Dimethyl-pepep: a DNA probe in two-photon excitation cellular imaging

Proteinaceous microstructure in a capillary: a study of non-linear bending dynamics

The flap of bendable structures under continuous flow impacts a variety of fields, ranging from energy harvesting to active mixing in microfluidic devices. Similar physical principles determine the flapping dynamics in a variety of systems with different sizes, but a thorough investigation of the bending dynamics at the microscale is still lacking. We employ here two-photon laser polymerization to fabricate elongated proteinaceous flexible microstructures directly within a micro-capillary and we characterize their bending dynamics. The elastic properties of the microstructures with different (circular and square) cross-sections are tested by Atomic Force Microscopy and by studying the deflection-flow dependence in microfluidic experiments at intermediate Reynolds numbers (Re_y ≲ 150). The retrieved Young's modulus of the fabricated matrix (100 kPa ≤ E ≤ 4 MPa) falls in the range of most typical biological tissues and solely depends on the laser fabrication intensity. The elastic constant of the microstructures falls in the range of 0.8 nN μm^-1 ≤ k ≤ 50 nN μm^-1, and fully agrees with the macroscopic Euler Bernoulli theory. For soft microstructures (0.8 nN μm^-1 ≤ k ≤ 8 nN μm^-1) we reveal undamped bending oscillations under continuous microfluidic flow, corresponding to ∼10% of the total structure deflection. This behavior is ascribed to the coupling of the viscoelasticity and non-linear elasticity of the polymer matrix with non-linear dynamics arising from the time-dependent friction coefficient of the bendable microstructures. We envision that similar instabilities may lead to the development of promising energy conversion nanoplatforms.

Synthesis and Spectroscopic Characterization of 2-(het)Aryl Perimidine Derivatives with Enhanced Fluorescence Quantum Yields

Perimidines are a particularly versatile family of heterocyclic compounds, whose properties are exploited in several applications ranging from industrial to medicinal chemistry. The molecular structure of perimidine incorporates a well-known efficient fluorophore, i.e.: 1,8-diaminonaphthalene. The high fluorescence quantum yield shared by most naphthalene derivatives, has enabled their use as stains for bio-imaging and biophysical characterizations. However, fluorescence is dramatically depressed in perimidine as well as in the few of its derivatives analysed so far to this respect. The use of perimidine-like molecules in life sciences might be notably fostered by enhancement of their fluorescence emission. Even more excitingly, the concomitance of both biologically active moieties and a fluorophore in the same molecular structure virtually discloses application of perimidines as drug compounds in state-of-art theranostics protocols. However, somewhat surprisingly, relatively few attempts were made until now in the direction of increasing the performances of perimidines as fluorescent dyes. In this work we present the synthesis and spectroscopic characterization of four perimidine derivatives designed to this aim, two of which result to be endowed with fluorescence quantum yields comparable to 1,8-diaminonaphthalene. A rationalization for such improved behaviour has been attempted employing TD-DFT calculations, which have unravelled the interrelations among bond structure, lone pair conjugation, local electron density changes and fluorescence quantum yield.

A New Design Strategy and Diagnostic to Tailor the DNA-Binding Mechanism of Small Organic Molecules and Drugs

The classical model for DNA groove binding states that groove binding molecules should adopt a crescent shape that closely matches the helical groove of DNA. Here, we present a new design strategy that does not obey this classical model. The DNA-binding mechanism of small organic molecules was investigated by synthesizing and examining a series of novel compounds that bind with DNA. This study has led to the emergence of structure-property relationships for DNA-binding molecules and/or drugs, which reveals that the structure can be designed to either intercalate or groove bind with calf thymus dsDNA by modifying the electron acceptor properties of the central heterocyclic core. This suggests that the electron accepting abilities of the central core play a key role in the DNA-binding mechanism. These small molecules were characterized by steady-state and ultrafast nonlinear spectroscopies. Bioimaging experiments were performed in live cells to evaluate cellular uptake and localization of the novel small molecules. This report paves a new route for the design and development of small organic molecules, such as therapeutics, targeted at DNA as their performance and specificity is dependent on the DNA-binding mechanism.

Uptake and localisation of small-molecule fluorescent probes in living cells: a critical appraisal of QSAR models and a case study concerning probes for DNA and RNA

Small-molecule fluorochromes are used in biology and medicine to generate informative microscopic and macroscopic images, permitting identification of cell structures, measurement of physiological/physicochemical properties, assessment of biological functions and assay of chemical components. Modes of uptake and precise intracellular localisation of a probe are typically significant factors in its successful application. These processes and localisations can be predicted using quantitative structure activity relations (QSAR) models, which correlate aspects of the physicochemical properties of the probes (expressed numerically) with the uptake/localisation. Pay-offs of such modelling include better understanding and trouble-shooting of current and novel probes, and easier design of future probes ("guided synthesis"). Uptake models discussed consider adsorptive (to lipid or protein domains), phagocytic and pinocytotic endocytosis, as well as passive diffusion. Localisation models discussed include those for cytosol, endoplasmic reticulum, Golgi apparatus, lipid droplets, lysosomes, mitochondria, nucleus and plasma membrane. A case example illustrates how such QSAR modelling of probe interactions can clarify localisation and mode of binding of probes to intracellular nucleic acids of living cells, including not only eukaryotic chromatin DNA and ribosomal RNA, but also prokaryote chromosomes.

Cell-permeant cytoplasmic blue fluorophores optimized for in vivo two-photon microscopy with low-power excitation

Because of the spreading of nonlinear microscopies in biology, there is a strong demand for specifically engineered probes in these applications. Herein, we report on the imaging properties in living cells and nude mice brains of recently developed water soluble blue fluorophores that show efficient diffusion through cell membranes and blood-brain barriers. They are characterized by two-photon absorption cross-sections of 100-150 Goeppert-Mayer range in the near IR and fluorescence efficiencies of up to 72% in water. They were found to stain homogeneously the cytoplasm of cultured living cells within minutes. Moreover, their diffusion times and fluorescence characteristics in the cytoplasm suggest a hydrophobic association with intracellular membranes. Their intracellular fluorescent decays were found to be almost mono-exponential, a very favorable feature for fluorescence lifetime imaging. Two photon images of living cells were obtained with a good signal to noise ratio using laser powers in the sub-milliwatt range. This allows continuous imaging without significant photobleaching for tens of minutes. In addition, these fluorophores allowed in vivo three-dimensional two-photon imaging of mice cortex vasculatures and extra vasculature structures, with no sign of toxicity.

Morphology, mechanical properties and viability of encapsulated cells

The morphological and mechanical properties of encapsulated yeast cells (Saccharomyces cerevisiae) have been investigated by atomic force microscopy (AFM). Single living cells have been coated through the alternate deposition of oppositely charged polyelectrolyte (PE) layers. The properties of cells coated by different numbers of PE layers and from PE solutions of different ionic strength have been investigated. AFM imaging indicates an increase in PE coating stability when decreasing the solution ionic strength. The Young's moduli of the different examined systems have been evaluated through a quantitative analysis of force-distance curves by using the Hertz-Sneddon model. The analysis indicates an increase in hybrid system stiffness when lowering the ionic strength of the PE solution. An evaluation of the viability of encapsulated cells was obtained by confocal laser scanning microscopy (CLSM) measurements. CLSM analysis indicates that cells preserve their subcellular structure and duplication capability after encapsulation. By coupling AFM and CLSM data, a correlation between local stiffness and duplication rate was obtained.

Conjugation of a New Two-Photon Fluorophore to Poly(ethylenimine) for Gene Delivery Imaging

We report herein the molecular engineering of an efficient two-photon absorbing (TPA) chromophore based on a donor-donor bis-stilbenyl entity to allow conjugation with biologically relevant molecules. The dye has been functionalized using an isothiocyanate moiety to conjugate it with the amine functions of poly(ethylenimine) (PEI), which is a cationic polymer commonly used for nonviral gene delivery. Upon conjugation, the basic architecture and photophysical properties of the active TPA chromophore remain unchanged. At the usual N/P ratio (ratio of the PEI positive charges to the DNA negative charges) of 10 used for transfection, the transfection efficiency and cytotoxicity of the labeled PEI/DNA complexes were found to be comparable to those of the unlabeled PEI/DNA complexes. Moreover, when used in combination with unlabeled PEI (at a ratio of 1 labeled PEI to 3 unlabeled PEI), the labeled PEI does not affect the size of the complexes with DNA. The labeled PEI was successfully used in two-photon fluorescence correlation spectroscopy measurements, showing that at N/P = 10 most PEI molecules are free and the diffusion coefficient of the complexes is consistent with the 360 nm size measured by quasielastic light scattering. Finally, two-photon images of the labeled PEI/DNA complexes confirmed that the complexes enter into the cytoplasm of HeLa cells by endocytosis and hardly escape from the endosomes. As a consequence, the functionalized TPA chromophore appears to be an adequate tool to label the numerous polyamines used in nonviral gene delivery and characterize their complexes with DNA in two-photon applications.

Vinyl-Pyridinium Triphenylamines: Novel Far-Red Emitters with High Photostability and Two-Photon Absorption Properties for Staining DNA

A series of mono-, bis- and trisvinyl-pyridinium triphenylamines (TP-py) has been synthesised and evaluated for its one- and two-photon absorption (2PA) induced-fluorescence properties under biological conditions. Interestingly, these compounds are only weakly fluorescent in water, whereas their fluorescence emissions are strongly restored (exaltation factors of 20-100) upon binding to double-stranded DNA. Additional measurements in glycerol indicate that the fluorescence increases are the result of immobilisation of the dyes in the DNA matrix, which inhibits rotational de-excitation modes. This particular feature is especially remarkable in the case of the bis and tris derivatives (TP-2 py, TP-3 py), which each display a high affinity (K(d) ~ microM) for dsDNA. TPIF measurements have shown that TP-2 py and TP-3 py each have a large 2PA cross section (delta up to 700 GM) both in glycerol and in the presence of DNA, which ranks them amongst the best 2PA biological fluorophores. Finally, one- and two-photon confocal imaging in cells revealed that these compounds perform red staining (lambda(em)=660-680 nm) of nuclear DNA with excellent contrast. The remarkable optical properties of the TP-py series, combined with their high photostability and their easy synthetic access, make these compounds extremely attractive for use in confocal and 2PA microscopy.

Multi-photon excitation microscopy

Multi-photon excitation (MPE) microscopy plays a growing role among microscopical techniques utilized for studying biological matter. In conjunction with confocal microscopy it can be considered the imaging workhorse of life science laboratories. Its roots can be found in a fundamental work written by Maria Goeppert Mayer more than 70 years ago. Nowadays, 2PE and MPE microscopes are expected to increase their impact in areas such biotechnology, neurobiology, embryology, tissue engineering, materials science where imaging can be coupled to the possibility of using the microscopes in an active way, too. As well, 2PE implementations in noninvasive optical bioscopy or laser-based treatments point out to the relevance in clinical applications. Here we report about some basic aspects related to the phenomenon, implications in three-dimensional imaging microscopy, practical aspects related to design and realization of MPE microscopes, and we only give a list of potential applications and variations on the theme in order to offer a starting point for advancing new applications and developments.

Novel nontoxic mitochondrial probe for confocal fluorescence microscopy

We propose a 2,5-Bis[1-(4-N-methylpyridinium)ethen-2-yl)]-N-methylpyrrole ditriflate (PEPEP) as a novel nontoxic, nonpotentiometric mitochondrial probe for confocal fluorescence microscopy. PEPEP is a representative chromophore of a large family of heterocyclic fluorescent dyes that show fluorescence emission in aqueous media and great DNA affinity. We check its cytotoxicity and intracellular localization in mammalian and yeast cell cultures. We demonstrate that PEPEP is a very efficient dye for fluorescence confocal microscopy and a valuable alternative to the most frequently used mitochondrial stains.