Chloroform induces outstanding crystallization of poly(hydroxybutyrate) (PHB) vesicles within bacteria.

Poly[(R)-3-hydroxyalkanoate]s or PHAs are aliphatic polyesters produced by numerous microorganisms. They are accumulated as energy and carbon reserve in the form of small intracellular vesicles. Poly[(R)-3-hydroxybutyrate] (PHB) is the most ubiquitous and simplest PHA. An atomic force microscope coupled with a tunable infrared laser (AFM-IR) was used to record highly spatially resolved infrared spectra of commercial purified PHB and native PHB within bacteria. For the first time, the crystallinity degree of native PHB within vesicle has been directly evaluated in situ without alteration due to the measure or extraction and purification steps of the polymer: native PHB is in crystalline state at 15% whereas crystallinity degree reaches 57% in commercial PHB. Chloroform addition on native PHB induces crystallization of the polymer within bacteria up to 60%. This possibility of probing and changing the physical state of polymer in situ could open alternative ways of production for PHB and others biopolymers. Graphical abstract An atomic force microscope coupled with a tunable infrared laser (AFM-IR) has been used to record local infrared spectra of biopolymer PHB within bacteria. Deconvolution of those spectra has allowed to determine in situ the crystallinity degree of native PHB.

Mutational control of bioenergetics of bacterial reaction center probed by delayed fluorescence.

The free energy gap between the metastable charge separated state P(+)QA(-) and the excited bacteriochlorophyll dimer P* was measured by delayed fluorescence of the dimer in mutant reaction center proteins of the photosynthetic bacterium Rhodobacter sphaeroides. The mutations were engineered both at the donor (L131L, M160L, M197F and M202H) and acceptor (M265I and M234E) sides. While the donor side mutations changed systematically the number of H-bonds to P, the acceptor side mutations modified the energetics of QA by altering the van-der-Waals and electronic interactions (M265IT) and H-bond network to the acidic cluster around QB (M234EH, M234EL, M234EA and M234ER). All mutants decreased the free energy gap of the wild type RC (~890meV), i.e. destabilized the P(+)QA(-) charge pair by 60-110meV at pH8. Multiple modifications in the hydrogen bonding pattern to P resulted in systematic changes of the free energy gap. The destabilization showed no pH-dependence (M234 mutants) or slight increase (WT, donor-side mutants and M265IT above pH8) with average slope of 10-15meV/pH unit over the 6-10.5pH range. In wild type and donor-side mutants, the free energy change of the charge separation consisted of mainly enthalpic term but the acceptor side mutants showed increased entropic (even above that of enthalpic) contributions. This could include softening the structure of the iron ligand (M234EH) and the QA binding pocket (M265IT) and/or increase of the multiplicity of the electron transfer of charge separation in the acceptor side upon mutation.

Multi-pathway excited state relaxation of adenine oligomers in aqueous solution: a joint theoretical and experimental study.

The singlet excited states of adenine oligomers, model systems widely used for the understanding of the interaction of ultraviolet radiation with DNA, are investigated by fluorescence spectroscopy and time-dependent (TD) DFT calculations. Fluorescence decays, fluorescence anisotropy decays, and time-resolved fluorescence spectra are recorded from the femtosecond to the nanosecond timescales for single strand (dA)20 in aqueous solution. These experimental observations and, in particular, the comparison of the fluorescence behavior upon UVC and UVA excitation allow the identification of various types of electronic transitions with different energy and polarization. Calculations performed for up to five stacked 9-methyladenines, taking into account the solvent, show that different excited states are responsible for the absorption in the UVC and UVA spectral domains. Independently of the number of bases, bright excitons may evolve toward two types of excited dimers having π-π* or charge-transfer character, each one distinguished by its own geometry and spectroscopic signature. According to the picture arising from the joint experimental and theoretical investigation, UVC-induced fluorescence contains contribution from 1) exciton states with a different degree of localization, decaying within a few ps, 2) "neutral" excited dimers decaying on the sub-nanosecond timescale, being the dominant species, and 3) charge-transfer states decaying on the nanosecond timescale. The majority of the photons emitted upon UVA excitation are related to charge-transfer states.

Electronic excited states responsible for dimer formation upon UV absorption directly by thymine strands: joint experimental and theoretical study.

The study addresses interconnected issues related to two major types of cycloadditions between adjacent thymines in DNA leading to cyclobutane dimers (T<>Ts) and (6-4) adducts. Experimental results are obtained for the single strand (dT)(20) by steady-state and time-resolved optical spectroscopy, as well as by HPLC coupled to mass spectrometry. Calculations are carried out for the dinucleoside monophosphate in water using the TD-M052X method and including the polarizable continuum model; the reliability of TD-M052X is checked against CASPT2 calculations regarding the behavior of two stacked thymines in the gas phase. It is shown that irradiation at the main absorption band leads to cyclobutane dimers (T<>Ts) and (6-4) adducts via different electronic excited states. T<>Ts are formed via (1)ππ* excitons; [2 + 2] dimerization proceeds along a barrierless path, in line with the constant quantum yield (0.05) with the irradiation wavelength, the contribution of the (3)ππ* state to this reaction being less than 10%. The formation of oxetane, the reaction intermediate leading to (6-4) adducts, occurs via charge transfer excited states involving two stacked thymines, whose fingerprint is detected in the fluorescence spectra; it involves an energy barrier explaining the important decrease in the quantum yield of (6-4) adducts with the irradiation wavelength.

Molecular spectroscopy: complexity of excited-state dynamics in DNA.

Absorption of ultraviolet light by DNA is known to lead to carcinogenic mutations, but the processes between photon absorption and the photochemical reactions are poorly understood. In their study of the excited-stated dynamics of model DNA helices using femtosecond transient absorption spectroscopy, Crespo-Hernández et al. observe that the picosecond component of the transient signals recorded for the adenine-thymine oligonucleotide (dA)18.(dT)18 is close to that for (dA)18, but quite different from that for (dAdT)9.(dAdT)9; from this observation, they conclude that excimer formation limits excitation energy to one strand at a time. Here we use time-resolved fluorescence spectroscopy to probe the excited-state dynamics, which reveals the complexity of these systems and indicates that the interpretation of Crespo-Hernández et al. is an oversimplification. We also comment on the pertinence of separating base stacking and base pairing in excited-state dynamics of double helices and question the authors' assignment of the long-lived signal component found for (dA)18.(dT)18 to adenine excimers.

Recent advances in non-plasmonic surface-enhanced Raman spectroscopy nanostructures for biomedical applications.

Surface-enhanced Raman spectroscopy (SERS) is an emerging powerful vibrational technique offering unprecedented opportunities in biomedical science for the sensitive detection of biomarkers and the imaging and tracking of biological samples. Conventional SERS detection is based on the use of plasmonic substrates (e.g., Au and Ag nanostructures), which exhibit very high enhancement factors (EF = 1010 -1011 ) but suffers from serious limitations, including light-induced local heating effect due to ohmic loss and expensive price. These drawbacks may limit detection accuracy and large-scaled practical applications. In this review, we focus on alternative approaches based on plasmon-free SERS detection on low-cost nanostructures, such as carbons, oxides, chalcogenides, polymers, silicons, and so forth. The mechanism of non-plasmonic SERS detection has been attributed to interfacial charge transfer between the substrate and the adsorbed molecules, with no photothermal side-effects but usually less EF compared with plasmonic nanostructures. The strategies to improve Raman signal detection, through the tailoring of substrate composition, structure, and surface chemistry, is reviewed and discussed. The biomedical applications, for example, SERS cell characterization, biosensing, and bioimaging are also presented, highlighting the importance of substrate surface functionalization to achieve sensitive, accurate analysis, and excellent biocompatibility. This article is categorized under: Diagnostic Tools > Diagnostic Nanodevices Diagnostic Tools > Biosensing Diagnostic Tools > In Vivo Nanodiagnostics and Imaging.

SERS tags derived from silver nanoparticles and aryl diazonium salts for cell Raman imaging.

The surface functionalization of silver nanoparticles (NPs) by Raman reporters has stimulated a wide interest in recent years for the design of Surface-Enhanced Raman Spectroscopy (SERS) labels. However, silver NPs are prone to oxidation and aggregation, which strongly limits their applications. The design of stable SERS tags based on Ag NPs still represents a major challenge for Raman bioimaging. We address this issue herein by taking advantage of aryl diazonium salt chemistry to obtain stable Ag NPs functionalized by multifunctional polyaryl layers bearing different Raman reporters (-NO2, -CN, -CCH). The resulting SERS-encoded Ag NPs were characterized by UV-vis absorption, transmission electron microscopy (TEM) and SERS. The formation of multilayers at the surface of Ag NPs gives access to new spectrally distinguishable SERS codes thus broadening the library of available Raman tags. Proof-of-concept Raman imaging experiments were performed on cancer cells (HeLa) after NP uptake, highlighting the large potentials of diazonium salt chemistry to design Ag NPs-based SERS labels for Raman bioimaging.

Anti-counterfeiting SERS security labels derived from silver nanoparticles and aryl diazonium salts.

The development of anti-counterfeiting inks based on surface-enhanced Raman scattering (SERS) labels have attracted great interest in recent years for their use as security labels in anti-counterfeiting applications. Indeed, they are promising alternatives to luminescent inks, which suffer from several limitations including emission peak overlap, toxicity and photobleaching. Most of the reported SERS security labels developed so far rely on the use of thiolate self-assembled monolayers (SAMs) for the immobilization of Raman reporters on metallic nanoparticle surface. However, SAMs are prone to spontaneous desorption and degradation under laser irradiation, thereby compromising the ink long-term stability. To overcome this issue, we develop herein a new generation of SERS security labels based on silver nanoparticles (Ag NPs) functionalized by aryl diazonium salts, carrying various substituents (-NO2, -CN, -CCH) with distinguishable Raman fingerprints. The resulting SERS tags were fully characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), UV-vis absorption and SERS. Then, they were incorporated into ink formulations to be printed on polyethylene naphthalate (PEN) substrates, using handwriting or inkjet printing. Proof-of-concept Raman imaging experiments confirmed the remarkable potential of diazonium salt chemistry to design Ag NPs-based SERS security labels.

Synergic Thermo- and pH-Sensitive Hybrid Microgels Loaded with Fluorescent Dyes and Ultrasmall Gold Nanoparticles for Photoacoustic Imaging and Photothermal Therapy.

Smart microgels (µGels) made of polymeric particles doped with inorganic nanoparticles have emerged recently as promising multifunctional materials for nanomedicine applications. However, the synthesis of these hybrid materials is still a challenging task with the necessity to control several features, such as particle sizes and doping levels, in order to tailor their final properties in relation to the targeted application. We report herein an innovative modular strategy to achieve the rational design of well-defined and densely filled hybrid particles. It is based on the assembly of the different building blocks, i.e., µGels, dyes, and small gold nanoparticles (<4 nm), and the tuning of nanoparticle loading within the polymer matrix through successive incubation steps. The characterization of the final hybrid networks using UV-vis absorption, fluorescence, transmission electron microscopy, dynamic light scattering, and small-angle X-ray scattering revealed that they uniquely combine the properties of hydrogel particles, including high loading capacity and stimuli-responsive behavior, the photoluminescent properties of dyes (rhodamine 6G, methylene blue and cyanine 7.5), and the features of gold nanoparticle assembly. Interestingly, in response to pH and temperature stimuli, the smart hybrid µGels can shrink, leading to the aggregation of the gold nanoparticles trapped inside the polymer matrix. This stimuli-responsive behavior results in plasmon band broadening and red shift toward the near-infrared region (NIR), opening promising prospects in biomedical science. Particularly, the potential of these smart hybrid nanoplatforms for photoactivated hyperthermia, photoacoustic imaging, cellular internalization, intracellular imaging, and photothermal therapy was assessed, demonstrating well controlled multimodal opportunities for theranostics.

Surface functionalization of nanomaterials by aryl diazonium salts for biomedical sciences.

Nanoparticles (NPs) can be prepared by simple reactions and methods from a number of materials. Their small size opens up a number of applications in different fields, among which biomedicine, including: i) drug delivery, ii) biosensors, iii) bioimaging, iv) antibacterial activity. To be able to perform such tasks, NPs must be modified with a variety of functional molecules, such as drugs, targeting groups, chemical tags or antibacterial agents, and must also be prevented from aggregation. The attachment must be stable to resist during the transportation to the targeted location. Diazonium salts, which have been widely used for coupling applications and surface modification, fulfil such criteria. Moreover, they are simple to prepare and can be easily substituted with a large number of organic groups. This review describes the use of these compounds in nanomedicine with a focus on the construction of nanohybrids derived from metal, oxide and carbon-based NPs as well as viruses.

Raman reporters derived from aryl diazonium salts for SERS encoded-nanoparticles.

Surface-enhanced Raman scattering (SERS) tags are usually prepared by immobilizing Raman reporters on plasmonic nanoparticles (NPs) via thiol-based self-assembled monolayers. We describe here the first example of SERS tags obtained by combining gold NPs and aryl diazonium salts. This strategy results in robust Au-C covalent bonds between the Raman reporter and the NPs, thus ensuring a high stability of the nanohybrid interface.

Fluorescence of the DNA double helix (dA)20 x (dT)20 studied by femtosecond spectroscopy--effect of the duplex size on the properties of the excited states.

The fluorescence of the DNA double-stranded oligomer (dA)20 x (dT)20 is studied at room temperature by fluorescence up-conversion at times shorter than 10 ps. The profile of the up-conversion spectra is similar to that of the steady-state fluorescence spectrum, showing that the majority of the photons are emitted within the probed time scale. At all the probed wavelengths, the fluorescence decays are slower than those of the monomeric chromophores dAMP and TMP. The fluorescence anisotropy decays show strong wavelength dependence. These data allow us to conclude that energy transfer takes place in this double helix and that this process involves exciton states. The spectral and dynamical properties of the oligomer are compared to those of the polymer poly(dA) x poly(dT), composed of about 2000 base pairs, reported previously. The oligomer absorption spectrum is characterized by a smaller hypsochromic shift and weaker hypochromism compared to the polymer. Moreover, the fluorescence decays of (dA)20 x (dT)20 are twice as fast as those of poly(dA) x poly(dT), and its fluorescence anisotropy decays more slowly. These differences are the fingerprints of a larger delocalization of the excited states induced by an increase in the size of the duplex.

Histidine is involved in coupling proton uptake to electron transfer in photosynthetic proteins.

In photosynthesis, the central step in transforming light energy into chemical energy is the coupling of light-induced electron transfer to proton uptake and release. Despite intense investigations of different photosynthetic protein complexes, including the photosystem II (PS II) in plants and the reaction center (RC) in bacteria, the molecular details of this fundamental process remain incompletely understood. In the RC of Rhodobacter (Rb.) sphaeroides, fast formation of the charge separated state, P(+)Q(A)(-), is followed by a slower electron transfer from the primary acceptor, Q(A), to the secondary acceptor, Q(B), and the uptake of a proton from the cytoplasm. The proton transfer to Q(B) takes place via a protonated water chain. Mutation of the amino acid AspL210 to Asn (L210DN mutant) near the entry of the proton pathway can disturb this water chain and consequently slow down proton uptake. Time-resolved step-scan Fourier transform infrared (FTIR) measurements revealed an intermediate X in the Q(A)(-)Q(B) to Q(A)Q(B)(-) transition. The nature of this transition remains a matter of debate. In this study, we investigated the role of the iron-histidine complex located between Q(A) and Q(B). We used time-resolved fast-scan FTIR spectroscopy to characterize the Rb. sphaeroides L210DN RC mutant marked with isotopically labeled histidine. FTIR marker bands of the intermediate X between 1120 cm(-1) and 1050 cm(-1) are assigned to histidine vibrations and indicate the protonation of a histidine, most likely HisL190, during the disappearance of the intermediate. Based on these results we propose a novel mechanism of the coupling of electron and proton transfer in photosynthesis.

Interaction between non-anionic phospholipids and cytochrome c induced by reactive oxygen species.

The oxidative interaction of cytochrome c (Cyt c) with liposomes of Palmitoyl Linoleyl Phosphatidyl Choline (PLPC) initiated by radio-induced free radicals was investigated. Results showed that the peroxidation of PLPC is decreased in the presence of Cyt c, meaning that this latter is the preferential target of hydroxyl radicals. In addition, when Cyt c was incubated with peroxidized PLPC, it was found to be able to decompose hydroperoxides of PLPC into hydroxides. The peroxidase activity of Cyt c proceeded via the opening of the tertiary structure of Cyt c, as suggested by the loss of the sixth coordination bond of the heme-iron. Even if it is known to preferentially interact with cardiolipin, this work shows that Cyt c is also able to interact with hydroperoxide species of non-anionic phospholipids.

Fluorescence of the DNA double helices (dAdT)n.(dAdT)n studied by femtosecond spectroscopy.

Polymeric and oligomeric DNA helices, poly(dAdT).poly(dAdT) and (dAdT)(10).(dAdT)(10), composed of 200-400 and 20 adenine-thymine base pairs, respectively, are studied by fluorescence upconversion. Fluorescence decays, anisotropy decays and time-resolved spectra, obtained for this alternating base sequence, are compared with those determined previously for the homopolymeric sequence (dA)(n).(dT)(n). It is shown that identical fluorescence decays may correspond to quite different anisotropy decays and vice versa, both varying with the emission wavelength, the base sequence and the duplex size. Our observations cannot be explained in terms of monomer and excimer emission exclusively, as concluded in the past on the basis of steady-state measurements. Excitons also contribute to the fluorescence. These are rapidly trapped by excimers, characterized by long-lived weak emission.

Proton uptake in the reaction center mutant L210DN from Rhodobacter sphaeroides via protonated water molecules.

The reaction center (RC) of Rhodobacter sphaeroides uses light energy to reduce and protonate a quinone molecule, QB (the secondary quinone electron acceptor), to form quinol, QBH2. Asp210 in the L-subunit has been shown to be a catalytic residue in this process. Mutation of Asp210 to Asn leads to a deceleration of reoxidation of QA- in the QA-QB --> QAQB- transition. Here we determined the structure of the Asp210 to Asn mutant to 2.5 A and show that there are no major structural differences as compared to the wild-type protein. We found QB in the distal position and a chain of water molecules between Asn210 and QB. Using time-resolved Fourier transform infrared (trFTIR) spectroscopy, we characterized the molecular reaction mechanism of this mutant. We found that QB- formation precedes QA- oxidation even more pronounced than in the wild-type reaction center. Continuum absorbance changes indicate deprotonation of a protonated water cluster, most likely of the water chain between Asn210 and QB. A detailed analysis of wild-type structures revealed a highly conserved water chain between Asp210 or Glu210 and QB in Rb. sphaeroides and Rhodopseudomonas viridis, respectively.

Collective behavior of Franck-Condon excited states and energy transfer in DNA double helices.

Absorption of UV radiation by DNA bases is known to induce carcinogenic mutations. The lesion distribution depends on the sequence around the hotspots, suggesting cooperativity between bases. Here we show that such cooperativity may intervene at the very first step of a cascade of events by formation of Franck-Condon states delocalized over several bases and subsequent energy transfer faster than 100 fs. Our study focuses on the double helix poly(dA).poly(dT), whose fluorescence, induced by femtosecond pulses at 267 nm, is probed by the upconversion technique and time-correlated single photon counting, over a large time domain (100 fs to 100 ns). The time-resolved fluorescence decays and fluorescence anisotropy decays are discussed in relation with the steady-state absorption and fluorescence spectra in the frame of exciton theory.