Synthesis and photophysical characterization of a pH-sensitive quadracyclic uridine (qU) analogue

Fluorescent base analogues (FBAs) have become useful tools for applications in biophysical chemistry, chemical biology, live-cell imaging, and RNA therapeutics. Herein, two synthetic routes towards a novel FBA of uracil named qU (quadracyclic uracil/uridine) are described. The qU nucleobase bears a tetracyclic fused ring system and is designed to allow for specific Watson-Crick base pairing with adenine. We find that qU absorbs light in the visible region of the spectrum and emits brightly with a quantum yield of 27 % and a dual-band character in a wide pH range. With evidence, among other things, from fluorescence lifetime measurements we suggest that this dual emission feature results from an excited-state proton transfer (ESPT) process. Furthermore, we find that both absorption and emission of qU are highly sensitive to pH. The high brightness in combination with excitation in the visible and pH responsiveness makes qU an interesting native-like nucleic acid label in spectroscopy and microscopy applications in, for example, the field of mRNA and antisense oligonucleotide (ASO) therapeutics.

HnRNPK maintains single strand RNA through controlling double-strand RNA in mammalian cells

Although antisense transcription is a widespread event in the mammalian genome, double-stranded RNA (dsRNA) formation between sense and antisense transcripts is very rare and mechanisms that control dsRNA remain unknown. By characterizing the FGF-2 regulated transcriptome in normal and cancer cells, we identified sense and antisense transcripts IER3 and IER3-AS1 that play a critical role in FGF-2 controlled oncogenic pathways. We show that IER3 and IER3-AS1 regulate each other's transcription through HnRNPK-mediated post-transcriptional regulation. HnRNPK controls the mRNA stability and colocalization of IER3 and IER3-AS1. HnRNPK interaction with IER3 and IER3-AS1 determines their oncogenic functions by maintaining them in a single-stranded form. hnRNPK depletion neutralizes their oncogenic functions through promoting dsRNA formation and cytoplasmic accumulation. Intriguingly, hnRNPK loss-of-function and gain-of-function experiments reveal its role in maintaining global single- and double-stranded RNA. Thus, our data unveil the critical role of HnRNPK in maintaining single-stranded RNAs and their physiological functions by blocking RNA-RNA interactions.

A new phosphoramidite enables orthogonal double labelling to form combination oligonucleotide probes

A novel phosphoramidite (AP-C3 dT) containing an alkyne and amine has been synthesized, enabling orthogonal labelling for combination oligonucleotides probes.

Light-induced modulation of DNA recognition by the Rad4/XPC damage sensor protein

Biomolecular structural changes upon binding/unbinding are key to their functions. However, characterization of such dynamical processes is difficult as it requires ways to rapidly and specifically trigger the assembly/disassembly as well as ways to monitor the resulting changes over time. Recently, various chemical strategies have been developed to use light to trigger changes in oligonucleotide structures, and thereby their activities. Here we report that photocleavable DNA can be used to modulate the DNA binding of the Rad4/XPC DNA repair complex using light. Rad4/XPC specifically recognizes diverse helix-destabilizing/distorting lesions including bulky organic adduct lesions and functions as a key initiator for the eukaryotic nucleotide excision repair (NER) pathway. We show that the 6-nitropiperonyloxymethyl (NPOM)-modified DNA is recognized by the Rad4 protein as a specific substrate and that the specific binding can be abolished by light-induced cleavage of the NPOM group from DNA in a dose-dependent manner. Fluorescence lifetime-based analyses of the DNA conformations suggest that free NPOM-DNA retains B-DNA-like conformations despite its bulky NPOM adduct, but Rad4-binding causes it to be heterogeneously distorted. Subsequent extensive conformational searches and molecular dynamics simulations demonstrate that NPOM in DNA can be housed in the major groove of the DNA, with stacking interactions among the nucleotide pairs remaining largely unperturbed and thus retaining overall B-DNA conformation. Our work suggests that photoactivable DNA may be used as a DNA lesion surrogate to study DNA repair mechanisms such as nucleotide excision repair.

Rad4/XPC DNA damage sensor protein specifically binds to a photocleavable NPOM-DNA adduct, and this recognition is abolished upon photo-cleavage of NPOM.

What Makes Thienoguanosine an Outstanding Fluorescent DNA Probe?

Thienoguanosine (^thG) is an isomorphic guanosine (G) surrogate that almost perfectly mimics G in nucleic acids. To exploit its full potential and lay the foundation for future applications, 20 DNA duplexes, where the bases facing and neighboring ^thG were systematically varied, were thoroughly studied using fluorescence spectroscopy, molecular dynamics simulations, and mixed quantum mechanical/molecular mechanics calculations, yielding a comprehensive understanding of its photophysics in DNA. In matched duplexes, ^thG's hypochromism was larger for flanking G/C residues but its fluorescence quantum yield (QY) and lifetime values were almost independent of the flanking bases. This was attributed to high duplex stability, which maintains a steady orientation and distance between nucleobases, so that a similar charge transfer (CT) mechanism governs the photophysics of ^thG independently of its flanking nucleobases. ^thG can therefore replace any G residue in matched duplexes, while always maintaining similar photophysical features. In contrast, the local destabilization induced by a mismatch or an abasic site restores a strong dependence of ^thG's QY and lifetime values on its environmental context, depending on the CT route efficiency and solvent exposure of ^thG. Due to this exquisite sensitivity, ^thG appears ideal for monitoring local structural changes and single nucleotide polymorphism. Moreover, ^thG's dominant fluorescence lifetime in DNA is unusually long (9-29 ns), facilitating its selective measurement in complex media using a lifetime-based or a time-gated detection scheme. Taken together, our data highlight ^thG as an outstanding emissive substitute for G with good QY, long fluorescence lifetimes, and exquisite sensitivity to local structural changes.

Deciphering the pH-dependence of ground- and excited-state equilibria of thienoguanine

The thienoguanine nucleobase (^thG_b) is an isomorphic fluorescent analogue of guanine. In aqueous buffer at neutral pH, ^thG_b exists as a mixture of two ground-state H1 and H3 keto-amino tautomers with distinct absorption and emission spectra and high quantum yield. In this work, we performed the first systematic photophysical characterization of ^thG_b as a function of pH (2 to 12). Steady-state and time-resolved fluorescence spectroscopies, supplemented with theoretical calculations, enabled us to identify three additional ^thG_b forms, resulting from pH-dependent ground-state and excited-state reactions. Moreover, a thorough analysis allowed us to retrieve their individual absorption and emission spectra as well as the equilibrium constants which govern their interconversion. From these data, the complete photoluminescence pathway of ^thG_b in aqueous solution and its dependence as a function of pH was deduced. As the identified forms differ by their spectra and fluorescence lifetime, ^thG_b could be used as a probe for sensing local pH changes under acidic conditions.

Cholesterol Based Surface Active Ionic Liquid That Can Form Microemulsions and Spontaneous Vesicles

In this article, we have reported the synthesis and physicochemical characterization of a novel l-glycine amino acid derived cholesterol based surface active ionic liquid (SAIL). This SAIL has been explored for the preparation of ionic liquid (IL)-in-oil microemulsions and vesicles. The formation of IL-in-oil microemulsion is characterized by construction of a ternary phase diagram, dynamic light scattering (DLS) measurement, proton nuclear magnetic resonance (¹H NMR) study, fluorescence measurement using coumarin 480 (C-480) as a molecular probe, and also by recording the diffusion behavior of the molecular probe rhodamine 6G (R6G) in microemulsion droplets through the fluorescence correlation spectroscopy (FCS) technique. Similarly, the spontaneous vesicle formation from the SAIL in water has been established using DLS, transmission electron microscopy (TEM), cryogenic-transmission electron microscopy (cryo-TEM), field emission scanning electron microscopy (FESEM), atomic force microscopy (AFM), FCS, and fluorescence lifetime imaging microscopy (FLIM) measurements. These aggregates may potentially serve as good biomimicking models and possible drug carriers.

Effect of the submicellar concentration of bile salts on structural alterations of β-casein micelles

The role of bile salts, sodium deoxycholate (NaDC) and sodium cholate (NaCh), on the self-assembly behavior of β-casein micelles (β-CMs) was investigated using various fluorescence techniques.

Spectroscopy and Fluorescence Lifetime Imaging Microscopy To Probe the Interaction of Bovine Serum Albumin with Graphene Oxide

The interaction of graphene oxide (GO) with bovine serum albumin (BSA) in aqueous buffer solution has been investigated with various spectroscopic and imaging techniques. At single molecular resolution this interaction has been performed using fluorescence correlation spectroscopy (FCS) and fluorescence lifetime imaging microscopy (FLIM) techniques. The conformational dynamics of BSA on GO's influence have been explored by FCS and circular dichroism (CD) spectroscopy. For the FCS studies BSA was labeled covalently by a fluorophore, Alexa Fluor 488. On the addition of GO in phosphate buffer of 10 mM at pH 7.4 the diffusion time (τD) and the hydrodynamic radius (Rh) of BSA increase due to adsorption of BSA. Conformational relaxation time components of native BSA drastically vary with the addition of GO, signifying the change of conformational dynamics of BSA after addition of GO. The adsorption isotherm also indicates significant adsorption of BSA on the GO surface. Adsorption of BSA on the GO surface has shown in direct images of atomic force microscopy (AFM) and FLIM. Fluorescence quenching study of BSA with addition of GO also indicates that there is strong interaction between BSA and GO.

How does the surface charge of ionic surfactant and cholesterol forming vesicles control rotational and translational motion of rhodamine 6G perchlorate (R6G ClO₄)?

The rotational dynamics and translational diffusion of a hydrophilic organic molecule, rhodamine 6G perchlorate (R6G ClO4) in small unilamellar vesicles formed by two different ionic surfactants, cetyltrimethylammonium bromide (CTAB) and sodium dodecyl sulfate (SDS), with cholesterol have been investigated using fluorescence spectroscopic methods. Moreover, in this article the formation of vesicle using anionic surfactant, SDS at different cholesterol-to-surfactant molar ratio (expressed by Q value (Q = [cholesterol]/[surfactant])) has also been reported. Visual observation, dynamic light scattering (DLS) study, turbidity measurement, steady state fluorescence anisotropy (r0) measurement, and eventually microscopic images reveal the formation of small unilamellar vesicles in aqueous solution. Also, in this study, an attempt has been made to observe whether the cationic probe molecule, rhodamine 6G (R6G) experiences similar or different microenvironment in cholesterol-SDS and cholesterol-CTAB assemblies with increase in cholesterol concentration. The influence of cholesterol on rotational and translational diffusion of R6G molecules has been investigated by monitoring UV-vis absorption, fluorescence, time-resolved fluorescence anisotropy, and finally fluorescence correlation spectroscopy (FCS) measurements. In cholesterol-SDS assemblies, due to the strong electrostatic attractive interaction between the negatively charged surface of vesicle and cationic R6G molecules, the rotational and diffusion motion of R6G becomes slower. However, in cholesterol-CTAB aggregates, the enhanced hydrophobicity and electrostatic repulsion induces the migration of R6G from vesicle bilayer to aqueous phase. The experimental observations suggest that the surface charge of vesicles has a stronger influence than the hydrophobicity of the vesicle bilayer on the rotational and diffusion motion of R6G molecules.

How does bile salt penetration affect the self-assembled architecture of pluronic P123 micelles? – light scattering and spectroscopic investigations

The triblock copolymer of the type (PEO)₂₀–(PPO)₇₀–(PEO)₂₀ (P123) forms a mixed supramolecular aggregate with different bile salts, sodium deoxycholate (NaDC) and sodium taurocholate (NaTC), having different hydrophobicity.

Modulation of the aggregation properties of sodium deoxycholate in presence of hydrophilic imidazolium based ionic liquid: water dynamics study to probe the structural alteration of the aggregates

In this article, we have investigated the effect of hydrophilic 1-butyl-3-methylimidazolium tetrafluoroborate on the aggregation properties of sodium deoxycholate (NaDC).

Effect of encapsulation of curcumin in polymeric nanoparticles: how efficient to control ESIPT process?

This paper demonstrates the photophysics of curcumin inside polymeric nanoparticles (NPs), which are being recently used as targeted drug delivery vehicles. For this purpose, we have prepared three polymeric NPs by ultrasonication method from three well-defined water-insoluble random copolymers. These copolymers having various degrees of hydrophobicity were synthesized via reversible addition-fragmentation transfer (RAFT) method using styrene and three different functional monomers, namely, 2-hydroxyethyl acrylate, 4-formylphenyl acrylate, and 4-vinylbenzyl chloride. The photophysics of the curcumin molecules inside the polymeric NPs have been monitored by applying tools like steady state and time-resolved fluorescence spectroscopy. An increase in fluorescence intensity along with an increase in the lifetime values indicated a perturbation of the excited state intramolecular proton transfer (ESIPT) process of curcumin inside the polymeric NPs.

Effect of confinement on excited-state proton transfer of firefly's chromophore D-luciferin in AOT reverse micelles

Excited-state intermolecular proton transfer of D-luciferin in reverse micelles has been investigated using steady-state and time-resolved fluorescence spectroscopy measurement. The different polar cores have been chosen for the study of proton transfer dynamics in aerosol-OT (AOT) reverse micelles. It is shown that aqueous reverse micelle is the suitable environment for the photoprotolytic reaction of D-luciferin. The neutral form of the chromophore is present both in ground and excited state at W0 = 0. The proton transfer in nanometer size water pool of water/AOT/n-heptane begins at W0 = 8 and increases with increasing W0 values. However, the intermolecular excited-state proton transfer (ESPT) of D-luciferin is inhibited in nonaquous reverse micelles with DMF and DMSO as a polar core. Thus, the requirement of ESPT of D-luciferin to take place in reverse micelles consists of polar protic solvent like water as a polar core.

Exploring the photophysics of curcumin in zwitterionic micellar system: an approach to control ESIPT process in the presence of room temperature ionic liquids (RTILs) and anionic surfactant

In this manuscript, we have modulated the photophysical properties of curcumin in a zwitterionic (N-hexadecyl-N,N-dimethylammonio-1-propanesulfonate (SB-16)) micellar aggregates with addition of room temperature ionic liquids (RTILs) as well as commonly used anionic surfactant (SDS), using steady-state and time-resolved spectroscopic techniques. To modulate the photophysics, first we studied its interaction with an SB-16 micellar system, then to further exploit its photophysics, three RTILs (EmimES, EmimBS, EmimHS) with variation of alkyl chain lengths as well as SDS were used. It is observed that the rate of degradation of curcumin is drastically decreased after partitioning into the zwitterionic micellar system. It is shown that the dynamics of excited state intramolecular proton transfer (ESIPT) processes can be controlled by using those RTILs and SDS. Our study also reveals that the hindrance of nonradiative processes of curcumin, i.e., ESIPT is more pronounced in the case of RTIL containing a long alkyl chain compared to a small one. However, most interestingly the addition of long chain (dodecyl) anionic surfactant (SDS) promotes the ESIPT process of curcumin. We have also studied the effect of the addition of inorganic salt and compared the results with RTILs. The present work demonstrates an effort to decipher the photophysics of curcumin in zwitterionic micellar systems by monitoring its excited state dynamics.

Spontaneous transition of micelle-vesicle-micelle in a mixture of cationic surfactant and anionic surfactant-like ionic liquid: a pure nonlipid small unilamellar vesicular template used for solvent and rotational relaxation study

The micelle-vesicle-micelle transition in aqueous mixtures of the cationic surfactant cetyl trimethyl ammonium bromide (CTAB) and the anionic surfactant-like ionic liquid 1-butyl-3-methylimidazolium octyl sulfate, [C4mim][C8SO4] has been investigated by using dynamic light scattering (DLS), transmission electron microscopy (TEM), surface tension, conductivity, and fluorescence anisotropy at different volume fractions of surfactant. The surface tension value decreases sharply with increasing CTAB concentration up to ∼0.38 volume fraction and again increases up to ∼0.75 volume fraction of CTAB. Depending upon their relative amount, these surfactants either mixed together to form vesicles and/or micelles, or both of these structures were in equilibrium. Fluorescence anisotropy of 1,6-diphenyl-1,3,5-hexatriene (DPH), incorporated in this system at different composition of surfactant indicates the formation of micelle and vesicle structures. The apparent hydrodynamic diameter of these large multilamellar vesicles is about ∼200 nm-300 nm obtained by DLS measurement and finally confirmed by TEM micrographs. The large multilamellar vesicles are transformed into small unilamellar ones by sonication using a Lab-line instruments probe sonicator with a diameter of ∼90-125 nm. To investigate the heterogeneity, solvent, and rotational relaxation of coumarin-153 (C-153) have been investigated in these unilamellar vesicles by using picosecond time-resolved fluorescence spectroscopic technique. The solvation dynamics of C-153 in these vesicles is found to be biexponential with average time constant ∼580 ps. This indicates the slow relaxation of water molecules in the surfactant bilayer. In accordance with solvation dynamics, fluorescence anisotropy analysis of C-153 in unilamellar vesicles also indicates hindered rotation compared to bulk water.

Fluorescence resonance energy transfer in microemulsions composed of tripled-chain surface active ionic liquids, RTILs, and biological solvent: an excitation wavelength dependence study

In this article we have reported the fluorescence resonance energy transfer (FRET) study in our earlier characterized surface active ionic liquids (SAILs)-containing microemulsion, i.e., N-methyl-N-propylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([P13][Tf2N])/[CTA][AOT]/isopropyl myristate ([IPM]) and N,N,N-trimethyl-N-propylammonium bis(trifluoromethanesulfonyl)imide ([N3111][Tf2N])/[CTA][AOT]/[IPM] microemulsions (Banerjee, C.; Mandal, S.; Ghosh, S.; Kuchlyan, J.; Kundu, N.; Sarkar, N. J. Phys. Chem. B 2013, 117, 3927-3934). The occurrence of effective FRET from the donor, coumarin-153 (C-153) to the acceptor rhodamine 6G (R6G) is evident from the decrease in the steady state fluorescence intensity of the donor with addition of acceptor and subsequent increase in the fluorescence intensity of the acceptor in the presence of donor. The excitation wavelength dependent FRET from C-153 to R6G has also been performed to assess the dynamic heterogeneity of these confined systems. In time-resolved experiments, the significant rise time of the acceptor in the presence of the donor further confirms the occurrence of FRET. The multiple donor-acceptor (D-A) distances, for various microemulsions, obtained from the rise times of the acceptor emission in the presence of a donor can be rationalized from the varying distribution of the donor, C-153, in the different regions of the microemulsion. Time-resolved measurement reveals that with increasing excitation wavelength from 408 to 440 nm, the contribution of the faster rise component of FRET increases significantly due to the close proximity of the C-153 and R6G in the polar region of the microemulsion where occurrence of FRET is very high. Moreover, we have also studied the FRET with variation of R (R = [room temperature ionic liquids (RTILs)]/[surfactant]) and shown that the effect of excitation wavelength on FRET is similar irrespective of R values.

Curcumin in reverse micelle: an example to control excited-state intramolecular proton transfer (ESIPT) in confined media

In this Article, we focused on the modulation of the photophysical properties of curcumin, an anti-cancer drug, in aqueous and nonaqueous reverse micelles of AOT in n-heptane using steady-state and time-resolved fluorescence spectroscopy. The instability of curcumin is a common problem which restricts its numerous applications like Alzheimer disease, HIV infections, cystic fibrosis, etc. Our study reveals that curcumin shows comparatively higher stability after encapsulation into the interfacial region of the reverse micelle. To get a vivid description of the microenvironment, we added hydrogen-bond-donor (HBD) as well as non-hydrogen-bond-donor (NBD) core solvents. For experimental purposes, we used water, ethylene glycol (EG), glycerol (GY) as HBD solvents and N,N-dimethyl formamide (DMF) as a NBD solvent. With increasing amount of core solvents, irrespective of HBD or NBD, the fluorescence intensity and lifetime of curcumin increase with remarkable red-shift inside the reverse micelle. This is attributed to the modulation of the nonradiative rates associated with the excited-state intermolecular hydrogen bonding between the pigment and the polar solvents. We obtained a high partition constant at W0 = 0 (W0 = [core solvent]/[AOT]) which is certainly due to the hydrogen bonding between the negatively charged sulfonate group of AOT and hydroxyl groups of curcumin. Steady-state anisotropy and time-resolved results give an idea about the microenvironment sensed by the curcumin molecules. The red-shift of emission spectra, increase in the value of ET(30), as well as the increase in the fluorescence lifetime were interpreted as being caused by the partition of the probe between the micellar interface and the polar core solvent. Indeed, we show here that it is possible to control the excited state intramolecular proton transfer (ESIPT) process of curcumin by simply changing the properties of the AOT reverse micelle interfaces by choosing the appropriate polar solvents to make the reverse micelle media.

Unique characteristics of ionic liquids comprised of long-chain cations and anions: a new physical insight

We have designed a unique class of surface active ionic liquids (SAILs) and utilized them to prepare IL-in-oil microemulsions as well as large unilamellar vesicles (LUVs). The IL-in-oil microemulsions were characterized by a phase behavior study, regular swelling behavior, and also by spectral shift of coumarin-480 probe molecules. The LUVs were characterized by dynamic light scattering and transmission electron microscope measurements. Our work opens up the possibility of creating a huge number of IL-in-oil microemulsions as well as LUVs simply by replacing the cation of NaAOT with a long chain cation.