Fast rate dual-comb spectrometer in the water-transparent 7.5-11.5†µm region.

We introduce a dual-comb spectrometer based on erbium fiber oscillators at 250 MHz that operates in the 7.5-11.5 µm spectral range over optical bandwidths up to 9 THz with a multi-kHz acquisition rate. Over an observation bandwidth of 0.8 THz, the signal-to-noise ratio per spectral point reaches 168 Hz0.5 at an acquisition rate of 26 kHz, which allows the investigation of transient processes in the gas phase at high temporal resolution. The system also represents an attractive solution for multi-species atmospheric gas detection in open paths due to the water transparency of the spectral window, the use of thermo-electrically cooled detectors, and the out-of-loop phase correction of the interferograms.

Mercury Clathration-Driven Phase Transition in a Luminescent Bipyrazolate Metal-Organic Framework: A Multitechnique Investigation.

Mercury is one of the most toxic heavy metals. By virtue of its triple bond, the novel ligand 1,2-bis(1H-pyrazol-4-yl)ethyne (H2BPE) was expressly designed and synthesized to devise metal-organic frameworks (MOFs) exhibiting high chemical affinity for mercury. Two MOFs, Zn(BPE) and Zn(BPE)·nDMF [interpenetrated i-Zn and noninterpenetrated ni-Zn·S, respectively; DMF = dimethylformamide], were isolated as microcrystalline powders. While i-Zn is stable in water for at least 15 days, its suspension in HgCl2 aqueous solutions prompts its conversion into HgCl2@ni-Zn. A multitechnique approach allowed us to shed light onto the observed HgCl2-triggered i-Zn-to-HgCl2@ni-Zn transformation at the molecular level. Density functional theory calculations on model systems suggested that HgCl2 interacts via the mercury atom with the carbon-carbon triple bond exclusively in ni-Zn. Powder X-ray diffraction enabled us to quantify the extent of the i-Zn-to-HgCl2@ni-Zn transition in 100-5000 ppm HgCl2 (aq) solutions, while X-ray fluorescence and inductively coupled plasma-mass spectrometry allowed us to demonstrate that HgCl2 is quantitatively sequestered from the aqueous phase. Irradiating at 365 nm, an intense fluorescence is observed at 470 nm for ni-Zn·S, which is partially quenched for i-Zn. This spectral benchmark was exploited to monitor in real time the i-Zn-to-HgCl2@ni-Zn conversion kinetics at different HgCl2 (aq) concentrations. A sizeable fluorescence increase was observed, within a 1 h time lapse, even at a concentration of 5 ppb. Overall, this comprehensive investigation unraveled an intriguing molecular mechanism, featuring the disaggregation of a water-stable MOF in the presence of HgCl2 and the self-assembly of a different crystalline phase around the pollutant, which is sequestered and simultaneously quantified by means of a luminescence change. Such a case study might open the way to new-conception strategies to achieve real-time sensing of mercury-containing pollutants in wastewaters and, eventually, pursue their straightforward and cost-effective purification.

High-resolution molecular fingerprinting in the 11.6-15†µm range by a quasi-CW difference-frequency-generation laser source.

We report an approach for high-resolution spectroscopy using a widely tunable laser emitting in the molecular fingerprint region. The laser is based on difference-frequency generation (DFG) in a nonlinear orientation-patterned GaAs crystal. The signal laser, a CO2 gas laser, is operated in a kHz-pulsed mode while the pump laser, an external-cavity quantum cascade laser, is finely mode-hop-free tuned. The idler radiation covers a spectral range of ∼11.6-15 µm with a laser linewidth of ∼ 2.3 MHz. We showcase the versatility and the potential for molecular fingerprinting of the developed DFG laser source by resolving the absorption features of a mixture of several species in the long-wavelength mid-infrared. Furthermore, exploiting the wide tunability and resolution of the spectrometer, we resolve the broadband absorption spectrum of ethylene (C2H4) over ∼13-14.2 µm and quantify the self-broadening coefficients of some selected spectral lines.

Standoff CARS spectroscopy and imaging using an ytterbium-based laser system.

A laser system for standoff coherent anti-Stokes Raman scattering (CARS) spectroscopy of various materials under ambient light conditions is presented. The system is based on an ytterbium laser and an ultrafast optical parametric amplifier for the generation of a broadband pump tunable from 880 to 930 nm, a Stokes at 1025 nm, and a narrowband probe at 512.5 nm. High-resolution Raman spectra encompassing the fingerprint region (400-1800 cm-1) are obtained in 5 ms for toluene, and 100 ms for two types of sugars, glucose and fructose, at a distance of 1 m. As a demonstration of the potential of the setup, hyperspectral images of a 2×2-cm2 target area are collected for a toluene cuvette and a glucose/fructose pressed disk. Our approach is suitable for implementation of a portable system for standoff CARS imaging of chemical and biological materials.

Double-stranded flanking ends affect the folding kinetics and conformational equilibrium of G-quadruplexes forming sequences within the promoter of KIT oncogene.

G-quadruplexes embedded within promoters play a crucial role in regulating the gene expression. KIT is a widely studied oncogene, whose promoter contains three G-quadruplex forming sequences, c-kit1, c-kit2 and c-kit*. For these sequences available studies cover ensemble and single-molecule analyses, although for kit* the latter were limited to a study on a promoter domain comprising all of them. Recently, c-kit2 has been reported to fold according to a multi-step process involving folding intermediates. Here, by exploiting fluorescence resonance energy transfer, both in ensemble and at the single molecule level, we investigated the folding of expressly designed constructs in which, alike in the physiological context, either c-kit2 or c-kit* are flanked by double stranded DNA segments. To assess whether the presence of flanking ends at the borders of the G-quadruplex affects the folding, we studied under the same protocols oligonucleotides corresponding to the minimal G-quadruplex forming sequences. Data suggest that addition of flanking ends results in biasing both the final equilibrium state and the folding kinetics. A previously unconsidered aspect is thereby unravelled, which ought to be taken into account to achieve a deeper insight of the complex relationships underlying the fine tuning of the gene-regulatory properties of these fascinating DNA structures.

Author Correction: Absolute spectroscopy near 7.8 µm with a comb-locked extended-cavity quantum-cascade-laser.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Comb-locked frequency-swept synthesizer for high precision broadband spectroscopy.

Frequency combs have made optical metrology accessible to hundreds of laboratories worldwide and they have set new benchmarks in multi-species trace gas sensing for environmental, industrial and medical applications. However, current comb spectrometers privilege either frequency precision and sensitivity through interposition of a cw probe laser with limited tuning range, or spectral coverage and measurement time using the comb itself as an ultra-broadband probe. We overcome this restriction by introducing a comb-locked frequency-swept optical synthesizer that allows a continuous-wave laser to be swept in seconds over spectral ranges of several terahertz while remaining phase locked to an underlying frequency comb. This offers a unique degree of versatility, as the synthesizer can be either repeatedly scanned over a single absorption line to achieve ultimate precision and sensitivity, or swept in seconds over an entire rovibrational band to capture multiple species. The spectrometer enables us to determine line center frequencies with an absolute uncertainty of 30 kHz and at the same time to collect absorption spectra over more than 3 THz with state-of-the-art sensitivity of a few 10-10 cm-1. Beyond precision broadband spectroscopy, the proposed synthesizer is an extremely promising tool to force a breakthrough in terahertz metrology and coherent laser ranging.

Comb-calibrated sub-Doppler spectroscopy with an external-cavity quantum cascade laser at 7.7 µm.

We study the frequency noise and the referencing to a near-infrared frequency comb of a widely tunable external-cavity quantum-cascade-laser that shows a relatively narrow free-running emission linewidth of 1.7 MHz. The frequency locking of the laser to the comb further narrows its linewidth to 690 kHz and enables sub-Doppler spectroscopy on an N2O transition of the ν1 band near 7.7 µm with sub-MHz resolution and absolute frequency calibration. The combined uncertainty on the measured transition center is estimated to be less than 50 kHz.

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.

Absolute spectroscopy near 7.8 µm with a comb-locked extended-cavity quantum-cascade-laser.

We report for the first time the frequency locking of an extended-cavity quantum-cascade-laser (EC-QCL) to a near-infrared frequency comb. The locked laser source is exploited to carry out molecular spectroscopy around 7.8 µm with a line-centre frequency combined uncertainty of ~63 kHz. The strength of the approach, in view of an accurate retrieval of line centre frequencies over a spectral range as large as 100 cm-1, is demonstrated on the P(40), P(18) and R(31) lines of the fundamental rovibrational band of N2O covering the centre and edges of the P and R branches. The spectrometer has the potential to be straightforwardly extended to other spectral ranges, till 12 µm, which is the current wavelength limit for commercial cw EC-QCLs.

Conjugating precision and acquisition time in a Doppler broadening regime by interleaved frequency-agile rapid-scanning cavity ring-down spectroscopy.

We propose a novel approach to cavity-ring-down-spectroscopy (CRDS) in which spectra acquired with a frequency-agile rapid-scanning (FARS) scheme, i.e., with a laser sideband stepped across the modes of a high-finesse cavity, are interleaved with one another by a sub-millisecond readjustment of the cavity length. This brings to time acquisitions below 20 s for few-GHz-wide spectra composed of a very high number of spectral points, typically 3200. Thanks to the signal-to-noise ratio easily in excess of 10 000, each FARS-CRDS spectrum is shown to be sufficient to determine the line-centre frequency of a Doppler broadened line with a precision of 2 parts over 1011, thus very close to that of sub-Doppler regimes and in a few-seconds time scale. The referencing of the probe laser to a frequency comb provides absolute accuracy and long-term reproducibility to the spectrometer and makes it a powerful tool for precision spectroscopy and line-shape analysis. The experimental approach is discussed in detail together with experimental precision and accuracy tests on the (30 012) ← (00 001) P12e line of CO2 at ∼1.57 µm.

Fluorimetric detection of the earliest events in amyloid ß oligomerization and its inhibition by pharmacologically active liposomes.

BACKGROUND: Amyloid ß (Aß) peptide aggregation is the main molecular mechanism underlying the development of Alzheimer's disease, the most widespread form of senile dementia worldwide. Increasing evidence suggests that the key factor leading to impaired neuronal function is accumulation of water-soluble Aß oligomers rather than formation of the senile plaques created by the deposition of large fibrillary aggregates of Aß. However, several questions remain about the preliminary steps and the progression of Aß oligomerization. METHODS: We show that the initial stages of the aggregation of fluorescently labeled Aß can be determined with a high degree of precision and at physiological (i.e., nanomolar) concentrations by using either steady-state fluorimetry or time-correlated single-photon counting. RESULTS: We study the dependence of the oligomerization extent and rate on the Aß concentration. We determine the chemical binding affinity of fluorescently labeled Aß for liposomes that have been recently shown to be pharmacologically active in vivo, reducing the Aß burden within the brain. We also probe their capacity to hinder the Aß oligomerization process in vitro. CONCLUSIONS: We introduced a fluorescence assay allowing investigation of the earliest steps of Aß oligomerization, the peptide involved in Alzheimer's disease. The assay proved to be sensitive even at Aß concentrations as low as those physiologically observed in the cerebrospinal fluid. GENERAL SIGNIFICANCE: This work represents an extensive and quantitative study on the initial events of Aß oligomerization at physiological concentration. It may enhance our comprehension of the molecular mechanisms leading to Alzheimer's disease, thus paving the way to novel therapeutic strategies.

Effects of non-CpG site methylation on DNA thermal stability: a fluorescence study.

Cytosine methylation is a widespread epigenetic regulation mechanism. In healthy mature cells, methylation occurs at CpG dinucleotides within promoters, where it primarily silences gene expression by modifying the binding affinity of transcription factors to the promoters. Conversely, a recent study showed that in stem cells and cancer cell precursors, methylation also occurs at non-CpG pairs and involves introns and even gene bodies. The epigenetic role of such methylations and the molecular mechanisms by which they induce gene regulation remain elusive. The topology of both physiological and aberrant non-CpG methylation patterns still has to be detailed and could be revealed by using the differential stability of the duplexes formed between site-specific oligonucleotide probes and the corresponding methylated regions of genomic DNA. Here, we present a systematic study of the thermal stability of a DNA oligonucleotide sequence as a function of the number and position of non-CpG methylation sites. The melting temperatures were determined by monitoring the fluorescence of donor-acceptor dual-labelled oligonucleotides at various temperatures. An empirical model that estimates the methylation-induced variations in the standard values of hybridization entropy and enthalpy was developed.

Full genotyping of a highly polymorphic human gene trait by time-resolved fluorescence resonance energy transfer.

The ability of detecting the subtle variations occurring, among different individuals, within specific DNA sequences encompassed in highly polymorphic genes discloses new applications in genomics and diagnostics. DQB1 is a gene of the HLA-II DQ locus of the Human Leukocyte Antigens (HLA) system. The polymorphisms of the trait of the DQB1 gene including codons 52-57 modulate the susceptibility to a number of severe pathologies. Moreover, the donor-receiver tissue compatibility in bone marrow transplantations is routinely assessed through crossed genotyping of DQB and DQA. For the above reasons, the development of rapid, reliable and cost-effective typing technologies of DQB1 in general, and more specifically of the codons 52-57, is a relevant although challenging task. Quantitative assessment of the fluorescence resonance energy transfer (FRET) efficiency between chromophores labelling the opposite ends of gene-specific oligonucleotide probes has proven to be a powerful tool to type DNA polymorphisms with single-nucleotide resolution. The FRET efficiency can be most conveniently quantified by applying a time-resolved fluorescence analysis methodology, i.e. time-correlated single-photon counting, which allows working on very diluted template specimens and in the presence of fluorescent contaminants. Here we present a full in-vitro characterization of the fluorescence responses of two probes when hybridized to oligonucleotide mixtures mimicking all the possible genotypes of the codons 52-57 trait of DQB1 (8 homozygous and 28 heterozygous). We show that each genotype can be effectively tagged by the combination of the fluorescence decay constants extrapolated from the data obtained with such probes.

Elucidation of the relationships between H-bonding patterns and excited state dynamics in cyclovalone.

Cyclovalone is a synthetic curcumin derivative in which the keto-enolic system is replaced by a cyclohexanone ring. This modification of the chemical structure might in principle result in an excited state that is more stable than that of curcumin, which in turn should produce an enhanced phototoxicity. Indeed, although curcumin exhibits photosensitized antibacterial activity, this compound is characterized by very fast excited-state dynamics which limit its efficacy as a photosensitizer. In previous works we showed that the main non-radiative decay pathway of keto-enolic curcuminoids is through excited-state transfer of the enolic proton to the keto-oxygen. Another effective deactivation pathway involves an intermolecular charge transfer mechanism occurring at the phenyl rings, made possible by intramolecular H-bonding between the methoxy and the hydroxyl substituent. In this paper we present UV-Vis and IR absorption spectra data with the aim of elucidating the intramolecular charge distribution of this compound and its solvation patterns in different environments, with particular focus on solute-solvent H-bonding features. Moreover, we discuss steady state and time-resolved fluorescence data that aim at characterizing the excited-state dynamics of cyclovalone, and we compare its decay photophysics to that of curcumin. Finally, because during the characterization procedures we found evidence of very fast photodegradation of cyclovalone, its photostability in four organic solvents was studied by HPLC and the corresponding relative degradation rates were calculated.

Spatial properties of twin-beam correlations at low- to high-intensity transition.

It is shown that spatial correlation functions measured for correlated photon pairs at the single-photon level correspond to speckle patterns visible at high intensities. This correspondence is observed for the first time in one experimental setup by using different acquisition modes of an intensified CCD camera in low and high intensity regimes. The behavior of intensity auto- and cross-correlation functions in dependence on pump-beam parameters including power and transverse profile is investigated.