Досліджено олігорибонуклеотидний склад сумарної дріжджової РНК, що входить до складу противірусно- го препарату широкого спектра дії Нуклекс. Для аналізу природних рибонуклеотидів використано методи рідинної хроматографії та мас-спектрометрії MALDI-Tof-Tof. У складі сумарної дріжджової РНК вста- новлено три основні фракції: перша — від 2 до 4 нуклеотидів, друга — від 4 до 7, третя — від 10 до 15. Зробле- но висновок, що досліджувана РНК містить олігорибонуклеотиди різної довжини, а саме від 4 до 15 ланок.

Optical imaging is a most useful and widespread technique for the investigation of the structure and function of the cellular genomes. However, an analysis of immensely convoluted and irregularly compacted DNA polymer is highly challenging even by modern super-resolution microscopy approaches. Here we propose fluorescence lifetime imaging (FLIM) for the advancement of studies of genomic structure including DNA compaction, replication as well as monitoring of gene expression. The proposed FLIM assay employs two independent mechanisms for DNA compaction sensing. One mechanism relies on the inverse quadratic relation between the fluorescence lifetimes of fluorescence probes incorporated into DNA and their local refractive index, variable due to DNA compaction density. Another mechanism is based on the Förster resonance energy transfer (FRET) process between the donor and the acceptor fluorophores, both incorporated into DNA. Both these proposed mechanisms were validated in cultured cells. The obtained data unravel a significant difference in compaction of the gene-rich and gene-poor pools of genomic DNA. We show that the gene-rich DNA is loosely compacted compared to the dense DNA domains devoid of active genes.

Abstract Background Biodistribution of photosensitizer (PS) in photodynamic therapy (PDT) can be assessed by fluorescence imaging that visualizes the accumulation of PS in malignant tissue prior to PDT. At the same time, excitation of the PS during an assessment of its biodistribution results in premature photobleaching and can cause toxicity to healthy tissues. Combination of PS with a separate fluorescent moiety, which can be excited apart from PS activation, provides a possibility for fluorescence imaging (FI) guided delivery of PS to cancer site, followed by PDT. Results In this work, we report nanoformulations (NFs) of core–shell polymeric nanoparticles (NPs) co-loaded with PS [2-(1-hexyloxyethyl)-2-devinyl pyropheophorbide-a, HPPH] and near infrared fluorescent organic dyes (NIRFDs) that can be excited in the first or second near-infrared windows of tissue optical transparency (NIR-I, ~ 700–950 nm and NIR-II, ~ 1000–1350 nm), where HPPH does not absorb and emit. After addition to nanoparticle suspensions, PS and NIRFDs are entrapped by the nanoparticle shell of co-polymer of N-isopropylacrylamide and acrylamide [poly(NIPAM-co-AA)], while do not bind with the polystyrene (polySt) core alone. Loading of the NIRFD and PS to the NPs shell precludes aggregation of these hydrophobic molecules in water, preventing fluorescence quenching and reduction of singlet oxygen generation. Moreover, shift of the absorption of NIRFD to longer wavelengths was found to strongly reduce an efficiency of the electronic excitation energy transfer between PS and NIRFD, increasing the efficacy of PDT with PS-NIRFD combination. As a result, use of the NFs of PS and NIR-II NIRFD enables fluorescence imaging guided PDT, as it was shown by confocal microscopy and PDT of the cancer cells in vitro. In vivo studies with subcutaneously tumored mice demonstrated a possibility to image biodistribution of tumor targeted NFs both using HPPH fluorescence with conventional imaging camera sensitive in visible and NIR-I ranges (~ 400–750 nm) and imaging camera for short-wave infrared (SWIR) region (~ 1000–1700 nm), which was recently shown to be beneficial for in vivo optical imaging. Conclusions A combination of PS with fluorescence in visible and NIR-I spectral ranges and, NIR-II fluorescent dye allowed us to obtain PS nanoformulation promising for see-and-treat PDT guided with visible-NIR-SWIR fluorescence imaging.

Nanoscopic optical imaging has made prominent progress in recent years, which provides a powerful tool for modern biology science. Superresolution optical imaging allows for the observation of ultra-fine structures of cells, cellular dynamics and cellular functions at nanometer scale or even single molecular level, which greatly promotes the development of life science and many other fields. However, challenges still exist for super-resolution optical imaging for live cells and thick samples in terms of imaging depth, imaging speed as well as biomedical applications. This talk will review the recent progress in superresolution optical microscopy and present our recent work. By combining stimulation emission depletion (STED) microscopy and fluorescence lifetime imaging (FLIM), a STED-FLIM superresolution microscopy was developed to improve the spatial resolution of STED and also perform FLIM imaging at nanometer resolution. A new fluorescent probe with low STED laser power was designed for live cell mitochondria imaging. STED-FLIM imaging of microtubules labeled with ATTO647N inside HeLa cells and the mitosis process was obtained, which provides new insight into the cell structure and functions. In addition, coherent adaptive optical technique (COAT) has been implemented in a stimulated emission depletion microscope to circumvent the scattering and aberration effect for thick sample imaging. Finally, stochastic optical reconstruction microscopy (STORM) superresolution imaging of mitochondrial membrane in live HeLa cells was obtained by the implementation of new fluorescent probes, improved imaging system and optimized single molecule localization algorithm. This provided an important tool and strategy for studying dynamic events and complex functions in living cells.

Photobiomodulation (PBM) involves light to activate cellular signaling pathways leading to cell proliferation or death. In this work, fluorescence and Coherent anti-Stokes Raman Scattering (CARS) imaging techniques were applied to assess apoptosis in human cervical cancer cells (HeLa) induced by near infrared (NIR) laser light (808 nm). Using the Caspase 3/7 fluorescent probe to identify apoptotic cells, we found that the pro-apoptotic effect is significantly dependent of irradiation dose. The highest apoptosis rate was noted for the lower irradiation doses, that is, 0.3 J/cm(2) (similar to 58%) and 3 J/cm(2) (similar to 28%). The impact of light doses on proteins/lipids intracellular metabolism and distribution was evaluated using CARS imaging, which revealed apoptosis-associated reorganization of nuclear proteins and cytoplasmic lipids after irradiation with 0.3 J/cm(2). Doses of NIR light causing apoptosis (0.3, 3 and 30 J/cm(2)) induced a gradual increase in the nuclear protein level over time, in contrast to proteins in cells non-irradiated and irradiated with 10 J/cm(2). Furthermore, irradiation of the cells with the 0.3 J/cm(2) dose resulted in lipid droplets (LDs) accumulation, which was apparently caused by an increase in reactive oxygen species (ROS) generation. We suggest that PBM induced apoptosis could be caused by the ability of NIR light to trigger excessive LDs formation which, in turn, induces cellular cytotoxicity.

A number of studies require sample fixation, aimed to preserve cells in a physiological state with minimal changes of morphology and intracellular molecular content. Sample fixation may significantly distort experimental data, which makes the data interpretation process more challenging. It is particularly important for study of lipid-related diseases, where the biochemical and morphological characteristics of the cells need to be well preserved for an accurate data analysis. This study investigates the effects of formaldehyde and ethanol (EtOH) fixatives on coherent anti-stokes Raman scattering (CARS) signal of proteins and lipids in major cellular compartments of neuronal and glial cells. We found that both fixatives induce alteration of proteins and lipids signal in studied cell lines. Furthermore, the impact of sample preservation methods on CARS signal varies between cell lines. For instance, our data reveals that EtOH fixation induces ~45% increase of CARS signal of proteins in the nucleolus of neuronal cells and ~35% decrease of CARS signal in glial cells. The results indicate that aldehyde fixation is a preferable method for preservation of neuronal and glial cells prior to CARS imaging, as it less affects both CARS signal and intracellular distribution of proteins and lipids.

Nuclear organelles are viscous droplets, created by concentration-dependent condensation and liquid-liquid phase separation of soluble proteins. Nuclear organelles have been actively investigated for their role in cellular regulation and disease. However, these studies are highly challenging to perform in live cells, and therefore, their physico-chemical properties are still poorly understood. In this study, we describe a fluorescence lifetime imaging approach for real-time monitoring of protein condensation in nuclear organelles of live cultured cells. This approach unravels surprisingly large cyclic changes in concentration of proteins in major nuclear organelles including nucleoli, nuclear speckles, Cajal bodies, as well as in the clusters of heterochromatin. Remarkably, protein concentration changes are synchronous for different organelles of the same cells. We propose a molecular mechanism responsible for synchronous accumulations of proteins in the nuclear organelles. This mechanism can serve for general regulation of cellular metabolism and contribute to coordination of gene expression.

CARS microscopy was employed to monitor the reorganization of intracellular lipids and proteins, as well as cellular transformations, after irradiation with near infrared (NIR) light. NIR light was shown to induce apoptosis in HeLa cells in vitro in a dose‐dependent manner. The progression of apoptosis assessed with CARS microscopy is apparently associated with the generation of reactive oxygen species followed by an excessive formation of lipid droplets and their peroxidation.Further details can be found in the article by Svitlana M. Levchenko, Andrey N. Kuzmin, Artem Pliss, et al. (e201900179) image

Oligonucleotides antiviral drugs have been actively implemented in medicine during the last decades nevertheless the molecular mechanism of their action is still unclear. As it was shown in our previous work, the combination of oligonucleotides with alcohol sugar D-mannitol leads to changes in their biological activity and efficiency. At this stage of our investigation, we studied the ability of oligoribonucleotides from total yeast RNA (ORNs) and oligoribonucleotides-D-mannitol complexes to affect the conformation and stability of interferon (IFN) α-2b – a key protein of the antiviral cell defense mechanism. To investigate that interaction, conformational changes and stability of IFN protein in the presence and/or absence of the ligands were studied by fluorescence and CD (circular dichroism) spectroscopies. All experiments were performed on spectrofluorometer Jasco FP- 8200 and CD spectrometer Jasco J-815 with a Peltier temperature cell holder. Obtained thermal denaturation profiles of IFN α–2b alone and in the presence of ORNs and ORNs-D-mannitol complexes show that the addition of these ligands led to an increase of thermal stabilization of protein of 2 and 1.8 0C respectively. The dissociation constant between INF and total yeast ORNs was Kd =2.88±1.14µM and between INF and ORNs with D-mannitol – Kd =0,92±0.23µM. The analysis of IFN secondary structure changes by Bestsel shows that addition of ORNs or ORNs-D-mannitol complexes led to a decrease of α-helix components in the protein structure and to an increase of antiparallel β-stand, β-turn, and random coil components. At the same time, the analysis of the tertiary structure shows that adding ORNs-D-mannitol changes the architecture of the protein from the 2-layer sandwich to alpha-beta complex. On the other hand, adding ORNs did not cause any change in the tertiary structure. We suppose that total yeast ORNs and ORNs-D-mannitol complexes act as compounds, altering the secondary and tertiary structures of the interferon and in this way can change its biological activity.

The alteration of the phospholipid composition within the cell, in particular the ratio between saturated and unsaturated fatty acids, can serve as an important biomarker to prognosis of the disease progression (e.g., fatty-liver disease, prostate cancer, or neurodegenerative disorders). Major techniques for lipid analysis in biological samples require a lipid extraction procedure that is not compatible with live cell studies. To address this challenge, we apply microRaman-Biomolecular Component Analysis (BCA) for comparative analysis of phospholipid composition and sensing the saturation degree of fatty acid lipid chain in live HeLa cells and lipids extracted from HeLa cells. After processing raw Raman data, acquired in lipid droplets (LDs) free cytoplasmic area, LDs and extracted lipids with BCA, the lipid component was isolated. Despite the similarity in general profiles of processed Raman spectra acquired in live cells and extracted lipids, some clear differences that reflect diversity in their phospholipids composition were revealed. Furthermore, using the direct relation between the number of double bonds in the fatty acid chain and the intensity ratio of the corresponding Raman bands, the saturation degree of fatty acids was estimated.

We present our recent work on the applications of fluorescence lifetime imaging microscopy(FLIM), including the monitoring of macromolecule dynamic changes in the nucleolar compartments and the auxiliary diagnosis of H and E-stained sections. We demonstrated the capability of FLIM to measure protein concentration in the specific cellular compartments in live cells. We proposed to use FLIM to monitor changes in intracellular protein concentration caused by various factors e.g. cell cycle progression, drug treatment etc. In the future, FLIM technology is expected to be combined with super-resolution optical imaging. FLIM with molecular resolution will have the potential to serve as a powerful tool for discovering new phenomena and revealing new mechanisms in biomedical research, which will effectively promote the development of life science.

It is known that lipids play an outstanding role in cellular regulation, and their dysfunction has been linked to many diseases. Thus, modulation of lipid metabolism may provide new pathways for disease treatment or prevention. In this work, near-infrared (NIR) light was applied to modulate lipid metabolism and increase intracellular lipid content in rat cortical neurons (RCN). Using label-free CARS microscopy, we have monitored the intracellular lipid content in RCN at a single-cell level. A major increase in average level of lipid per cell after treatment with laser diode at 808 nm was found, nonlinearly dependent on the irradiation dose. Moreover, a striking formation of lipid droplets (LDs) in the irradiated RCN was discovered. Further experiments and analysis reveal a strong correlation between NIR light induced generation of reactive oxygen species (ROS), lipids level, and LDs formation in RCN. Our findings can contribute to a development of therapeutic approaches for neurological disorders via NIR light control of lipid metabolism in neuronal cells.

Recent developments in Raman spectroscopy instrumentation and data processing algorithms have led to the emergence of Ramanomics - an independent discipline with unprecedented capabilities to map the distribution of distinct molecular groups in live cells. Here, we introduce a method for probing the absolute concentrations of proteins, RNA and lipids in single organelles of live cultured cells by biomolecular component analysis using microRaman data. We found significant cell-to-cell variations in the molecular profiles of organelles, thus providing a physiologically relevant set of markers of cellular heterogeneity. At the same cell the molecular profiles of different organelles can strongly correlate, reflecting tight coordination of their functions. This correlation was significant in WI-38 diploid fibroblasts and weak in HeLa cells, indicating profound differences in the regulation of biochemical processes in these cell lines.

Fluorescence lifetime imaging (FLIM) is an effective noninvasive bioanalytical tool based on measuring fluorescent lifetime of fluorophores. A growing number of FLIM studies utilizes genetically engineered fluorescent proteins targeted to specific subcellular structures to probe local molecular environment, which opens new directions in cell science. This paper highlights the unconventional applications of FLIM for studies of molecular processes in diverse organelles of live cultured cells.

To advance an understanding of cellular regulation and function it is crucial to identify molecular contents in cellular organelles, which accommodate specific biochemical processes. Toward achievement of this goal, we applied micro-Raman-Biomolecular Component Analysis assay for molecular profiling of major organelles in live cells. We used this assay for comparative analysis of proteins 3D conformation and quantification of proteins, RNA, and lipids concentrations in nucleoli, endoplasmic reticulum, and mitochondria of WI 38 diploid lung fibroblasts and HeLa cancer cells. Obtained data show substantial differences in the concentrations and conformations of proteins in the studied organelles. Moreover, differences in the intraorganellar concentrations of RNA and lipids between these cell lines were found. We report the biological significance of obtained macromolecular profiles and advocate for micro-Raman BCA assay as a valuable proteomics tool.

Комплексоутворення РНК з манітолом, його спектральні характеристики та біологічна активність (Представлено членом-кореспондентом НАН України Д.М

The steady-state and time-resolved linear spectral properties, two-photon absorption spectra and fast relaxation processes in the excited states of styryl base-type derivatives were investigated. The nature of linear absorption, fluorescence and excitation anisotropy spectra were analyzed in solvents of different polarity at room temperature and specific dependence of the solvatochromic behavior on the donor-acceptor strength of the terminal substituents was shown. Two-photon absorption (2PA) efficiency of styryl dye bases was determined in a broad spectral range using two-photon induced fluorescence technique, and cross-sections maxima of ~ 100 GM were found. The excited state absorption (ESA) and fast relaxation processes in the molecular structures were investigated by transient absorption femtosecond pump-probe methodology. The role of twisted intramolecular charge transfer (TICT) effect in the excited state of styryl dye base with dimethylamino substituent was shown. The experimental spectroscopic data were also verified by quantum chemical calculations at the Time Dependent Density Functional Theory level, combined with a polarizable continuum model.

Quantum-chemical and spectroscopic study of fluorine atoms as substituents in the trimethine and pentamethine chain influence on the electronic structure in polymethine dyes has been performed. According to the calculation data that were experimentally confirmed by RCA and C-13 NMR spectroscopy fluorination of polymethine chain leads to the small C-C bond lengths changes in chromophore and appreciably changes of the atomic charges. It was established that the introduction of fluorine atoms in the chromophore is accompanied by the significant shifting of the frontier and nearest levels and hence by changing the electronic transitions energies. The simultaneous analysis of the absorption and fluorescence excitation anisotropy spectra as well as results of the calculations of electronic transitions has shown that the S-0 -> S-1 transition is more sensitive to the fluorine substituents than the S-0 -> S-2 transition. (C) 2015 Elsevier Ltd. All rights reserved.

The interaction between 2-5?(3)oligonucleotides and recombinant -interferon was studied by MALDI-TOF mass spectrometry and fluorescence spectroscopy methods. The ability of this key protein of antiviral cell defense system to bind up to 5 molecules of oligoadenylates depending on their structure was established. The presence of interaction in oligoadenylate-interferon system was also confirmed by fluorescence studies. Investigated compounds quenched the emission of -interferon from 40 to 63%. The efficiency of quenching of the fluorescence of -interferon also depends on the oligoadenylates structure.