11 research outputs found
Understanding the unfolding mechanism of human telomeric G-quadruplex using steered molecular dynamics simulationÂ
The unfolding pathway of human telomeric G-quadruplex with three G-tetrads in presence of K+ and Na+ ions, separately using steered molecular dynamics (SMD) simulation is reported. The isothermal-isobaric all-atoms classical molecular dynamics simulation results show that three K+ and three Na+ ions are required within the central channel of the G-quadruplex (PDB ID: 143D and 2HY9, respectively) to stabilize the respective overall structure. To obtain the unfolded G-quadruplex which is ~5-6 times of its initial contour length, SMD simulation has been carried out by fixing one end of the G-quadruplex and constraining the other end to move only along the long axis (z-axis). The SMD results suggest that the unfolding of G-quadruplex occurs via G-triplex intermediates independent of the presence of cations (K+, Na+).
A Thiazole Coumarin (TC) turn-on fluorescence probe for AT-base pair detection and multipurpose applications in different biological systems
Sequence-specific recognition of DNA by small turn-on fluorescence probes is a promising tool for bioimaging, bioanalytical and biomedical applications. Here, the authors report a novel cell-permeable and red fluorescent hemicyanine-based Thiazole Coumarin (TC) probe for DNA recognition, nuclear staining and cell cycle analysis. TC exhibited strong fluorescence enhancement in the presence of DNA containing AT-base pairs, but did not fluoresce with GC sequences, single-stranded DNA, RNA and proteins. The fluorescence staining of HeLa S3 and HEK 293 cells by TC followed by DNase and RNase digestion studies depicted the selective staining of DNA in the nucleus over the cytoplasmic region. Fluorescence-Activated Cell Sorting (FACS) analysis by flow cytometry demonstrated the potential application of TC in cell cycle analysis in HEK 293 cells. Metaphase chromosome and malaria parasite DNA imaging studies further confirmed the in vivo diagnostic and therapeutic applications of probe TC. Probe TC may find multiple applications in fluorescence spectroscopy, diagnostics, bioimaging and molecular and cell biology
Understanding the unfolding mechanism of human telomeric G-quadruplex using steered molecular dynamics simulation
907-912The unfolding pathway of human telomeric G-quadruplex with three G-tetrads in presence of K+ and Na+ ions, separately using steered molecular dynamics (SMD) simulation is reported. The isothermal-isobaric all-atoms classical molecular dynamics simulation results show that three K+ and three Na+ ions are required within the central channel of the G-quadruplex (PDB ID: 143D and 2HY9, respectively) to stabilize the respective overall structure. To obtain the unfolded G-quadruplex which is ~5-6 times of its initial contour length, SMD simulation has been carried out by fixing one end of the G-quadruplex and constraining the other end to move only along the long axis (z-axis). The SMD results suggest that the unfolding of G-quadruplex occurs via G-triplex intermediates independent of the presence of cations (K+, Na+)
Exploring Thioxanthone Derivatives as Singlet Oxygen Photosensitizers for Photodynamic Therapy at the Near-IR Region
In
the lowest excited triplet state, the excited photosensitizer
reacts with tissue oxygen and forms reactive oxygen species (ROS),
which kills tissue cells in photodynamic therapy (PDT). Metal-free
thio-based pure organic molecules and analogous nucleobases can be
used as photosensitizers for PDT applications. Using quantum chemical
methods, we studied one- and two-photon optical absorptions, fluorescence,
and other excited-state properties of substituted thioxanthone derivatives
for their potential as photosensitizers for PDT. Our calculated values
were compared with the available experimental data. The calculation
of the intersystem crossing rate constant for these photosensitizers
explains the high quantum yield of the formation of ROS, as reported
experimentally. The excited triplet-state population of the photosensitizer
occurs through the 1ÏâÏ* â 3nâÏ* channel of intersystem crossing and increases
in the presence of halogen substitution
Tuning of Hyperpolarizability, One- and Two-Photon Absorption of D-A and D-A-A Type Intramolecular Charge Transfer Based Sensors
Solvents play an important role in shaping the
intramolecular charge transfer (ICT) properties of Ï-conjugated molecules,
which in turn can affect their one-photon absorption (OPA) and two-photon
absorption (TPA) as well as the static (hyper)polarizabilities. Here, we study
the effect of solvent and donor-acceptor arrangement on linear and nonlinear
optical (NLO) response properties of two novel ICT-based fluorescent sensors,
one consisting of hemicyanine and dimethylaniline as electron withdrawing and
donating groups (molecule 1), respectively and its boron-dipyrromethene
(BODIPY, molecule 2)-fused counterpart (molecule 3). Density functional
theoretical (DFT) calculations using long-range corrected CAM-B3LYP and M06-2X
functionals, suitable for studying properties of ICT molecules, are employed to
calculate the desired properties. The dipole moment (”) as well as the total
first hyperpolarizability (ÎČtotal) of the studied molecules in the
gas phase is dominantly dictated by the component in the direction of charge
transfer. The ratios of vector component of first hyperpolarizability (ÎČvec)
to ÎČtotal also reveal unidirectional charge transfer process. The
properties of the medium significantly affect the OPA, hyperpolarizability and
TPA properties of the studied molecules. Time dependent DFT (TDDFT)
calculations suggest interchanging between two lowest excited states of molecule 3 from the gas phase to
salvation. The
direction of charge polarization and dominant transitions among molecular
orbitals involved in the OPA and TPA processes are studied. The results
presented are expected to be useful in tuning the NLO response of many
ICT-based chromophores, especially those with BODIPY acceptors.<br /
Computational studies on structural and optical properties of single-stranded DNA encapsulated silver/gold clusters
Using a combined approach of molecular dynamics (MD) and density functional theoretical (DFT) calculations, we perform the investigation of structures, energetics and optical properties of Ag12 and Au12 clusters in the presence of single-stranded DNA (ssDNA) scaffold of various nucleobase sequences (i.e. ssdA12, ssdT12, ssdG12 and ssdC12). The individual ssDNA undergoes various conformational changes in the presence of different metal clusters during the course of 1.5 ns MD simulations in aqueous media. We find that ssdG12 interacts strongly with the Ag12 cluster while ssdA12 shows greater binding affinity towards the Au12 cluster. We also find that the two different kinds of binding modes of a nucleobase play a key role in deciding the overall structure and stability of the complex while interacting with metal clusters. The metal clusters form nanocomposites with ssDNA either via p-stacking and/or by the interaction mediated through specific atoms (nitrogen and/or oxygen) present in the nucleobases. The optical response properties of these Ag12/Au12-ssDNA composites together with the bare metal clusters are calculated with the MD simulated structures alone, which are comparable with experimental results. The optical absorption characteristics of metal clusters are little affected by the presence of ssDNA scaffold due to the frontier orbital localization mainly on the metal clusters or ssDNA
Understanding the Binding Mechanism of Various Chiral SWCNTs and ssDNA: A Computational Study
Molecular dynamics (MD) simulations have been carried
out to understand
the binding mechanism of various chiral single-walled carbon nanotubes
(SWCNTs) and single-stranded DNA (ssDNA) of four different nucleobase
sequences (i.e., ssdA<sub>14</sub>, ssdT<sub>14</sub>, ssdG<sub>14</sub>, and ssdC<sub>14</sub>, where, A, T, G, and C are adenine, thymine,
guanine, and cytosine, respectively) in aqueous media at room temperature
(300 K) and atmospheric pressure (1 atm). The simulations studies
reveal that ssDNA undergoes rapid structural changes and wrap around
the SWCNTs via Ï-stacking interactions between SWCNTâs
wall and the nucleobases of ssDNA. Our computations demonstrate that
the length of the ssDNA plays an important role during the wrapping
process. Moreover, it suggests that the length of the sequence should
be proportional to the diameter of the SWCNT, in order to overcome
the intralocked Ï-stacking interactions between the nucleobases
of ssDNA sequence. Also, in our classical MD simulation, we do not
observe the correlation between the diameter of SWCNTs and the sequences
of ssDNA, which indicates the importance of electronic factors of
these systems. In order to understand the electronic contributions
of these systems, the quantum calculations have been performed at
HartreeâFock level for the 17 ns MD simulated structures. The
quantum chemical calculations provide evidence that the highly stable
ssDNA@SWCNT hybrid possesses a larger HOMOâLUMO gap
Up-Conversion Intersystem Crossing Rates in Organic Emitters for Thermally Activated Delayed Fluorescence: Impact of the Nature of Singlet vs Triplet Excited States
The rates for up-conversion
intersystem crossing (UISC) from the
T<sub>1</sub> state to the S<sub>1</sub> state are calculated for
a series of organic emitters with an emphasis on thermally activated
delayed fluorescence (TADF) materials. Both the spinâorbit
coupling and the energy difference between the S<sub>1</sub> and T<sub>1</sub> states (Î<i>E</i><sub>ST</sub>) are evaluated,
at the density functional theory (DFT) and time-dependent DFT levels.
The calculated UISC rates and Î<i>E</i><sub>ST</sub> values are found to be in good agreement with available experimental
data. Our results underline that small Î<i>E</i><sub>ST</sub> values and sizable spinâorbit coupling matrix elements
have to be simultaneously realized in order to facilitate UISC and
ultimately TADF. Importantly, the spatial separation of the highest
occupied and lowest unoccupied molecular orbitals of the emitter,
a widely accepted strategy for the design of TADF molecules, does
not necessarily lead to a sufficient reduction in Î<i>E</i><sub>ST</sub>; in fact, either a significant charge-transfer (CT)
contribution to the T<sub>1</sub> state or a minimal energy difference
between the local-excitation and charge-transfer triplet states is
required to achieve a small Î<i>E</i><sub>ST</sub>. Also, having S<sub>1</sub> and T<sub>1</sub> states of a different
nature is found to strongly enhance spinâorbit coupling, which
is consistent with the El-Sayed rule for ISC rates. Overall, our results
indicate that having either similar energies for the local-excitation
and charge-transfer triplet states or the right balance between a
substantial CT contribution to T<sub>1</sub> and somewhat different
natures of the S<sub>1</sub> and T<sub>1</sub> states, paves the way
toward UISC enhancement and thus TADF efficiency improvement
Enhancing Selectivity and Kinetics in Oxidative Photocyclization by Supramolecular Control
International audiencePhotochemical reactions typically proceed via multiple reaction pathways, yielding a variety of isomers and products. Enhancing the selectivity is challenging. Now, the potential of supramolecular control for oxidative photocyclization of a tetraarylethylene, containing a stereogenic -C=C- bond, is demonstrated. In solution, this photochemical reaction produces three constitutional isomers (substituted phenanthrenes), with slow kinetics. When the reactant is assembled into a crystalline framework, only one product forms with accelerated kinetics. Key to this selectivity enhancement is the integration into a surface grown metal-organic framework (SURMOF); the dramatic gain in selectivity is ascribed to the hindrance of the rotational freedom of the -C=C- double bond. The structure of the MOF is key; the corresponding reaction in the solid does not result in such a high increase in selectivity. A striking change of luminescence properties after photocyclization is observed