Interaction of a Julolidine-Based Neutral Ultrafast Molecular Rotor with Natural DNA: Spectroscopic and Molecular Docking Studies

Abstract

Ultrafast molecular rotors (UMRs) are reported to be one of the best fluorescent sensors to study different microenvironments, including biomolecules. In the present work, we have explored the possibility of application of a julolidine-based neutral UMR, 9-(2,2-dicyano vinyl) julolidine (DCVJ), as a DNA sensor and studied its mode of binding with DNA in detail using spectroscopic and molecular docking techniques. Our spectroscopic studies indicate that association of DCVJ with DNA leads to a very large enhancement in its emission intensity. Detailed investigation reveals that, despite being a neutral molecule, binding of DCVJ with DNA is largely modulated in the presence of salt. Such an unusual salt effect has been explained by invoking the ion-dipole interaction between DCVJ and the phosphate backbone of DNA. The ion-dipole interaction has also been established by studying the interaction of DCVJ with nucleosides. Detailed time-resolved studies show that the twisting motion around the vinyl bond in DCVJ gets retarded to a great extent because of its association with DNA molecules. Through competitive binding studies, it has also been established that DCVJ also binds to DNA through intercalation. Finally, quantum chemical calculations and molecular docking studies have been performed to confirm the mode of binding of DCVJ with DNA.

Exploring the Nucleobase-Specific Hydrophobic Interaction of Cryptolepine Hydrate with RNA and Its Subsequent Sequestration

“…The protonated form of CRYP shows a relatively shorter lifetime of 1.69 ns after excitation at 375 nm. ,, The interaction of the drug with RNA is characterized by a biexponential decay in which the short (major) component closely resembles the lifetime of the unbound drug along with a longer (minor) component reflecting the contribution from the bound counterpart of the drug molecules. It is also noted that with increasing RNA concentration, the amplitude of the longer lifetime component gradually increases with a concomitant decrease of the amplitude of the shorter component, which in turn corresponds to a gradually increasing fraction of bound drug molecules. − The fluorescence quantum yield (Φ f ) of CRYP has been estimated with respect to the standard quantum yield of flavin adenine dinucleotide (FAD) in aqueous medium (Φ f = 0.03) and is found to be in good agreement with the reported literature . The radiative ( k r ) and nonradiative ( k nr ) decay rate constants were then calculated according to the standard equations: k r = Φ f / τ avg and k nr = 1/ τ avg – k r .…”

Cation–dipole interaction that creates ordered ion channels in an anion exchange membrane for fastOH−conduction

“…27,28 Ion-dipole interactions represent another attractive force (electrostatic attraction between an ion and a neutral dipolar molecule), 29,30 where the more substantial interaction strengths (20-200 kJ mol −1 ) are known to significantly contributes to the self-assembly of biological macromolecules such as DNA and proteins. [31][32][33][34] Mimicking the structure of the biological iondipole interactions (and their functions) in polyelectrolyte will potentially yield AEMs containing highly ordered morphologies. As AEMs contain high concentration of cationic sites, incorporation of additional polar segments (containing centrally distributed dipoles) onto the polymer backbones will facilitate cation-dipole interactions, which is expected to regulate the self-assembled morphology of the resulting AEMs.…”

“…For example, hydrogen bonding and π − π stacking commonly have interaction strengths of 5–60 kJ mol −1 and 0–50 kJ mol −1 , respectively 27,28 . Ion‐dipole interactions represent another attractive force (electrostatic attraction between an ion and a neutral dipolar molecule), 29,30 where the more substantial interaction strengths (20–200 kJ mol −1 ) are known to significantly contributes to the self‐assembly of biological macromolecules such as DNA and proteins 31‐34 . Mimicking the structure of the biological ion‐dipole interactions (and their functions) in polyelectrolyte will potentially yield AEMs containing highly ordered morphologies.…”

Synthesis and Derivatization of Julolidine: A Powerful Heterocyclic Structure

“…Some examples include the use of julolidines as probes for measurement of blood viscosity, to photoinduced releasing of neurotransmitter amino acids, and as bio‐image (e.g. DNA, RNA, lysosome, and mitochondrial images) sensors …”