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An investigation of the photophysical properties of minor groove bound and intercalated molecular probes for nucleic acids, through QM and spectroscopic tools
No full textAn investigation of the photophysical properties of minor groove bound and intercalated DAPI through quantum-mechanical and spectroscopic tools
No full textThe fluorescent probe 4',6-diamidino-2-phenylindole (DAPI) is a dye known to interact with
polynucleotides in a non-univocal manner, both intercalation and minor groove binding modes being
possible, and to specifically change its photophysical properties according to the different
environments. To investigate this behavior, quantum-mechanical calculations using time-dependent
density functional theory (TDDFT), coupled with polarizable continuum and/or atomistic models,
were performed in combination with spectroscopic measurements of the probe in the different
environments, ranging from a homogeneous solution to the minor groove or intercalation pockets of
double stranded nucleic acids. According to our simulation, the electronic transition involves a
displacement of the electron charge towards the external amidine groups and this feature makes the
absorption energies very environment-sensitive while a much smaller sensitivity is seen in the
fluorescence energies. Moreover, the calculations show that the DAPI molecule, when minor groove
bound to the nucleic acid, presents both a reduced geometrical flexibility because of the rigid DNA
pocket and a reduced polarization due to the very ‘‘apolar’’ microenvironment. All these effects can be
used to better understand the observed enhancement of the fluorescence, which makes it an excellent
marker for DNA
Modelling environment effects on intercalating and minor groove-binding molecular probes for nuclear acids: a combined quantum-mechanical and spectroscopic study
No full textFluorescent dyes in the context of DNA-binding: The case of Thioflavin T
No full textThioflavin T (ThT) is a dye characterized by a strong fluorescence light-up on binding to biosubstrates. Although this effect is known to be related to the inhibition of intramolecular torsion on excitation, the binding modes and their role in affecting photoinduced processes are by no means adequately understood. Here, a combined molecular dynamics and quantum chemical modeling is used to study the tuning of the photophysical properties of ThT when moving from solution to DNA binding. The binding mechanism of ThT to B-DNA was found to be very complex as a result of an uncommon interplay between different binding modes, for example, monomer intercalation and external binding but also groove binding of the dimer. The detailed analysis of the relation between the different binding modes and the structural and electronic properties of ThT can be used to better understand the interaction with other biosubstrates
Modelling fluorescence of intercalating and minor groove binding molecular probes for nucleic acids: a combined quantum-mechanical and spectroscopic study
No full textQuantum-mechanical and spectral studies on the Thiazole Orange (TO) fluorophore: dimerisation and DNA intercalation
No full textDespite the unquestionable importance of fluorescent dyes, theoretical studies, aimed to
an in dept understanding of the photophysical characteristics of these molecules, are still
limited. In all cases, at the best of our knowledge, the effects of different environments
have never been considered in a detailed fashion.
In this communication we present a combination of a Time-dependent Density
Functional Theory (TDDFT) study of the absorbance and fluorescence emission
characteristics of the cyanine thiazole orange (TO) free in solution and when intercalated in
DNA with spectro-photometric and -fluorometric experiments under different conditions
(temperature, concentration, solvent viscosity). Moreover, the DH and DS values for TO
dimerisation are evaluated by T-jump experiments.
The comparison between experimental and calculated photo-physical properties shows
that (TD)DFT approaches when combined with spectroscopic measurements represent a valid
strategy not only to reproduce the experimental solvatochromic shifts, induced by both
dimerisation and intercalation in the DNA, but also to rationalize quenching/enhancing of
fluorescence when changing the environment conditions
What is solvatochromism?
No full textSolvatochromism is commonly used in many fields of chemical and biological research to study bulk and local polarity in macrosystems (membranes, etc.), or even the conformation and binding of proteins. Despite its wide use, solvatochromism still remains a largely unknown phenomenon due to the extremely complex coupling of many different interactions and dynamical processes which characterize it. In this study we analyze the influence of different solvents on the photophysical properties of selected charge-transfer probes (4-AP, PRODAN, and FR0). The purpose is to achieve a microscopic understanding of the intermolecular effects which govern the absorption and fluorescence properties of solvated molecular probes, such as solvent-induced structural modifications, polarization effects, solubility, solute-solvent hydrogen-bonding interactions, and solute aggregation. To this aim we have exploited a time dependent density functional theory (TDDFT) approach
coupled to complementary solvation approaches (continuum, discrete and mixed discrete and continuum). Such an integration has allowed us to clearly disentangle the complex interplay between specific and nonspecific interactions of the solvent with the probes and show that strong H-bonding effects not only can lead to large solvatochromic shifts but also can affect the nature of the emitting species with resulting reduction of the quantum yield
Plasmon-Controlled Light-Harvesting: Design Rules for Biohybrid Devices via Multiscale Modeling
No full textPhotosynthesis is triggered by the absorption of light by light-harvesting (LH) pigment−protein complexes followed by excitation energy transfer to the reaction center(s). A promising strategy to achieve control on and to improve light harvesting is to complement the LH complexes with plasmonic particles. Here a recently developed QM/MM/continuum approach is used to investigate the LH process of the peridinin-chlorophyll-protein (PCP) complex on a silver island film. The simulations not only reproduce and interpret the experiments but they also suggest general rules to design novel biohybrid devices; hot-spot configurations in which the LH complex is sandwiched between couples of metal aggregates are found to produce the largest amplifications. Indications about the best distances and orientations are also reported together with illumination and emission geometries of the PCP−NP system necessary to achieve the maximum enhancement
Mechanistic aspects of thioflavin-T self-aggregation and DNA binding: evidence for dimer attack on DNA grooves
Get PDFThioflavin-T (TFT) is a fluorescent marker widely employed in biomedical research but the mechanism of
its binding to polynucleotides has been poorly understood. This paper presents a study of the mechanisms
of TFT self-aggregation and binding to DNA. Relaxation kinetics of TFT solutions show that the cyanine
undergoes dimerization followed by dimer isomerisation. The interaction of TFT with DNA has been
investigated using static methods, such as spectrophotometric and spectrofluorometric titrations under
different conditions (salt content, temperature), fluorescence quenching, viscometric experiments and the
T-jump relaxation method. The combined use of these techniques enabled us to show that the TFT
monomer undergoes intercalation between the DNA base pairs and external binding according to a
branched mechanism. Moreover, it has also been observed that, under dye excess conditions, the TFT
dimer binds to the DNA grooves. The molecular structures of intercalated TFT and the groove-bound
TFT dimer are obtained by performing QM/MM MD simulations
Accurate and Inexpensive Prediction of the Color Optical Properties of Anthocyanins in Solution
No full textThe simulation of the color optical properties of molecular dyes in liquid solution requires the calculation of time evolution of the solute absorption spectra fluctuating in the solvent at finite temperature. Time-averaged spectra can be directly evaluated by combining ab initio CarParrinello molecular dynamics and time-dependent density functional theory calculations. The inclusion of hybrid exchange-correlation functionals, necessary for the prediction of the correct transition frequencies, prevents one from using these techniques for the simulation of the optical properties of large realistic systems. Here we present an alternative approach for the prediction of the color of natural dyes in solution with a low computational cost. We applied this approach to representative anthocyanin dyes: the excellent agreement between the simulated and the experimental colors makes this method a straightforward and inexpensive tool for the high-throughput prediction of colors of molecules in liquid solvents.THEO
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