Photophysics of a nucleic acid-protein crosslinking model strongly depends on solvation dynamics: an experimental and theoretical study.

We present a combined experimental and theoretical study of the photophysics of 5-benzyluracil (5BU) in methanol, which is a model system for interactions between nucleic acids and proteins. A molecular dynamics study of 5BU in solution through efficient DFT-based hybrid ab initio potentials revealed a remarkable conformational flexibility - allowing the population of two main conformers - as well as specific solute-solvent interactions, which both appear as relevant factors for the observed 5BU optical absorption properties. The simulated absorption spectrum, calculated on such an ensemble, enabled a molecular interpretation of the experimental UV-Vis lowest energy band, which is also involved in the induced photo-reactivity upon irradiation. In particular, the first two excited states (mainly involving the uracil moiety) both contribute to the 5BU lowest energy absorption. Moreover, as a key finding, the nature and brightness of such electronic transitions are strongly influenced by 5BU conformation and the microsolvation of its heteroatoms.

The Effectiveness of Cyrene as a Solvent in Exfoliating 2D TMDs Nanosheets.

The pursuit of environmentally friendly solvents has become an essential research topic in sustainable chemistry and nanomaterial science. With the need to substitute toxic solvents in nanofabrication processes becoming more pressing, the search for alternative solvents has taken on a crucial role in this field. Additionally, the use of toxic, non-economical organic solvents, such as N-methyl-2 pyrrolidone and dimethylformamide, is not suitable for all biomedical applications, even though these solvents are often considered as the best exfoliating agents for nanomaterial fabrication. In this context, the success of producing two-dimensional transition metal dichalcogenides (2D TMDs), such as MoS2 and WS2, with excellent captivating properties is due to the ease of synthesis based on environment-friendly, benign methods with fewer toxic chemicals involved. Herein, we report for the first time on the use of cyrene as an exfoliating agent to fabricate monolayer and few-layered 2D TMDs with a versatile, less time-consuming liquid-phase exfoliation technique. This bio-derived, aprotic, green and eco-friendly solvent produced a stable, surfactant-free, concentrated 2D TMD dispersion with very interesting features, as characterized by UV-visible and Raman spectroscopies. The surface charge and morphology of the fabricated nanoflakes were analyzed using ς-potential and scanning electron microscopy. The study demonstrates that cyrene is a promising green solvent for the exfoliation of 2D TMD nanosheets with potential advantages over traditional organic solvents. The ability to produce smaller-sized-especially in the case of WS2 as compared to MoS2-and mono/few-layered nanostructures with higher negative surface charge values makes cyrene a promising candidate for various biomedical and electronic applications. Overall, the study contributes to the development of sustainable and environmentally friendly methods for the production of 2D nanomaterials for various applications.

A systematic study of the valence electronic structure of cyclo(Gly-Phe), cyclo(Trp-Tyr) and cyclo(Trp-Trp) dipeptides in the gas phase.

The electronic energy levels of cyclo(glycine-phenylalanine), cyclo(tryptophan-tyrosine) and cyclo(tryptophan-tryptophan) dipeptides are investigated with a joint experimental and theoretical approach. Experimentally, valence photoelectron spectra in the gas phase are measured using VUV radiation. Theoretically, we first obtain low-energy conformers through an automated conformer-rotamer ensemble sampling scheme based on tight-binding simulations. Then, different first principles computational schemes are considered to simulate the spectra: Hartree-Fock (HF), density functional theory (DFT) within the B3LYP approximation, the quasi-particle GW correction, and the quantum-chemistry CCSD method. Theory allows assignment of the main features of the spectra. A discussion on the role of electronic correlation is provided, by comparing computationally cheaper DFT scheme (and GW) results with the accurate CCSD method.

Spectroscopic Properties of Two 5'-(4-Dimethylamino)Azobenzene Conjugated G-Quadruplex Forming Oligonucleotides.

The synthesis of two 5'-end (4-dimethylamino)azobenzene conjugated G-quadruplex forming aptamers, the thrombin binding aptamer (TBA) and the HIV-1 integrase aptamer (T30695), was performed. Their structural behavior was investigated by means of UV, CD, fluorescence spectroscopy, and gel electrophoresis techniques in K+-containing buffers and water-ethanol blends. Particularly, we observed that the presence of the 5'-(4-dimethylamino)azobenzene moiety leads TBA to form multimers instead of the typical monomolecular chair-like G-quadruplex and almost hampers T30695 G-quadruplex monomers to dimerize. Fluorescence studies evidenced that both the conjugated G-quadruplexes possess unique fluorescence features when excited at wavelengths corresponding to the UV absorption of the conjugated moiety. Furthermore, a preliminary investigation of the trans-cis conversion of the dye incorporated at the 5'-end of TBA and T30695 showed that, unlike the free dye, in K+-containing water-ethanol-triethylamine blend the trans-to-cis conversion was almost undetectable by means of a standard UV spectrophotometer.

Exploring the Photodynamic Properties of Two Antiproliferative Benzodiazopyrrole Derivatives.

The identification of molecules whose biological activity can be properly modulated by light is a promising therapeutic approach aimed to improve drug selectivity and efficacy on the molecular target and to limit the side effects compared to traditional drugs. Recently, two photo-switchable diastereomeric benzodiazopyrrole derivatives 1RR and 1RS have been reported as microtubules targeting agents (MTAs) on human colorectal carcinoma p53 null cell line (HCT 116 p53-/-). Their IC50 was enhanced upon Light Emitting Diode (LED) irradiation at 435 nm and was related to their cis form. Here we have investigated the photo-responsive behavior of the acid derivatives of 1RR and 1RS, namely, d1RR and d1RS, in phosphate buffer solutions at different pH. The comparison of the UV spectra, acquired before and after LED irradiation, indicated that the trans→cis conversion of d1RR and d1RS is affected by the degree of ionization. The apparent rate constants were calculated from the kinetic data by means of fast UV spectroscopy and the conformers of the putative ionic species present in solution (pH range: 5.7-8.0) were modelled. Taken together, our experimental and theoretical results suggest that the photo-conversions of trans d1RR/d1RS into the corresponding cis forms and the thermal decay of cis d1RR/d1RS are dependent on the presence of diazonium form of d1RR/d1RS. Finally, a photo-reaction was detected only for d1RR after prolonged LED irradiation in acidic medium, and the resulting product was characterized by means of Liquid Chromatography coupled to High resolution Mass Spectrometry (LC-HRMS) and Nuclear Magnetic Resonance (NMR) spectroscopy.

A multi-scale time-resolved study of photoactivated dynamics in 5-benzyl uracil, a model for DNA/protein interactions.

We combine fluorescence up-conversion and time correlated single photon counting experiments to investigate the 5-benzyl uracil excited state dynamics in methanol from 100 fs up to several ns. This molecule has been proposed as a model for DNA/protein interactions. Our results show emission bands at about 310 and 350 nm that exhibit bi-exponential sub-ps decays. Calculations, including solvent effects by a mixed discrete-continuum model, indicate that the Franck Condon region is characterized by significant coupling between the excited states of the benzyl and the uracil moieties, mirrored by the short-lived emission at 310 nm. Two main ground state recovery pathways are identified, both contributing to the 350 nm emission. The first 'photophysical' decay path involves a ππ* excited state localized on the uracil and is connected to the ground electronic state by an easily accessible crossing with S0, accounting for the short lifetime component. Simulations indicate that a possible second pathway is characterized by exciplex formation, with partial benzene → uracil charge transfer character, that may lead instead to photocyclization. The relevance of our results is discussed in view of the photoactivated dynamics of DNA/protein complexes, with implications on their interaction mechanisms.

Identification of novel direct protein-protein interactions by irradiating living cells with femtosecond UV laser pulses.

The identification of protein-protein interaction networks in living cells is becoming increasingly fundamental to elucidate main biological processes and to understand disease molecular bases on a system-wide level. We recently described a method (LUCK, Laser UV Cross-linKing) to cross-link interacting protein surfaces in living cells by UV laser irradiation. By using this innovative methodology, that does not require any protein modification or cell engineering, here we demonstrate that, upon UV laser irradiation of HeLa cells, a direct interaction between GAPDH and alpha-enolase was "frozen" by a cross-linking event. We validated the occurrence of this direct interaction by co-immunoprecipitation and Immuno-FRET analyses. This represents a proof of principle of the LUCK capability to reveal direct protein interactions in their physiological environment.

Femtosecond UV-laser pulses to unveil protein-protein interactions in living cells.

A hallmark to decipher bioprocesses is to characterize protein-protein interactions in living cells. To do this, the development of innovative methodologies, which do not alter proteins and their natural environment, is particularly needed. Here, we report a method (LUCK, Laser UV Cross-linKing) to in vivo cross-link proteins by UV-laser irradiation of living cells. Upon irradiation of HeLa cells under controlled conditions, cross-linked products of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were detected, whose yield was found to be a linear function of the total irradiation energy. We demonstrated that stable dimers of GAPDH were formed through intersubunit cross-linking, as also observed when the pure protein was irradiated by UV-laser in vitro. We proposed a defined patch of aromatic residues located at the enzyme subunit interface as the cross-linking sites involved in dimer formation. Hence, by this technique, UV-laser is able to photofix protein surfaces that come in direct contact. Due to the ultra-short time scale of UV-laser-induced cross-linking, this technique could be extended to weld even transient protein interactions in their native context.

Detection of parathion pesticide by quartz crystal microbalance functionalized with UV-activated antibodies.

Photonic immobilization technique (PIT) has been used to develop an immunosensor for the detection of parathion. An antibody solution has been activated by breaking the disulfide bridge in the triad Trp/Cys-Cys through absorption of ultrashort UV laser pulses. The free thiol groups so produced interact with gold lamina making the antibody oriented upside, that is, with its variable parts exposed to the environment, thereby greatly increasing the detection efficiency. PIT has been applied to anchor polyclonal antiparathion antibodies to the gold electrode of a Quartz Crystal Microbalance (QCM) giving rise to very high detection sensitivity once the parathion is made heavier by complexion with BSA (bovine serum albumin), this latter step only required by the mass based transducer used in this case. The comparison of the sensor response with irradiated antibodies against different analytes shows that the high degree of antibody specificity is not affected by PIT nor is it by the complexion of parathion with BSA. These results pave the way to important applications in biosensing, since the widespread occurrence of the Trp/Cys-Cys residues triads in proteins make our procedure very general and effective to detect light analytes.

Influence of generalized focusing of few-cycle Gaussian pulses in attosecond pulse generation.

In contrast to the case of quasi-monochromatic waves, a focused optical pulse in the few-cycle limit may exhibit two independent curved wavefronts, associated with phase and group retardations, respectively. Focusing optical elements will generally affect these two wavefronts differently, thus leading to very different behavior of the pulse near focus. As limiting cases, we consider an ideal diffractive lens introducing only phase retardations and a perfect non-dispersive refractive lens (or a curved mirror) introducing equal phase and group retardations. We study the resulting diffraction effects on the pulse, finding both strong deformations of the pulse shape and shifts in the spectrum. We then show how important these effects can be in highly nonlinear optics, by studying their role in attosecond pulse generation. In particular, the focusing effects are found to affect substantially the generation of isolated attosecond pulses in gases from few-cycle fundamental optical fields.

Ultraviolet laser-induced cross-linking in peptides.

RATIONALE: The aim of this study was to demonstrate, and to characterize by high-resolution mass spectrometry that it is possible to preferentially induce covalent cross-links in peptides by using high-energy femtosecond ultraviolet (UV) laser pulses. The cross-link is readily formed only when aromatic amino acids are present in the peptide sequence. METHODS: Three peptides, xenopsin, angiotensin I, and interleukin, individually or in combination, were exposed to high-energy femtosecond UV laser pulses, either alone or in the presence of spin trapping molecules, the reaction products being characterized by high resolution mass spectrometry. RESULTS: High-resolution mass spectrometry and spin trapping strategies showed that cross-linking occurs readily, proceeds via a radical mechanism, and is the highly dominant reaction, proceeding without causing significant photo-damage in the investigated range of experimental parameters. CONCLUSIONS: High-energy femtosecond UV laser pulses can be used to induce covalent cross-links between aromatic amino acids in peptides, overcoming photo-oxidation processes, that predominate as the mean laser pulse intensity approaches illumination conditions achievable with conventional UV light sources.

Analysis of simulated fluorescence intensities decays by a new maximum entropy method algorithm.

A new algorithm for the Maximum Entropy Method (MEM) is proposed for recovering the lifetime distribution in time-resolved fluorescence decays. The procedure is based on seeking the distribution that maximizes the Skilling entropy function subjected to the chi-squared constraint χ(2) ~ 1 through iterative linear approximations, LU decomposition of the Hessian matrix of the lagrangian problem and the Golden Section Search for backtracking. The accuracy of this algorithm has been investigated through comparisons with simulated fluorescence decays both of narrow and broad lifetime distributions. The proposed approach is capable to analyse datasets of up to 4,096 points with a discretization ranging from 100 to 1,000 lifetimes. A good agreement with non linear fitting estimates has been observed when the method has been applied to multi-exponential decays. Remarkable results have been also obtained for the broad lifetime distributions where the position is recovered with high accuracy and the distribution width is estimated within 3%. These results indicate that the procedure proposed generates MEM lifetime distributions that can be used to quantify the real heterogeneity of lifetimes in a sample.

Low-lying excited-states of 5-benzyluracil.

A numerical study is reported concerning the first and second singlet excited-states of 5-benzyluracil using the multireference self-consistent field (state-averaged CASSCF) method. The vertical excitation energies of low-lying excited-states were characterized using the SA-CASSCF method, as well as using higher-level methods, such as CASPT2, MRCI and EOM-CCSD. The local minima and conical intersections found on the potential energy surfaces (PESs) were characterized in terms of molecular geometry and natural population analysis. Different relaxation pathways on the PESs are identified and discussed by comparing with the similar pathways found for the individual monomers of uracil and benzene. The molecule can be thought of as a model system for the study of crosslink reaction between DNA and proteins induced by UV light.

Periodic Surface Structuring of Copper with Spherical and Cylindrical Lenses.

The use of a cylindrical lens in femtosecond laser surface structuring is receiving attention to improve the processing efficiency. Here, we investigate the structures produced on a copper target, in air, by exploiting both spherical and cylindrical lenses for beam focusing, aiming at elucidating similarities and differences of the two approaches. The morphological features of the surface structures generated by ≈180 fs laser pulses at 1030 nm over areas of 8 × 8 mm2 were analyzed. For the spherical lens, micron-sized parallel channels are formed on the target surface, which is covered by subwavelength ripples and nanoparticles. Instead, the cylindrical lens leads to a surface decorated with ripples and nanoparticles with a negligible presence of micro-channels. Moreover, the morphological features achieved by focusing ≈180 fs laser pulses at 515 nm with the cylindrical lens and varying the scanning parameters were also studied. The experimental results evidence a direct effect of the hatch distance used in the scanning process on the target surface that contains dark and bright bands corresponding to regions where the rippled surface contains a richer decoration or a negligible redeposition of nanoparticles. Our findings can be of interest in large area surface structuring for the selection of the more appropriate focusing configuration according to the final application of the structured surface.

Single-Cell Photothermal Analysis Induced by MoS2 Nanoparticles by Raman Spectroscopy.

Two-dimensional nanomaterials, such as MoS2 nanosheets, have been attracting increasing attention in cancer diagnosis and treatment, thanks to their peculiar physical and chemical properties. Although the mechanisms which regulate the interaction between these nanomaterials and cells are not yet completely understood, many studies have proved their efficient use in the photothermal treatment of cancer, and the response to MoS2 nanosheets at the single-cell level is less investigated. Clearly, this information can help in shedding light on the subtle cellular mechanisms ruling the interaction of this 2D material with cells and, eventually, to its cytotoxicity. In this study, we use confocal micro-Raman spectroscopy to reconstruct the thermal map of single cells targeted with MoS2 under continuous laser irradiation. The experiment is performed by analyzing the water O-H stretching band around 3,400 cm-1 whose tetrahedral structure is sensitive to the molecular environment and temperature. Compared to fluorescence-based approaches, this Raman-based strategy for temperature measurement does not suffer fluorophore instability, which can be significant under continuous laser irradiation. We demonstrate that irradiation of human breast cancer MCF7 cells targeted with MoS2 nanosheets causes a relevant photothermal effect, which is particularly high in the presence of MoS2 nanosheet aggregates. Laser-induced heating is strongly localized near such particles which, in turn, tend to accumulate near the cytoplasmic membrane. Globally, our experimental outcomes are expected to be important for tuning the nanosheet fabrication process.

Glucose sensing by time-resolved fluorescence of sol-gel immobilized glucose oxidase.

A monolithic silica gel matrix with entrapped glucose oxidase (GOD) was constructed as a bioactive element in an optical biosensor for glucose determination. Intrinsic fluorescence of free and immobilised GOD was investigated in the visible range in presence of different glucose concentrations by time-resolved spectroscopy with time-correlated single-photon counting detector. A three-exponential model was used for analysing the fluorescence transients. Fractional intensities and mean lifetime were shown to be sensitive to the enzymatic reaction and were used for obtaining calibration curve for glucose concentration determination. The sensing system proposed achieved high resolution (up to 0.17 mM) glucose determination with a detection range from 0.4 mM to 5 mM.

DNA Mutations via Chern-Simons Currents.

We test the validity of a possible schematization of DNA structure and dynamics based on the Chern-Simons theory, that is a topological field theory mostly considered in the context of effective gravity theories. By means of the expectation value of the Wilson Loop, derived from this analogue gravity approach, we find the point-like curvature of genomic strings in KRAS human gene and COVID-19 sequences, correlating this curvature with the genetic mutations. The point-like curvature profile, obtained by means of the Chern-Simons currents, can be used to infer the position of the given mutations within the genetic string. Generally, mutations take place in the highest Chern-Simons current gradient locations and subsequent mutated sequences appear to have a smoother curvature than the initial ones, in agreement with a free energy minimization argument.

Interplay between group-delay-dispersion-induced polarization gating and ionization to generate isolated attosecond pulses from multicycle lasers.

We implemented a new experimental scheme for the generation of single-shot extreme-UV continua that exploits a combination of transform-limited 15 fs, 800 nm pulses and chirped 35 fs, 800 nm pulses with orthogonal polarizations. Continua are interpreted as the formation of a single attosecond pulse and attributed to the interplay between polarization, ionization gating, and trajectory selection operated by suitable phase-matching conditions.

Combating Actions of Green 2D-Materials on Gram Positive and Negative Bacteria and Enveloped Viruses.

Interactions of novel bi-dimensional nanomaterials and live matter such as bacteria and viruses represent an extremely hot topic due to the unique properties of the innovative nanomaterials, capable in some cases to exhibit bactericide and antiviral actions. The interactions between bacteria and viruses and two dimensional nanosheets are here investigated. We extensively studied the interaction between a gram-negative bacterium, Escherichia coli, and a gram-positive bacterium, Staphylococcus aureus, with two different types of 2D nanoflakes such as MoS2, belonging to the Transition Metal Dichalcogenides family, and Graphene Oxide. The same two types of nanomaterials were employed to study their antiviral action toward the Herpes simplex virus type-1, (HSV-1). The experimental results showed different bactericide impacts as well as different antiviral power between the two nanomaterials. The experimental findings were interpreted in bacteria on the base of the Derjaguin-Landau-Verwey-Overbeek theory. A simple kinetic model of bacterial growth in the presence of the interacting nanosheets is also elaborated, to explain the observed results. The experimental results in viruses are really novel and somewhat surprising, evidencing a stronger antiviral action of Graphene Oxide as compared to MoS2. Results in viruses are complicated to quantitatively interpret due to the complexity of the system under study, constituted by virus/host cell and nanoflake, and due to the lack of a well assessed theoretical context to refer to. Thus, these results are interpreted in terms of qualitative arguments based on the chemical properties of the interactors in the given solvent medium.

Generating single attosecond pulse using multi-cycle lasers in a polarization gate.

We analyze the macroscopic effects which are responsible for producing clean isolated pulses lasting few hundreds of attoseconds when starting from multi-cycle fundamental pulses. In particular, we consider a polarization gating scheme and show that, at high fundamental peak intensities, in the range 0.7-1 PWcm(-2), it usually produces three-four main attosecond pulses of radiation at single dipole level, just located in the leading edge of the laser pulse. We describe the physical mechanisms contributing to the formation of a single attosecond pulse by using a three dimensional non-adiabatic model and a quantum trajectory phase calculation. An analysis of the scheme optimization and stability against various parameters is performed in view of an experimental scheme implementation.