Ultrafast Dynamics of Solvation and Charge Transfer in a DNA‐Based Biomaterial

Choudhury, Samiran; Batabyal, Subrata; Mondol, Tanumoy; Sao, Dilip; Lemmens, P.; Pal, Samir Kumar

doi:10.1002/asia.201400062

Cited by 19 publications

(18 citation statements)

References 61 publications

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“…All the picosecond‐resolved fluorescence transients were measured by using a commercially available time‐correlated single‐photon counting (TCSPC) setup with MCP‐PMT from Edinburgh Instrument, UK [instrument response function (IRF) ≈75 ps] using a 375 nm excitation laser source. Details of the time‐resolved fluorescence setup have been discussed in our previous reports . For fluorescence anisotropy measurements, the emission polarizer was adjusted to be parallel and perpendicular to that of the excitation beam, and the corresponding fluorescence transients were collected as I para and I per , respectively.…”

Section: Methodsmentioning

confidence: 99%

Modulation of Kinetic Pathways of Enzyme–Substrate Interaction in a Microfluidic Channel: Nanoscopic Water Dynamics as a Switch

Singh

Mukherjee

Singha

et al. 2019

Chemistry A European J

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Enzyme‐mediated catalysis is attributed to enzyme–substrate interactions, with models such as “induced fit” and “conformational selection” emphasizing the role of protein conformational transitions. The dynamic nature of the protein structure, thus, plays a crucial role in molecular recognition and substrate binding. As large‐scale protein motions are coupled to water motions, hydration dynamics play a key role in protein dynamics, and hence, in enzyme catalysis. Here, microfluidic techniques and time‐dependent fluorescence Stokes shift (TDFSS) measurements are employed to elucidate the role of nanoscopic water dynamics in the interaction of an enzyme, α‐Chymotrypsin (CHT), with a substrate, Ala‐Ala‐Phe‐7‐amido‐4‐methylcoumarin (AMC) in the cationic reverse micelles of benzylhexadecyldimethylammonium chloride (BHDC/benzene) and anionic reverse micelles of sodium bis(2‐ethylhexyl)sulfosuccinate (AOT/benzene). The kinetic pathways unraveled from the microfluidic setup are consistent with the “conformational selection” fit for the interaction of CHT with AMC in the cationic reverse micelles, whereas an “induced fit” mechanism is indicated for the anionic reverse micelles. In the cationic reverse micelles of BHDC, faster hydration dynamics (≈550 ps) aid the pathway of “conformational selection”, whereas in the anionic reverse micelles of AOT, the significantly slower dynamics of hydration (≈1600 ps) facilitate an “induced fit” mechanism for the formation of the final enzyme–substrate complex. The role of water dynamics in dictating the mechanism of enzyme–substrate interaction becomes further manifest in the neutral reverse micelles of Brij‐30 and Triton X‐100. In the former, the faster water dynamics aid the “conformational selection” pathway, whereas the significantly slower dynamics of water molecules in the latter are conducive to the “induced fit” mechanism in the enzyme–substrate interaction. Thus, nanoscopic water dynamics act as a switch in modulating the pathway of recognition of an enzyme (CHT) by the substrate (AMC) in reverse micelles.

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Section: Methodsmentioning

confidence: 99%

Modulation of Kinetic Pathways of Enzyme–Substrate Interaction in a Microfluidic Channel: Nanoscopic Water Dynamics as a Switch

Singh

Mukherjee

Singha

et al. 2019

Chemistry A European J

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“…26 The average lifetime (amplitude-weighted) of a multi-exponential decay is expressed as t av ¼ P N i¼1 c i t i . It should be noted that we can resolve at least one quarter of the instrument response time constants with our time resolved instrument after the de-convolution of the IRF.…”

Section: Methodsmentioning

confidence: 99%

“…26 Time-resolved area normalised emission spectra (TRANES) were constructed following an earlier work. 26 Time-resolved area normalised emission spectra (TRANES) were constructed following an earlier work.…”

Section: Methodsmentioning

confidence: 99%

Ultrafast differential flexibility of Cro-protein binding domains of two operator DNAs with different sequences

Choudhury

Ghosh

Singh

et al. 2016

Phys. Chem. Chem. Phys.

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The nature of the interface of specific protein-DNA complexes has attracted immense interest in contemporary molecular biology. Although extensive studies on the role of flexibility of DNA in the specific interaction in the genetic regulatory activity of lambda Cro (Cro-protein) have been performed, the exploration of quantitative features remains deficient. In this study, we have mutated (site directed mutagenesis: SDM) Cro-protein at the 37th position with a cysteine residue (G37C) retaining the functional integrity of the protein and labelled the cysteine residue, which is close to the interface, with a fluorescent probe (AEDANS), for the investigation of its interface with operator DNAs (OR3 and OR2). We have employed picosecond resolved polarization gated fluorescence spectroscopy and the well known strategy of solvation dynamics for the exploration of physical motions of the fluorescent probes and associated environments, respectively. Even though this particular probe on the protein (AEDANS) shows marginal changes in its structural flexibility upon interaction with the DNAs, a non-covalent DNA bound probe (DAPI), which binds to the minor groove, shows a major differential alteration in the dynamical flexibility in the OR3-Cro complex when compared to that of the OR2 complex with the Cro-protein. We attempt to correlate the observed significant structural fluctuation of the Cro-protein binding domain of OR3 for the specificity of the protein to the operator DNA.

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“…[27,28] For the fluorescence anisotropy measurements, the emission polarizer was adjusted to be parallel and perpendicular to that of the excitation and the corresponding fluorescence transients are collected as I para and I per , respectively. All the picosecond resolved fluorescence transients were measured by using commercially available timecorrelated single-photon counting (TCSPC) setup with MCP-PMT from Edinburgh instrument, U.K. (instrument response function (IRF) of~75 ps) using a 375 nm excitation laser source.…”

Section: Characterization Techniquesmentioning

confidence: 99%

Modulation of Solvation and Molecular Recognition of a Lipid Bilayer under Dynamical Phase Transition

et al. 2018

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It is well accepted in contemporary biology that an ∼30 Å thick lipid bilayer film around living cells is a matter of life and death as the film typically delimits the environments that serve as a crucial margin. The dynamic organization of lipid molecules both across the lipid bilayer and in the lateral dimension are known to be crucial for cellular transport and molecular recognition by important biological macromolecules. Here, we study dilute (20 mM) Dioctadecyldimethylammonium bromide (DODAB) vesicles at different temperatures in aqueous dispersion with well-defined phases namely liquid crystalline, gel and subgel. The spectroscopic studies on two fluorescent probes 8-anilino-1-naphthalene sulfonic acid ammonium salt (ANS) and Coumarin 500 (C500), former in the head group region of the lipid-water interface and later located deeper in the lipid bilayer follow dynamics (solvation and fluidity) of their local environments in the vesicles. Binding of an anti-tuberculosis drug rifampicin has also been studied employing Förster resonance energy transfer (FRET) technique. The molecular insight concerning the effect of dynamical organization of the lipid molecules on the local dynamics of aqueous environments in different phases leading to molecular recognition becomes evident in our study.

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Ultrafast Dynamics of Solvation and Charge Transfer in a DNA‐Based Biomaterial

Cited by 19 publications

References 61 publications

Modulation of Kinetic Pathways of Enzyme–Substrate Interaction in a Microfluidic Channel: Nanoscopic Water Dynamics as a Switch

Modulation of Kinetic Pathways of Enzyme–Substrate Interaction in a Microfluidic Channel: Nanoscopic Water Dynamics as a Switch

Ultrafast differential flexibility of Cro-protein binding domains of two operator DNAs with different sequences

Modulation of Solvation and Molecular Recognition of a Lipid Bilayer under Dynamical Phase Transition

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