlinear Brillouin spectroscopy based on impulsive stimulated Brillouin scattering offers a number of significant advantages over conventional spontaneous and stimulated Brillouin scattering. In this report, we evaluate the accuracy of Brillouin shift measurements in spontaneous and nonlinear Brillouin microscopy by calculating the Allan variance for both CW excited spontaneous Brillouin measurements and nonlinear Brillouin scattering measurements made with both nanosecond and picosecond pulse excitation. We find that impulsive stimulated Brillouin spectroscopy is superior to spontaneous Brillouin spectroscopy in terms of the accuracy of such measurements and demonstrate its application for assessing tiny changes in Brillouin frequency shifts associated with low concentrations of biologically relevant solutions.