Browsing by Author "Patra, Satyajit"

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Antagonistic effects of natural osmolyte mixtures and hydrostatic pressure on the conformational dynamics of a DNA hairpin probed at the single-molecule level
(RSC, 2018-03) Patra, Satyajit
Organisms are thriving in the deep sea at pressures of up to the 1 kbar level. To withstand such harsh conditions, they accumulate particular osmolyte mixtures to counteract the pressure stress imposed. We explored the combined effects of pressure and osmolyte mixtures known from deep sea organisms on the closed-to-open conformational transition of a DNA hairpin (Hp). To this end, single-molecule Förster resonance energy transfer (smFRET) experiments were carried out in an optimized high-pressure capillary optical cell. In the absence of osmolytes, pressure shifts the conformational equilibrium of the DNA Hp towards the open, unfolded state owing to a volume decrease of about −20 cm3 mol−1. We show that the deep-sea osmolyte mixture, largely composed of TMAO, is able to rescue the DNA Hp from unfolding even up to almost 1 kbar, which is supposed to be essentially due to a distinct excluded volume effect.
Crowders and Cosolvents—Major Contributors to the Cellular Milieu and Efficient Means to Counteract Environmental Stresses
(Wiley, 2017-08) Patra, Satyajit
The free energy and conformational landscape of biomolecular systems as well as biochemical reactions depend not only on temperature and pressure, but also on the particular solution conditions. Such conditions include the effects of cosolvents (for example osmolytes) and macromolecular crowding, which are crucial components to understand the energetics and kinetics of biological processes in living system. Such conditions are also important for the understanding of many debilitating diseases, such as those where misfolding and amyloid formation of proteins are involved. Moreover, understanding their effects on biomolecular processes is prerequisite for designing industrially relevant enzymatic reactions, which seldom take place under neat conditions. Here, we review and discuss experimental and theoretical studies on the characterization of cosolvent and crowding induced effects in biologically relevant systems, approaching even the complexity of living organisms. In particular, we focus on cosolvent and crowding effects on the conformational equilibrium and folding kinetics of proteins and nucleic acids as well as on enzymatic reactions, including their effects on the temperature and pressure dependence of these processes. By presenting a few representative examples, we show how such effects are unveiled and described in thermodynamic and kinetic terms.
The Deep Sea Osmolyte Trimethylamine N-Oxide and Macromolecular Crowders Rescue the Antiparallel Conformation of the Human Telomeric G-Quadruplex from Urea and Pressure Stress
(Wiley, 2018-07) Patra, Satyajit
Organismsare thriving in the deepsea at pres-suresup to the 1kbar level,whichimposessevere stresson the conformationaldynamics and stabilityof theirbio-molecules.The impactofosmolytesand macromolecularcrowders, mimickingintracellular conditions,on the effectof pressure on the conformationaldynamics of ahumantelomeric G-quadruplex (G4)DNAis exploredin this studyemployingsingle-moleculeFçrsterresonanceenergytransfer(FRET)experiments.Inneat buffer,pressurizationfavorsthe parallel/hybridstateof the G4-DNAoverthe an-tiparallel conformationat 400 bar,finallyleadingtoun-foldingbeyond1000 bar.High-pressure NMRdatasupportthesefindings.The foldedtopological conformershavedifferentsolvent accessible surfaceareasandcavityvol-umes,leadingto differentvolumetricpropertiesandhencepressure stabilities.Thedeep-seaosmolytetri-methylamineN-oxide(TMAO)and macromolecular crowd-ing agentsare ableto effectively rescuethe G4-DNAfromunfolding in the wholepressure rangeencounteredonEart
Deep Ultraviolet Plasmonic Enhancement of Single Protein Autofluorescence in Zero-Mode Waveguides
(ACS, 2019-09) Patra, Satyajit
Single molecule detection provides detailed information about molecular structures and functions but it generally requires the presence of a fluorescent marker which can interfere with the activity of the target molecule or complicate the sample production. Detecting a single protein with its natural UV autofluorescence is an attractive approach to avoid all the issues related to fluorescence labeling. However, the UV autofluorescence signal from a single protein is generally extremely weak. Here, we use aluminum plasmonics to enhance the tryptophan autofluorescence emission of single proteins in the UV range. Zero-mode waveguide nanoapertures enable the observation of the UV fluorescence of single label-free β-galactosidase proteins with increased brightness, microsecond transit times, and operation at micromolar concentrations. We demonstrate quantitative measurements of the local concentration, diffusion coefficient, and hydrodynamic radius of the label-free protein over a broad range of zero-mode waveguide diameters. Although the plasmonic fluorescence enhancement has generated a tremendous interest in the visible and near-infrared parts of the spectrum, this work pushes further the limits of plasmonic-enhanced single molecule detection into the UV range and constitutes a major step forward in our ability to interrogate single proteins in their native state at physiological concentrations.
Diffusion of organic dyes in bovine serum albumin solution studied by fluorescence correlation spectroscopy
(RSC, 2012-05) Patra, Satyajit
The understanding of the transport of drugs and naturally occurring molecules in living cells and tissues requires a thorough knowledge of the diffusion behaviour of the molecular systems in these media. In this work, we studied the translational diffusion of three fluorescent molecules, electrically neutral coumarin 102 (C102), cationic rhodamine 6G (R6G) and anionic fluorescein (FL) in phosphate-buffered (pH 7) aqueous solutions of bovine serum albumin (BSA) protein in the absence and presence of common salt and urea using fluorescence correlation spectroscopy (FCS) by monitoring the fluorescence intensity fluctuations in a small confocal observation volume. The diffusion due to both free and BSA-bound molecules is observed in the case of the C102-BSA system. While no exchange between the bound and free states of the molecule is observed in this case, a rapid exchange between the two states is observed in the case of electrically charged hydrophilic dyes R6G and FL. This molecular picture, which is the first of its kind, is a reflection of a weaker binding of R6G and FL compared to C102 with the protein molecule. The binding sites of the probe molecules in BSA were identified based on the urea-induced change of diffusion of the probes in BSA.
Effect of Capping Agent and Medium on Light-Induced Variation of the Luminescence Properties of CdTe Quantum Dots: A Study Based on Fluorescence Correlation Spectroscopy, Steady State and Time-Resolved Fluorescence Techniques
(ACS, 2014-07) Patra, Satyajit
The influence of ligand and solvent on light-induced modulation of the emission behavior of the quantum dots (QDs) has been studied for CdTe QDs capped with hexadecylamine (HDA), mercaptopropionic acid (MPA), and 1-(1-undecanethiol)-3-methyl imidazolium bromide (SMIM) in CHCl3, H2O, and [bmim][PF6] ionic liquid, respectively, using steady state and time-resolved fluorescence and fluorescence correlation spectroscopy techniques. While an aqueous solution of CdTe/MPA QDs exhibits fluorescence enhancement and a small blue shift of the emission peak (λmaxem) in the early stages of the light irradiation, such enhancement could not be observed in the case of CHCl3 solution of CdTe/HDA and [bmim][PF6] solution of CdTe/SMIM. Instead, exposure to light leads to a rapid reduction in luminescence intensity and large blue shift of λmaxem in the case of CHCl3 solution of CdTe/HDA and a very slow decrease of luminescence intensity with negligible shift of λmaxem in the case of an ionic liquid solution of CdTe/SMIM. The time-resolved fluorescence behavior of the QDs is found to be consistent with the steady state results. Fluorescence correlation spectroscopy measurements on the other hand reveal a large decrease of the amplitude of correlation at time zero [G(0)] for the aqueous solution of CdTe/MPA and negligible change in the G(0) value for the ionic liquid solution of CdTe/SMIM with increasing excitation power. The mechanism of these light-induced changes of the luminescence behavior of the QDs is investigated.
Effect of Controlled Deposition of ZnS Shell on the Photostability of CdTe Quantum Dots as Studied by Conventional Fluorescence and FCS Techniques
(Wiley, 2015-10) Patra, Satyajit
The effect of one and two monolayers of ZnS shells on the photostability of CdTe quantum dots (QDs) in aqueous and nonaqueous media has been studied by monitoring the fluorescence behavior of the QDs under ensemble and single-molecule conditions. ZnS capping of the CdTe QDs leads to significant enhancement of the fluorescence brightness of these QDs. Considerable enhancement of the photostability of the shell-protected QDs, including the suppression of photoactivation, is also observed. Fluorescence correlation spectroscopy measurements reveal an increase in the number of particles undergoing reversible fluorescent on–off transitions in the volume under observation with increasing excitation power; this effect is found to be more pronounced in the case of core-only QDs than for core–shell QDs.
Effect of Pressure on the Conformational Landscape of a Large Loop DNA Hairpin in the Presence of Salts and Osmolytes
(Cell Press, 2018-02) Patra, Satyajit
The effect of pressure on the conformational landscape of a DNA hairpin has been investigated in the absence and presence of salts and osmolytes using both ensemble and single-molecule Förster resonance energy transfer (FRET) techniques.1 We use monovalent (K+), divalent (Mg2+) and trivalent (Co3+) salts and urea as well as TMAO as osmolytes. Unlike the canonical DNA duplex structures of similar melting points, this large loop DNA hairpin is rather sensitive to pressure.2 The transition volume upon unfolding is found to be −17 cm3 mol−1 in neat buffer solution. We found that the stabilizing effect of salt follows the order Co3+ > Mg2+ > K+. Above 1 mM Mg2+ and 0.3 mM Co3+, pressure has a negligible effect on the conformation of the DNA hairpin, which is due to the compensation of the negative charge density of the phosphate backbone, favoring the formation of loops by base pairing of complementary sequences, and thus the closed conformation. The compatible osmolyte TMAO also stabilizes the closed conformation even at high pressures and temperatures, while urea destabilizes the closed conformation synergistically with pressure and temperature. Intermediate states are populated by urea and high temperatures, indicating that the conformational landscape of the DNA hairpin is in fact a rugged one. The results obtained are interpreted in terms of preferential hydration and interaction effects of the cations and osmolytes.
Exploring the effects of cosolutes and crowding on the volumetric and kinetic profile of the conformational dynamics of a poly dA loop DNA hairpin: a single-molecule FRET study
(OUP, 2019-01) Patra, Satyajit
We investigated the volumetric and kinetic profile of the conformational landscape of a poly dA loop DNA hairpin (Hp) in the presence of salts, osmolytes and crowding media, mimicking the intracellular milieu, using single-molecule FRET methodology. Pressure modulation was applied to explore the volumetric and hydrational characteristics of the free-energy landscape of the DNA Hp, but also because pressure is a stress factor many organisms have to cope with, e.g. in the deep sea where pressures even up to the kbar level are encountered. Urea and pressure synergistically destabilize the closed conformation of the DNA Hp due to a lower molar partial volume in the unfolded state. Conversely, multivalent salts, trimethylamine-N-oxide and Ficoll strongly populate the closed state and counteract deteriorating effects of pressure. Complementary smFRET measurements under immobilized conditions at ambient pressure allowed us to dissect the equilibrium data in terms of folding and unfolding rate constants of the conformational transitions, leading to a deeper understanding of the stabilization mechanisms of the cosolutes. Our results show that the free-energy landscape of the DNA Hp is a rugged one, which is markedly affected by the ionic strength of the solution, by preferential interaction and exclusion of cosolvents as well as by pressure.
Extending Single-Molecule Förster Resonance Energy Transfer (FRET) Range beyond 10 Nanometers in Zero-Mode Waveguides
(ACS, 2019-07) Patra, Satyajit
Single-molecule Förster resonance energy transfer (smFRET) is widely used to monitor conformations and interaction dynamics at the molecular level. However, conventional smFRET measurements are ineffective at donor–acceptor distances exceeding 10 nm, impeding the studies on biomolecules of larger size. Here, we show that zero-mode waveguide (ZMW) apertures can be used to overcome the 10 nm barrier in smFRET. Using an optimized ZMW structure, we demonstrate smFRET between standard commercial fluorophores up to 13.6 nm distance with a significantly improved FRET efficiency. To further break into the classical FRET range limit, ZMWs are combined with molecular constructs featuring multiple acceptor dyes to achieve high FRET efficiencies together with high fluorescence count rates. As we discuss general guidelines for quantitative smFRET measurements inside ZMWs, the technique can be readily applied for monitoring conformations and interactions on large molecular complexes with enhanced brightness.
Fast interaction dynamics of G-quadruplex and RGG-rich peptides unveiled in zero-mode waveguides
(OUP, 2021-12) Patra, Satyajit
G-quadruplexes (GQs), a non-canonical form of DNA, are receiving a huge interest as target sites for potential applications in antiviral and anticancer drug treatments. The biological functions of GQs can be controlled by specifically binding proteins known as GQs binding proteins. Some of the GQs binding proteins contain an arginine and glycine-rich sequence known as RGG peptide. Despite the important role of RGG, the GQs-RGG interaction remains poorly understood. By single molecule measurements, the interaction dynamics can be determined in principle. However, the RGG–GQs interaction occurs at micromolar concentrations, making conventional single-molecule experiments impossible with a diffraction-limited confocal microscope. Here, we use a 120 nm zero-mode waveguide (ZMW) nanoaperture to overcome the diffraction limit. The combination of dual-color fluorescence cross-correlation spectroscopy (FCCS) with FRET is used to unveil the interaction dynamics and measure the association and dissociation rates. Our data show that the RGG–GQs interaction is predominantly driven by electrostatics but that a specific affinity between the RGG sequence and the GQs structure is preserved. The single molecule approach at micromolar concentration is the key to improve our understanding of GQs function and develop its therapeutic applications by screening a large library of GQs-targeting peptides and proteins.
Fluorescence Blinking and Photoactivation of All-Inorganic Perovskite Nanocrystals CsPbBr3 and CsPbBr2I
(ACS, 2016-01) Patra, Satyajit
Study of the emission behavior of all-inorganic perovskite nanocrystals CsPbBr3 and CsPbBr2I as a function of the excitation power employing fluorescence correlation spectroscopy and conventional techniques reveals fluorescence blinking in the microsecond time scale and photoinduced emission enhancement. The observation provides insight into the radiative and nonradiative deactivation pathways of these promising substances. Because both blinking and photoactivation processes are intimately linked to the charge separation efficiency and dynamics of the nanocrystals, these key findings are likely to be helpful in realizing the true potential of these substances in photovoltaic and optoelectronic applications.
Fluorescence Brightness, Photostability, and Energy Transfer Enhancement of Immobilized Single Molecules in Zero-Mode Waveguide Nanoapertures
(ACS, 2022-05) Patra, Satyajit
Zero-mode waveguide (ZMW) nanoapertures are widely used to monitor single molecules beyond the range accessible to normal microscopes. However, several aspects of the ZMW influence on the photophysics of fluorophores remain inadequately documented and sometimes controversial. Here, we thoroughly investigate the ZMW influence on the fluorescence of single immobilized Cy3B and Alexa 647 molecules, detailing the interplays between brightness, lifetime, photobleaching time, the total number of emitted photons, and Förster resonance energy transfer (FRET). Despite the plasmonic-enhanced excitation intensity in the ZMW, we find that the photostability is preserved with similar photobleaching times as on the glass reference. Both the fluorescence brightness and the total number of photons detected before photobleaching are increased, with an impressive gain of nearly five times that found for Alexa 647 dyes. Finally, the single-molecule data importantly allow a loophole-free characterization of the ZMW influence on the FRET process. We show that the FRET rate constant is enhanced by 50%, demonstrating that nanophotonics can mediate the energy transfer. These results deepen our understanding of the fluorescence enhancement in ZMWs and are of immediate relevance for single-molecule biophysical applications.
A Fluorescence Correlation Spectroscopy, Steady-State, and Time-Resolved Fluorescence Study of the Modulation of Photophysical Properties of Mercaptopropionic Acid Capped CdTe Quantum Dots upon Exposure to Light
(ACS, 2013-10) Patra, Satyajit
Light-induced modulation of the fluorescence behavior of mercaptopropionic acid (MPA) capped CdTe quantum dots (QDs) in aqueous solution is studied by a combination of fluorescence correlation spectroscopy (FCS) and steady-state and time-resolved fluorescence techniques. These investigations reveal a dramatic variation in the fluorescence properties of the QDs under exposure to light. In the FCS measurement, a large decrease in amplitude and change in shape of the correlation curves are observed with increasing excitation power. The change in the shape of the correlation curves, particularly at short lag time, e.g., a faster relaxation at high excitation power, is attributed to the increasing contribution of the off state of the QDs. Interestingly, despite this increasing contribution of the off state, which reduces the effective number of emitters in the observation volume and hence should increase the amplitude of the correlation curve, the latter actually decreases at high excitation power. This apparent contradiction is resolved by considering light-induced transformation of the dark QDs to bright QDs due to surface passivation of the QDs with increasing excitation power. Enhancement of the steady-state fluorescence intensity under light irradiation, both in aerated and deaerated environments, supports the mechanism of passivation of the surface trap states by photoadsorption of water molecules. Fluorescence lifetime data is also shown to be consistent with this light-induced surface passivation mechanism.
Fluorescence Quenching of CdS Quantum Dots by 4-Azetidinyl-7-Nitrobenz-2-Oxa-1,3-Diazole: A Mechanistic Study
(Wiley, 2011-08) Patra, Satyajit
Fluorescence quenching of CdS quantum dots (QDs) by 4-azetidinyl-7-nitrobenz-2-oxa-1,3-diazole (NBD), where the two quenching partners satisfy the spectral overlap criterion necessary for Förster resonance energy transfer (FRET), is studied by steady-state and time-resolved fluorescence techniques. The fluorescence quenching of the QDs is accompanied by an enhancement of the acceptor fluorescence and a reduction of the average fluorescence lifetime of the donor. Even though these observations are suggestive of a dynamic energy transfer process, it is shown that the quenching actually proceeds through a static interaction between the quenching partners and is probably mediated by charge-transfer interactions. The bimolecular quenching rate constant estimated from the Stern–Volmer plot of the fluorescence intensities, is found to be exceptionally high and unrealistic for the dynamic quenching process. Hence, a kinetic model is employed for the estimation of actual quencher/QD ratio dependent exciton quenching rate constants of the fluorescence quenching of CdS by NBD. The present results point to the need for a deeper analysis of the experimental quenching data to avoid erroneous conclusions.
Influence of isoform-specific Ras lipidation motifs on protein partitioning and dynamics in model membrane systems of various complexity
(De Gruyter, 2016-12) Patra, Satyajit
The partitioning of the lipidated signaling proteins N-Ras and K-Ras4B into various membrane systems, ranging from single-component fluid bilayers, binary fluid mixtures, heterogeneous raft model membranes up to complex native-like lipid mixtures (GPMVs) in the absence and presence of integral membrane proteins have been explored in the last decade in a combined chemical-biological and biophysical approach. These studies have revealed pronounced isoform-specific differences regarding the lateral distribution in membranes and formation of protein-rich membrane domains. In this context, we will also discuss the effects of lipid head group structure and charge density on the partitioning behavior of the lipoproteins. Moreover, the dynamic properties of N-Ras and K-Ras4B have been studied in different model membrane systems and native-like crowded milieus. Addition of crowding agents such as Ficoll and its monomeric unit, sucrose, gradually favors clustering of Ras proteins in forming small oligomers in the bulk; only at very high crowder concentrations association is disfavored.
Long-Range Single-Molecule Förster Resonance Energy Transfer between Alexa Dyes in Zero-Mode Waveguides
(ACS, 2020-03) Patra, Satyajit
Zero-mode waveguide (ZMW) nano-apertures milled in metal films were proposed to improve the Förster resonance energy transfer (FRET) efficiency and enable single-molecule FRET detection beyond the 10 nm barrier, overcoming the restrictions of diffraction-limited detection in a homogeneous medium. However, the earlier ZMW demonstrations were limited to the Atto 550–Atto 647N fluorophore pair, asking the question whether the FRET enhancement observation was an artifact related to this specific set of fluorescent dyes. Here, we use Alexa Fluor 546 and Alexa Fluor 647 to investigate single-molecule FRET at large donor–acceptor separations exceeding 10 nm inside ZMWs. These Alexa fluorescent dyes feature a markedly different chemical structure, surface charge, and hydrophobicity as compared to their Atto counterparts. Our single molecule data on Alexa 546–Alexa 647 demonstrate enhanced FRET efficiencies at large separations exceeding 10 nm, extending the spatial range available for FRET and confirming the earlier conclusions. By showing that the FRET enhancement inside a ZMW does not depend on the set of fluorescent dyes, this report is an important step to establish the relevance of ZMWs to extend the sensitivity and detection range of FRET, while preserving its ability to work on regular fluorescent dye pairs.
Mechanistic insights into the C-myc G-quadruplex and berberine binding inside an aqueous two-phase system mimicking biomolecular condensates
(ACS, 2024-08) Patra, Satyajit
We investigated the binding between the c-MYC G-quadruplex (GQ) and berberine chloride (BCl) in an aqueous two-phase system (ATPS) with 12.3 wt % polyethylene glycol and 5.6 wt % dextran, mimicking the highly crowded intracellular biomolecular condensates formed via liquid–liquid phase separation. We found that in the ATPS, complex formation is significantly altered, leading to an increase in affinity and a change in the stoichiometry of the complex with respect to neat buffer conditions. Thermodynamic studies reveal that binding becomes more thermodynamically favorable in the ATPS due to entropic effects, as the strong excluded volume effect inside ATPS droplets reduces the entropic penalty associated with binding. Finally, the binding affinity of BCl for the c-MYC GQ is higher than those for other DNA structures, indicating potential specific interactions. Overall, these findings will be helpful in the design of potential drugs targeting the c-MYC GQ structures in cancer-related biocondensates.
Microheterogeneity of Some Imidazolium Ionic Liquids As Revealed by Fluorescence Correlation Spectroscopy and Lifetime Studies
(ACS, 2012-10) Patra, Satyajit
The microscopic structure and dynamics of the room temperature ionic liquids (RTILs) that are responsible for some of the peculiar properties of this class of solvents continue to intrigue the researchers and stimulate new investigations. Herein, we use the fluorescence correlation spectroscopy (FCS) technique to study the diffusion of some probe molecules in RTILs, the results of which, when combined with those obtained from fluorescence lifetime studies, provide insights into the microscopic structural details of this class of novel solvents. Experiments performed with three charged and neutral probe molecules in five carefully selected 1-alkyl-3-methylimidazolium ionic liquids reveal that unlike in conventional solvents these probes exhibit a bimodal diffusion behavior in RTILs thus indicating the presence of two distinct environments. It is found that the contribution of the slow component of the diffusion increases with increasing alkyl chain length of the cation. Not only are these results supported by the biexponential decay behavior of the fluorescence intensity of the systems, but the individual values of the lifetime components and their weight allow determination of the nature of the two major environments. In essence, the results point to the potential of the two combined techniques in unraveling some of the complex features of the ionic liquids.
Osmolyte Effects on the Conformational Dynamics of a DNA Hairpin at Ambient and Extreme Environmental Conditions
(Wiley, 2017-04) Patra, Satyajit
The structural dynamics of a DNA hairpin (Hp) are studied in the absence and presence of the two natural osmolytes trimethylamine-N-oxide (TMAO) and urea at ambient and extreme environmental conditions, including high pressures and high temperatures, by using single-molecule Förster resonance energy transfer and fluorescence correlation spectroscopy. The effect of pressure on the conformational dynamics of the DNA Hp is investigated on a single-molecule level, providing novel mechanistic insights into its conformational conversions. Different from canonical DNA duplex structures of similar melting points, the DNA Hp is found to be rather pressure sensitive. The combined temperature and pressure dependent data allow dissection of the folding free energy into its enthalpic, entropic, and volumetric contributions. The folded conformation is effectively stabilized by the compatible osmolyte TMAO not only at high temperatures, but also at high pressures and in the presence of the destabilizing co-solute urea.