The LexA-RecA* structure reveals a cryptic lock-and-key mechanism for SOS activation

The bacterial SOS response plays a key role in adaptation to DNA damage, including genomic stress caused by antibiotics. SOS induction begins when activated RecA*, an oligomeric nucleoprotein filament that forms on single-stranded DNA, binds to and stimulates autoproteolysis of the repressor LexA. Here, we present the structure of the complete Escherichia coli SOS signal complex, constituting full-length LexA bound to RecA*. We uncover an extensive interface unexpectedly including the LexA DNA-binding domain, providing a new molecular rationale for ordered SOS gene induction. We further find that the interface involves three RecA subunits, with a single residue in the central engaged subunit acting as a molecular key, inserting into an allosteric binding pocket to induce LexA cleavage. Given the pro-mutagenic nature of SOS activation, our structural and mechanistic insights provide a foundation for developing new therapeutics to slow the evolution of antibiotic resistance.

Highly tunable bimane-based fluorescent probes: design, synthesis, and application as a selective amyloid binding dye

Small molecule fluorescent probes are indispensable tools for a broad range of biological applications. Despite many probes being available, there is still a need for probes where photophysical properties and biological selectivity can be tuned as desired. Here, we report the rational design and synthesis of a palette of fluorescent probes based on the underexplored bimane scaffold. The newly developed probes with varied electronic properties show tunable absorption and emission in the visible region with large Stokes shifts. Probes featuring electron-donating groups exhibit rotor effects that are sensitive to polarity and viscosity by "intramolecular charge transfer" (ICT) and twisted intramolecular charge transfer (TICT) mechanisms, respectively. These properties enable their application as "turn-on" fluorescent probes to detect fibrillar aggregates of the α-synuclein (αS) protein that are a hallmark of Parkinson's disease (PD). One probe shows selective binding to αS fibrils relative to soluble proteins in cell lysates and amyloid fibrils of tau and amyloid-β. Finally, we demonstrate the diagnostic potential of the probe in selectively detecting αS fibrils amplified from PD with dementia (PDD) patient samples.

FRETing about the details: Case studies in the use of a genetically encoded fluorescent amino acid for distance-dependent energy transfer

Förster resonance energy transfer (FRET) is a valuable method for monitoring protein conformation and biomolecular interactions. Intrinsically fluorescent amino acids that can be genetically encoded, such as acridonylalanine (Acd), are particularly useful for FRET studies. However, quantitative interpretation of FRET data to derive distance information requires careful use of controls and consideration of photophysical effects. Here we present two case studies illustrating how Acd can be used in FRET experiments to study small molecule induced conformational changes and multicomponent biomolecular complexes.

Engineered RecA Constructs Reveal the Minimal SOS Activation Complex

The SOS response is a bacterial DNA damage response pathway that has been heavily implicated in bacteria's ability to evolve resistance to antibiotics. Activation of the SOS response is dependent on the interaction between two bacterial proteins, RecA and LexA. RecA acts as a DNA damage sensor by forming lengthy oligomeric filaments (RecA*) along single-stranded DNA (ssDNA) in an ATP-dependent manner. RecA* can then bind to LexA, the repressor of SOS response genes, triggering LexA degradation and leading to induction of the SOS response. Formation of the RecA*-LexA complex therefore serves as the key "SOS activation signal." Given the challenges associated with studying a complex involving multiple macromolecular interactions, the essential constituents of RecA* that allow LexA cleavage are not well defined. Here, we leverage head-to-tail linked and end-capped RecA constructs as tools to define the minimal RecA* filament that can engage LexA. In contrast to previously postulated models, we found that as few as three linked RecA units are capable of ssDNA binding, LexA binding, and LexA cleavage. We further demonstrate that RecA oligomerization alone is insufficient for LexA cleavage, with an obligate requirement for ATP and ssDNA binding to form a competent SOS activation signal with the linked constructs. Our minimal system for RecA* highlights the limitations of prior models for the SOS activation signal and offers a novel tool that can inform efforts to slow acquired antibiotic resistance by targeting the SOS response.

One- and Two-Photon Uncaging of Carbon Monoxide (CO) with Real-Time Monitoring: On-Demand Carbazole-Based Dual CO-Releasing Platform to Test over Single and Combinatorial Approaches for the Efficient Regression of Orthotopic Murine Melanoma In Vivo

Herein, we report three new metal-free, photochemically active single, dual, and combinatorial CORMs (photoCORMs) based on a carbazole-fused 1,3-dioxol-2-one moiety which released one equivalent of CO, two equivalent of CO, and a combination of one equivalent of each CO and anticancer drug upon one- and two-photon excitation, respectively. The photoCORMs exhibited good cellular uptake and real-time monitoring ability of CO uncaging by a color change approach in cancerous B16F10 cells. Interestingly, the cytotoxicity assay on B16F10 cells indicated that the dual photoCORM has increased anticancer activity over the single and combinatorial photoCORMs upon irradiation. Our results also showed that CO could accelerate the effectiveness of the well-known anticancer drug (chlorambucil). Finally, the in vivo evaluation of the dual photoCORM on an established murine melanoma tumor (C57BL/6J mouse model) manifested a significant regression of tumor volume and led to significant improvement (>50%) in the overall survivability.

An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET

With the recent explosion in high-resolution protein structures, one of the next frontiers in biology is elucidating the mechanisms by which conformational rearrangements in proteins are regulated to meet the needs of cells under changing conditions. Rigorously measuring protein energetics and dynamics requires the development of new methods that can resolve structural heterogeneity and conformational distributions. We have previously developed steady-state transition metal ion fluorescence resonance energy transfer (tmFRET) approaches using a fluorescent noncanonical amino acid donor (Anap) and transition metal ion acceptor to probe conformational rearrangements in soluble and membrane proteins. Here, we show that the fluorescent noncanonical amino acid Acd has superior photophysical properties that extend its utility as a donor for tmFRET. Using maltose-binding protein (MBP) expressed in mammalian cells as a model system, we show that Acd is comparable to Anap in steady-state tmFRET experiments and that its long, single-exponential lifetime is better suited for probing conformational distributions using time-resolved FRET. These experiments reveal differences in heterogeneity in the apo and holo conformational states of MBP and produce accurate quantification of the distributions among apo and holo conformational states at subsaturating maltose concentrations. Our new approach using Acd for time-resolved tmFRET sets the stage for measuring the energetics of conformational rearrangements in soluble and membrane proteins in near-native conditions.

Genetic encoding of a highly photostable, long lifetime fluorescent amino acid for imaging in mammalian cells

Acridonylalanine (Acd) is a fluorescent amino acid that is highly photostable, with a high quantum yield and long fluorescence lifetime in water. These properties make it superior to existing genetically encodable fluorescent amino acids for monitoring protein interactions and conformational changes through fluorescence polarization or lifetime experiments, including fluorescence lifetime imaging microscopy (FLIM). Here, we report the genetic incorporation of Acd using engineered pyrrolysine tRNA synthetase (RS) mutants that allow for efficient Acd incorporation in both E. coli and mammalian cells. We compare protein yields and amino acid specificity for these Acd RSs to identify an optimal construct. We also demonstrate the use of Acd in FLIM, where its long lifetime provides strong contrast compared to endogenous fluorophores and engineered fluorescent proteins, which have lifetimes less than 5 ns.

Protein labeling for FRET with methoxycoumarin and acridonylalanine

Site-specific protein labeling can be used to monitor protein motions and interactions in real time using Förster resonance energy transfer (FRET). While there are many fluorophores available for protein labeling, few FRET pairs are suitable for monitoring intramolecular protein motions without being disruptive to protein folding and function. Here, we describe the synthesis and use of a minimally perturbing FRET pair comprised of methoxycoumarin maleimide (Mcm-Mal) and acridonylalanine (Acd). Acd can be incorporated into a protein through unnatural amino acid mutagenesis. Mcm-Mal is fluorogenic when reacted with cysteine and can label cysteine/Acd double mutant proteins. This labeling strategy provides an easy to install FRET pair with a working range or 15-40Å, making it ideal for monitoring most intramolecular motions. Additionally, Mcm/Acd FRET can be combined with tryptophan fluorescence for monitoring multiple protein motions via three color FRET.

Real-time monitoring of a photoactivated hydrogen persulfide donor for biological entities

Hydrogen persulfide (H2S2) plays an important role in sulfur-based redox signaling mechanisms. Herein, we developed a visible light activated ESIPT based H2S2 donor using a p-hydroxyphenacyl phototrigger. The unique feature of the designed H2S2 donor system is the ability to monitor the H2S2 release in real time through a non-invasive fluorescence color change approach, with the color changing from green to blue. Next, we demonstrated the detection and quantification of H2S2 using a fluorescein based "turn-on" fluorescent probe. Furthermore, in vitro studies of the designed H2S2 donor demonstrated the real-time monitored H2S2 release and cytoprotective ability in the highly oxidizing cellular environment of MDA-MB-468 cells.

An improved tumor-specific therapeutic strategy by the spatio-temporally controlled in situ formation of a Cu(ii) complex, leading to prompt cell apoptosis via photoactivation of a prodrug

Biotin tagged one and two photon activable Cu chelating prodrug as a target-specific and spatio-temporal generations of Cu complex for improved cancer treatment.

One- and two-photon responsive sulfur dioxide (SO2) donors: a combinatorial drug delivery for improved antibiotic therapy

Light-activated sulfur dioxide donors have been developed and explored their applicability for combinatorial antibiotic therapy with self-monitoring ability.

One- and Two-Photon Uncaging: Carbazole Fused o-Hydroxycinnamate Platform for Dual Release of Alcohols (Same or Different) with Real-Time Monitoring

A one- and two-photon activated photoremovable protecting group (PRPG) was designed based on a carbazole fused o-hydroxycinnamate platform for the dual (same or different) release of alcohols. The mechanism for the dual release proceeds through a stepwise pathway and also monitors the first and second photorelease in real time by an increase in fluorescence intensity and color change, respectively. Further, its application in staining live neurons and ex vivo imaging with two-photon excitation is shown.

Light triggered uncaging of hydrogen sulfide (H2S) with real-time monitoring

An ESIPT based light activated hydrogen sulfide (H₂S) donor using a p-hydroxyphenacyl phototrigger has been developed. The unique feature of our H₂S donor system is that it provides real-time monitoring of H₂S release by a non-invasive fluorescence colour change approach.

Coumarin polycaprolactone polymeric nanoparticles: light and tumor microenvironment activated cocktail drug delivery

Highly sensitive hypoxia (H₂O₂)-activated photoresponsive polymeric nanoparticles for cocktail delivery of anticancer drugs doxorubicin (Dox) and chlorambucil (Cbl) were developed.

Redox-responsive xanthene–coumarin–chlorambucil-based FRET-guided theranostics for “activatable” combination therapy with real-time monitoring

A FRET-based theranostic agent, xanthene–coumarin–chlorambucil, exhibited redox-responsive “activatable” synergic treatment involving PDT and chemotherapy with fluorescence-change from green to blue.

Cascade photocaging of diazeniumdiolate: a novel strategy for one and two photon triggered uncaging with real time reporting

We report a new strategy, viz. cascade photocaging, for protecting diethylamine diazeniumdiolate (O²-position), a light sensitive molecule.

Photocaging of Single and Dual (Similar or Different) Carboxylic and Amino Acids by Acetyl Carbazole and its Application as Dual Drug Delivery in Cancer Therapy

A new fluorescent photoremovable protecting group (FPRPG) based on acetylcarbazole framework has been explored for the first time release of single and dual (similar or different) substrates from single chromophore. Mechanistic studies of the photorelease process revealed that photorelease of two (similar or different) substrates from acetyl carbazole proceeds via a stepwise pathway. Further, we constructed photoresponsive dual drug delivery system (DDS) to release two different anticancer drugs (caffeic acid and chlorambucil, 1 equiv each). In vitro study reveals that our DDS exhibit excellent properties like biocompatibility, cellular uptake, and photoregulated dual drug release.

Diffusive and non-diffusive photo-induced proton coupled electron transfer from hydrogen bonded phenols to meso-tetrakis-5,10,15,20-pentafluorophenyl porphyrin

Enhanced reductive fluorescence quenching of meso-tetrakis-5,10,15,20-pentafluorophenyl porphyrin (H2F20TPP) by two different phenols, 4-methoxy phenol (4-MeOPhOH) and 2,6-dimethoxy phenol (2,6-DiMeOPhOH) in the presence of various pyridine bases in dichloromethane solution is studied using steady state and time resolved fluorescence spectroscopic methods by employing time correlated single photon counting (TCSPC) and fluorescence up-conversion techniques. An enhanced quenching behaviour of H2F20TPP is observed when phenols are hydrogen bonded to various pyridine bases. Quenching observed in the steady state and time resolved studies in the nanosecond time domain follows second order kinetics and generates quenching rate constants and hydrogen bond equilibrium constants, the latter of which agree quite closely with those obtained from independent spectroscopic measurements. A significant kinetic deuterium isotope effect is observed, indicating the importance of proton movement in the quenching processes. This quenching effect is attributed to be due to a tri-molecular transition state involving H2F20TPP and a hydrogen bonded phenol complex, in which electron transfer from phenol to excited H2F20TPP is concerted with proton movement from the phenol to hydrogen bonded base. Observed quenching behaviours are rationalized by invoking diffusion controlled proton coupled electron transfer. Fluorescence up-conversion studies in the 100 ps time domain confirm ultrafast PCET for 4-MeOPhOH and base pairs which fall in a non-diffusive regime.