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1.
Chemistry ; 30(18): e202303539, 2024 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-38230625

RESUMO

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.


Assuntos
Corantes Fluorescentes , Ácidos Nucleicos , Uridina/química , Corantes Fluorescentes/química , Concentração de Íons de Hidrogênio , Uracila
2.
Org Biomol Chem ; 20(44): 8618-8622, 2022 11 16.
Artigo em Inglês | MEDLINE | ID: mdl-36314563

RESUMO

Oligonucleotides labelled with thiazole orange intercalator and a reporter dye on the same thymine base have been synthesized. The key phosphoramidite (AP-C3 dT) contains an alkyne and amine, enabling dual orthogonal labelling of the nucleobase. Multiple monomers can be added to produce heavily functionalised oligonucleotides. In their DNA and 2'-OMe RNA formats these combination probes display high duplex stability and fluorescence when bound to complementary DNA and RNA.


Assuntos
Corantes Fluorescentes , Oligonucleotídeos , Sondas de Oligonucleotídeos , RNA
3.
J Am Chem Soc ; 142(40): 16999-17014, 2020 10 07.
Artigo em Inglês | MEDLINE | ID: mdl-32915558

RESUMO

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.


Assuntos
Sondas de DNA/química , DNA/química , Corantes Fluorescentes/química , Guanosina/análogos & derivados , Guanosina/química , Cinética , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico , Solventes/química , Espectrometria de Fluorescência , Relação Estrutura-Atividade
4.
Phys Chem Chem Phys ; 22(14): 7381-7391, 2020 Apr 14.
Artigo em Inglês | MEDLINE | ID: mdl-32211689

RESUMO

The thienoguanine nucleobase (thGb) is an isomorphic fluorescent analogue of guanine. In aqueous buffer at neutral pH, thGb 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 thGb 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 thGb 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 thGb in aqueous solution and its dependence as a function of pH was deduced. As the identified forms differ by their spectra and fluorescence lifetime, thGb could be used as a probe for sensing local pH changes under acidic conditions.


Assuntos
Corantes Fluorescentes/química , Guanina/análogos & derivados , Guanina/química , Concentração de Íons de Hidrogênio , Luminescência , Espectrometria de Fluorescência , Água/química
5.
Langmuir ; 33(23): 5891-5899, 2017 06 13.
Artigo em Inglês | MEDLINE | ID: mdl-28514858

RESUMO

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.

6.
Langmuir ; 31(51): 13793-801, 2015 Dec 29.
Artigo em Inglês | MEDLINE | ID: mdl-26646418

RESUMO

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.


Assuntos
Grafite/química , Microscopia de Fluorescência , Sondas Moleculares/química , Soroalbumina Bovina/química , Análise Espectral , Animais , Bovinos , Dicroísmo Circular , Estrutura Molecular , Rodaminas/química , Succinimidas/química
7.
Langmuir ; 31(8): 2310-20, 2015 Mar 03.
Artigo em Inglês | MEDLINE | ID: mdl-25643899

RESUMO

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.


Assuntos
Colesterol/química , Rodaminas/química , Tensoativos/química , Íons/química , Tamanho da Partícula , Rotação , Propriedades de Superfície
8.
Phys Chem Chem Phys ; 17(38): 25216-27, 2015 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-26353033

RESUMO

In this article, we have investigated the effect of a hydrophilic ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim]-BF4), on the aggregation properties of a biological surfactant, sodium deoxycholate (NaDC), in water. In solution, unlike conventional surfactants it shows stepwise aggregation and the effect of the conventional ionic liquid on the aggregation properties is rather interesting. We have observed concentration dependent dual role of the ionic liquid; at their low concentration, the aggregated structure of NaDC reorganizes itself into an elongated rod like structure. However, the aggregated network is disintegrated into small aggregates upon further addition of ionic liquid. TEM (Transmission Electron Microscopy), SEM (Scanning Electron Microscopy) and FLIM (Fluorescence Lifetime Imaging Microscopy) images also confirmed the structural alteration of NaDC upon varying the concentration of the ionic liquid. The proton NMR data indicate that hydrophobic as well as electrostatic interaction is solely responsible for such structural adaptation of NaDC in the presence of an ionic liquid. The host-guest interaction inside the aggregates is monitored using Coumarin-153 (C-153) and the location of C-153 is probed by varying the excitation wavelength from 375 nm to 440 nm and the two binding sites of the aggregates are affected in a different fashion in the presence of ionic liquid. Excitation in the blue region selects the fluorophores which preferably bind to the buried region of the aggregates, whereas 440 nm excitation corresponds to the guest molecules which are exposed to the solvent molecules. The average solvation time of C-153 is increased in the presence of 1.68 wt% [bmim]-BF4 at λexc = 440 nm i.e. the probe molecules relocate themselves to a more restricted region. However, the average solvation time became 2.6 times faster in the presence of 11.2 wt% [bmim]-BF4, which corresponds to a more polar and exposed region. The time resolved anisotropy measurements and polarity determined by pyrene also supported our results in addition to solvation dynamics measurements. In summary, ionic liquids can modulate the host-guest interaction of bile salt aggregates, which can be used as nanocarriers for drug delivery.


Assuntos
Ácido Desoxicólico/química , Líquidos Iônicos/química , Água/química , Cumarínicos/química , Interações Hidrofóbicas e Hidrofílicas , Imidazóis/química , Espectroscopia de Ressonância Magnética , Microscopia Eletrônica de Transmissão , Pirenos/química
9.
Phys Chem Chem Phys ; 17(30): 19977-90, 2015 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-26172987

RESUMO

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. These mixed micellar systems have been investigated through dynamic light scattering (DLS) and other various spectroscopic techniques. DLS measurements reveal that the bile salts penetrate into the core-corona region of the P123 micelle and further addition of bile salts causes formation of a new supramolecular aggregate. Further CONTIN analysis confirms existence of two types of complexes at higher molar ratios of bile salt-P123 (>1 : 3). Due to the bile salt penetration, the polarity of the core-corona region of bile salt-P123 mixed micelle increases which results in red shift in the absorption and emission spectra of coumarin 153 (C153) and coumarin 480 (C480). The rotational diffusion of the hydrophobic probe C153 and a hydrophilic probe C480 has been investigated in these bile salt-P123 mixed systems and for both the probes a decrease in the average reorientation time has been observed. The reason behind this decrease in the average reorientation time is the increase in both polarity and hydration of the core-corona region in these mixed micelles. Moreover, these bile salt-P123 mixed micelles are characterized by fluorescence correlation spectroscopy (FCS) techniques. As hydrophobic solute 4-(dicyanomethylene)-2-methyl-6-(p-dimethylamino-styryl)-4H-pyran (DCM) resides in the core region of the bile salt-P123 mixed micelles, the translational diffusion of DCM becomes faster in these mixed micelles compared to that in pure P123 micelle. However, for cationic probe rhodamine 6G perchlorate (R6G), a totally opposite trend in the translational diffusion coefficients has been observed. Both anisotropy and FCS measurements confirm that bile salts affect the core region of the P123 micelle more than the corona region. Besides, all these characterizations confirm that more hydrophobic NaDC interacts in a better way than NaTC with the P123 micelle.


Assuntos
Micelas , Poloxaleno/química , Cumarínicos/química , Difusão Dinâmica da Luz , Microscopia Eletrônica de Transmissão , Rodaminas/química , Espectrometria de Fluorescência
10.
J Chem Phys ; 142(5): 054505, 2015 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-25662652

RESUMO

In this work, we have investigated the composition dependent anomalous behavior of dimethyl sulfoxide (DMSO)-water binary mixture by collecting the ultrafast solvent relaxation response around a well known solvation probe Coumarin 480 (C480) by using a femtosecond fluorescence up-conversion spectrometer. Recent molecular dynamics simulations have predicted two anomalous regions of DMSO-water binary mixture. Particularly, these studies encourage us to investigate the anomalies from experimental background. DMSO-water binary mixture has repeatedly given evidences of its dual anomalous nature in front of our systematic investigation through steady-state and time-resolved measurements. We have calculated average solvation times of C480 by two individual well-known methods, among them first one is spectral-reconstruction method and another one is single-wavelength measurement method. The results of both the methods roughly indicate that solvation time of C480 reaches maxima in the mole fraction of DMSO XD = 0.12-0.17 and XD = 0.27-0.35, respectively. Among them, the second region (XD = 0.27-0.35) is very common as most of the thermodynamic properties exhibit deviation in this range. Most probably, the anomalous solvation trend in this region is fully guided by the shear viscosity of the medium. However, the first region is the most interesting one. In this region due to formation of strongly hydrogen bonded 1DMSO:2H2O complexes, hydration around the probe C480 decreases, as a result of which solvation time increases.


Assuntos
Dimetil Sulfóxido/química , Solventes/química , Água/química , Absorção Fisico-Química , Cumarínicos/química , Ligação de Hidrogênio , Cinética , Quinolizinas/química , Espectrometria de Fluorescência
11.
Chemphyschem ; 15(16): 3544-53, 2014 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-25195786

RESUMO

The spontaneous micelle-to-vesicle transition in an aqueous mixture of two surface-active ionic liquids (SAILs), namely, 1-butyl-3-methylimidazolium n-octylsulfate ([C4mim][C8SO4]) and 1-dodecyl-3-methylimidazoium chloride ([C12mim]Cl) is described. In addition to detailed structural characterization obtained by using dynamic light scattering, transmission electron microscopy (TEM), and cryogenic TEM techniques, ultrafast fluorescence resonance energy transfer (FRET) from coumarin 153 (C153) as a donor (D) to rhodamine 6G (R6G) as an acceptor (A) is also used to study micelle-vesicle transitions in the present system. Structural transitions of SAIL micelles ([C4mim][C8SO4] or [C12mim]Cl micelles) to mixed SAIL vesicles resulted in significantly increased D-A distances, and therefore, increased timescale of FRET. In [C4mim][C8SO4] micelles, FRET between C153 and R6G occurs on an ultrafast timescale of 3.3 ps, which corresponds to a D-A distance of about 15 Å. As [C4mim][C8SO4] micelles are transformed into mixed micelles upon the addition of a 0.25 molar fraction of [C12mim]Cl, the timescale of FRET increases to 300 ps, which suggests an increase in the D-A distance to 31 Å. At a 0.5 molar fraction of [C12mim]Cl, unilamellar vesicles are formed in which FRET occurs on multiple timescales of about 250 and 2100 ps, which correspond to D-A distances of 33 and 47 Å. Although in micelles and mixed micelles the obtained D-A distances are well correlated with their radius, in vesicles the obtained D-A distance is within the range of the bilayer thickness.

12.
Langmuir ; 30(36): 10834-44, 2014 Sep 16.
Artigo em Inglês | MEDLINE | ID: mdl-25148375

RESUMO

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.


Assuntos
Curcumina/química , Nanopartículas/química , Polímeros/química , Prótons , Interações Hidrofóbicas e Hidrofílicas , Tamanho da Partícula , Polímeros/síntese química , Espectrometria de Fluorescência , Propriedades de Superfície
13.
Phys Chem Chem Phys ; 16(45): 25024-38, 2014 Dec 07.
Artigo em Inglês | MEDLINE | ID: mdl-25327647

RESUMO

The fluorescence and optical properties of membrane potential probes are widely used to measure cellular transmembrane potentials. Hemicyanine dyes are also able to bind to membranes. The spectral properties of these molecules depend upon the charge shift from the donor moiety to the acceptor moiety. Changes in their spectral properties, i.e. absorption and emission maxima or intensities, are helpful in characterizing model membranes, microheterogeneous media, etc. In this article, we have demonstrated the binding interaction of a membrane potential probe, 1-ethyl-2-(4-(p-dimethylaminophenyl)-1,3-butadienyl)-pyridinium perchlorate (LDS 698), with various supramolecular confined environments. The larger dipole moment in the ground state compared to the excited state is a unique feature of hemicyanine dyes. Due to this unique feature, red shifts in the absorption maxima are observed in hydrophobic environments, compared with bulk solvent. On addition of surfactants and CT DNA to an aqueous solution containing LDS 698, significant increase in the emission intensity along with the quantum yield and lifetime indicate partition of the probe molecules into organized assemblies. In the case of the sodium dodecyl sulfate (SDS)-water system, due to interactions between the cationic LDS 698 and the anionic dodecyl sulfate moiety, the fluorescence intensity at ∼666 nm decreases and an additional peak at ∼590 nm appears at premicellar concentration (∼0.20 mM-4.50 mM). But at ∼5.50 mM SDS concentration, the absorbance in the higher wavelength region increases again, indicating encapsulation of the probe in micellar aggregates. This observation indicates that the premicellar aggregation behavior of SDS can also be judged by observing the changes in the UV-vis and fluorescence spectral patterns. The temperature dependent study also indicates that non-radiative deactivation of the dye molecules is highly restricted in the DNA micro-environment, compared with micelles. Besides, we have also investigated the specific interaction of surfactant micelles with DNA. Our observations reveal that, in the presence of CT DNA, LDS 698 interacts exclusively with SDS micelles, but that it preferentially releases from micelles and relocates to DNA surfaces in solutions containing TX-100 micelles.


Assuntos
Alcenos/química , DNA/química , Portadores de Fármacos/química , Potenciais da Membrana , Sondas Moleculares/química , Nanoestruturas/química , Compostos de Piridínio/química , Tensoativos/química , Animais , Butadienos , Carbocianinas/química , Bovinos , Corantes/química , Liberação Controlada de Fármacos , Micelas , Espectrometria de Fluorescência , Propriedades de Superfície , Temperatura
14.
Phys Chem Chem Phys ; 16(32): 17272-83, 2014 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-25018085

RESUMO

This paper describes the intermolecular interactions of gold nanoclusters (Au NCs) with cyanine dyes, namely HITC P, DTTC I, and IR 144. All the cyanine dyes quenched the fluorescence of Au NCs effectively. Steady-state and time-resolved measurements were performed to understand the competition between electron transfer and energy transfer in the Au NCs and cyanine dye system. A significant spectral overlap between the emission spectrum of the Au NCs and the absorption spectrum of cyanine dyes was observed, making both ideal for studying FRET interactions. However, after careful inspection of the steady state spectra and time resolved decays we concluded that photoinduced electron transfer (PET) could be the major pathway to quench the fluorescence intensity of Au NCs. To elucidate the interaction mechanism between Au NCs and cyanine dyes, docking studies were also performed. The docking studies reveal that the quencher molecules, i.e. cyanine dyes, come in close proximity with the 34-cysteine (Cys) in BSA where the Au clusters are located to enable the electron transfer process.


Assuntos
Carbocianinas/química , Corantes/química , Ouro/química , Raios Infravermelhos , Nanoestruturas , Fluorescência , Microscopia Eletrônica de Transmissão
15.
Langmuir ; 29(32): 10066-76, 2013 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-23859437

RESUMO

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.


Assuntos
Compostos de Cetrimônio/química , Imidazóis/química , Líquidos Iônicos/química , Octanos/química , Tensoativos/química , Ânions/química , Cátions/química , Cetrimônio , Hidrodinâmica , Micelas , Estrutura Molecular , Tamanho da Partícula , Rotação , Solventes/química , Propriedades de Superfície , Água/química
16.
Nat Commun ; 13(1): 4865, 2022 08 29.
Artigo em Inglês | MEDLINE | ID: mdl-36038571

RESUMO

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.


Assuntos
Fator 2 de Crescimento de Fibroblastos , RNA de Cadeia Dupla , Animais , Fator 2 de Crescimento de Fibroblastos/metabolismo , Regulação da Expressão Gênica , Mamíferos/genética , Estabilidade de RNA/genética , RNA Antissenso/genética , RNA Antissenso/metabolismo , RNA de Cadeia Dupla/genética
17.
RSC Chem Biol ; 2(2): 523-536, 2021 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-34041491

RESUMO

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.

18.
J Phys Chem B ; 119(6): 2310-22, 2015 Feb 12.
Artigo em Inglês | MEDLINE | ID: mdl-25133782

RESUMO

In this work, we have focused on the supramolecular interactions of a water-soluble host Cucurbit[7]uril (CB[7]) with an excited state intramolecular proton transfer (ESIPT) probe 1'-hydroxy-2'-acetonaphthone (HAN) through steady-state and time-resolved fluorescence measurements. In water HAN is almost nonfluorescent in nature with a very low fluorescence quantum yield (Φ = 0.009). With gradual addition of CB[7] absorption maximum of HAN is red-shifted (292 cm(-1)) and hence confirming the formation of an inclusion complex in the ground state between HAN and CB[7]. Due to this complexation CB[7] offers a hydrophobic microenvironment to the HAN which is completely different from that of homogeneous water. Upon encapsulation into the nanocavity of CB[7], HAN exhibits a 20-fold increase in fluorescence intensity along with a 36 nm (1618 cm(-1)) hypsochromic shift in emission maxima. This hypsochromic shift is an indication about the modulation of excited state photophysical behavior of HAN due to the formation of HAN-CB[7] inclusion complex. Moreover, huge partition coefficient of HAN from water to CB[7] along with a∼ 12-fold increase in fluorescence lifetime confirm the favorable interaction between HAN and CB[7]. We have also observed the stimuli-sensitive (temperature and cationic stimuli) breathing of CB[7] cavity i.e., in the presence of different additives the portals of CB[7] open up to release HAN in water and take up the additives. Time-resolved anisotropy measurements further indicate about the probable location of HAN inside the CB[7]. The observation of a 1.7 ns component in the presence of CB[7] signifies the highly restricted rotational motion of HAN inside the cavity of CB[7] corroborates our finding.


Assuntos
Hidrocarbonetos Aromáticos com Pontes/química , Imidazóis/química , Naftóis/química , Absorção Fisico-Química , Cálcio/química , Polarização de Fluorescência , Líquidos Iônicos/química , Sódio/química , Temperatura
19.
J Phys Chem B ; 119(26): 8285-92, 2015 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-26053544

RESUMO

The stable unilamellar vesicles formation, having large potential applications in biological as well as biomedical fields, has been investigated in aqueous solution composed of a zwitterionic surfactant, N-hexadecyl-N,N-dimethylammonio-1-propanesulfonate (SB-16), and water-soluble cationic poly(amino acid), poly-L-lysine (PLL). Dynamic light scattering (DLS), transmission electron microscopy (TEM), and other optical spectroscopic techniques revealed the transformation of SB-16 micelles in aqueous solutions into stable unilamellar vesicles above a certain concentration (0.008 to 0.1% w/v) of PLL. Solvation and rotational dynamics of coumarin 480 (C-480) give the information on hydration behavior around the headgroup regions of SB-16 micelle and SB-16/PLL vesicle. It was observed that the hydration nature around the headgroup regions of SB-16/PLL vesicular system is higher than the head group regions of micellar system. Thus, PLL permits more water molecules in the headgroup regions of vesicular system.


Assuntos
Micelas , Polilisina/química , Compostos de Amônio Quaternário/química , Cumarínicos/química , Microscopia Crioeletrônica/métodos , Difusão Dinâmica da Luz , Condutividade Elétrica , Microscopia Eletrônica de Transmissão , Nefelometria e Turbidimetria/métodos , Quinolizinas/química , Tensoativos/química , Lipossomas Unilamelares/química
20.
J Phys Chem B ; 118(48): 13946-53, 2014 Dec 04.
Artigo em Inglês | MEDLINE | ID: mdl-25415652

RESUMO

In this article we have investigated intermolecular excited-state proton transfer (ESPT) of firefly's chromophore D-luciferin in DMSO-water binary mixtures using steady-state and time-resolved fluorescence spectroscopy. The unusual behavior of DMSO-water binary mixture as reported by Bagchi et al. (J. Phys. Chem. B 2010, 114, 12875-12882) was also found using D-luciferin as intermolecular ESPT probe. The binary mixture has given evidence of its anomalous nature at low mole fractions of DMSO (below XD = 0.4) in our systematic investigation. Upon excitation of neutral D-luciferin molecule, dual fluorescence emissions (protonated and deprotonated form) are observed in DMSO-water binary mixture. A clear isoemissive point in the time-resolved area normalized emission spectra further indicates two emissive species in the excited state of D-luciferin in DMSO-water binary mixture. DMSO-water binary mixtures of different compositions are fascinating hydrogen bonding systems. Therefore, we have observed unusual changes in the fluorescence emission intensity, fluorescence quantum yield, and fluorescence lifetime of more hydrogen bonding sensitive anionic form of D-luciferin in low DMSO content of DMSO-water binary mixture.


Assuntos
Benzotiazóis/química , Dimetil Sulfóxido/química , Vaga-Lumes/química , Água/química , Animais , Vaga-Lumes/metabolismo , Ligação de Hidrogênio , Prótons , Espectrometria de Fluorescência
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