Sameena Yousuf

Isolation of Prunin from the fruit shell of Bixa orellana and the effect of β-cyclodextrin on its binding with calf thymus DNA.

Naringenin-7-O-glucoside [Prunin (Pru)] was isolated from the fruit shell of Bixa orellana L. The binding of Pru with calf thymus DNA (ctDNA) and the influence of cyclomaltoheptaose (β-cyclodextrin, β-CD) on the binding were studied by absorption and fluorescence spectroscopic techniques. The comparison of the binding modes of Pru/β-CD and ctDNA-Pru/β-CD suggested that β-CD extracted Pru from DNA for forming inclusion complex. Molecular modeling gave added support to the above results. Fluorescence microscopy was used to visualize the effect of β-CD on the bindings.

The Unusual Fluorescence Quenching of Coumarin 314 by β-Cyclodextrin and the Effect of β-Cyclodextrin on its Binding with Calf Thymus DNA

This paper discusses the binding of a laser dye, Coumarin 314 with β-cyclodextrin, studied mainly by UV-visible spectroscopy, 2D rotating-frame nuclear Overhauser effect spectroscopy (ROESY), steady-state spectroscopy and time-resolved fluorescence spectroscopy. The role of β-cyclodextrin on the binding of Coumarin 314 with calf thymus DNA was investigated. Coumarin 314 shows a hyperchromic shift of absorption and a quenching of fluorescence due to binding with β-cyclodextrin. The fluorescence quenching is non-linear and the reason for the non-linearity is discussed. The unusual fluorescence quenching on Coumarin 314–β-cyclodextrin binding is rationalised from the effect of acidity on absorption, fluorescence, and molecular modelling studies. Additional proof for the mode of binding is given by 2D ROESY. The capped and exposed portions of the Coumarin 314 molecule in the Coumarin 314–β-cyclodextrin complex when binding with calf thymus DNA were visualised based on spectral and molecular modelling studies.

On the accessibility of surface-bound drugs on magnetic nanoparticles. Encapsulation of drugs loaded on modified dextran-coated superparamagnetic iron oxide by β-cyclodextrin.

We report the loading of drugs on aminoethylaminodextran-coated iron oxide nanoparticles, their superparamagnetic behavior, loading of drugs on them, and the β-cyclodextrin-complex formation of the drugs on the surface of the nanoparticles. The magnetic behavior is studied using vibrating sample magnetometry and X-ray photoelectron spectroscopy is used to analyze the elemental composition of drug-loaded nanoparticles. Scanning electron microscopy shows ordered structures of drug-loaded nanoparticles. UV-visible absorption and fluorescence spectroscopy are used to study the binding of the surface-loaded drugs to β-cyclodextrin. All of the drugs form 1:1 host-guest complexes. The iodide ion quenching of fluorescence of free- and iron oxide-attached drugs are compared. The binding strengths of the iron oxide surface-loaded drugs-β-cyclodextrin binding are smaller than those of the free drugs.

Picking Out Logic Operations in a Naphthalene β-Diketone Derivative by Using Molecular Encapsulation, Controlled Protonation, and DNA Binding.

On–off switching and molecular logic in fluorescent molecules are associated with what chemical inputs can do to the structure and dynamics of these molecules. Herein, we report the structure of a naphthalene derivative, the fashion of its binding to β-cyclodextrin and DNA, and the operation of logic possible using protons, cyclodextrin, and DNA as chemical inputs. The compound crystallizes out in a keto-amine form, with intramolecular N−H⋅⋅⋅O bonding. It shows stepwise formation of 1:1 and 1:2 inclusion complexes with β-cyclodextrin. The aminopentenone substituents are encapsulated by β-cyclodextrin, leaving out the naphthalene rings free. The binding constant of the β-cyclodextrin complex is 512 m−1. The pKa value of the guest molecule is not greatly affected by the complexation. Dual input logic operations, based on various chemical inputs, lead to the possibility of several molecular logic gates, namely NOR, XOR, NAND, and Buffer. Such chemical inputs on the naphthalene derivative are examples of how variable signal outputs based on binding can be derived, which, in turn, are dependent on the size and shape of the molecule.

Binding Interactions of Naringenin and Naringin with Calf Thymus DNA and the Role of β-Cyclodextrin in the Binding

The interaction of naringenin (Nar) and its neohesperidoside, naringin (Narn), with calf thymus deoxyribonucleic acid (ctDNA) in the absence and the presence of β-cyclodextrin (β-CD) was investigated. The interaction of Nar and Narn with β-CD/ctDNA was analyzed by using absorption, fluorescence, and molecular modeling techniques. Docking studies showed the existence of hydrogen bonding, electrostatic and phobic interaction of Nar and Narn with β-CD/DNA. 1:2 stoichiometric inclusion complexes were observed for Nar and Narn with β-CD. With the addition of ctDNA, Nar and Narn resulted into the fluorescence quenching phenomenon in the aqueous solution and β-CD solution. The binding constant Kb and the number of binding sites were found to be different for Nar and Narn bindings with DNA in aqueous and β-CD solution. The difference is attributed to the structural difference between Nar and Narn with neohesperidoside moiety present in Narn.

Spectroscopic investigation of interaction of 6-methoxyflavanone and its β-cyclodextrin inclusion complex with calf thymus DNA

The interaction of 6-methoxyflavanone (6MF, 6-methoxy-2-phenyl-4H-1-benzopyran-4-one) with calf thymus DNA (ctDNA) was investigated by absorption spectroscopy, fluorescence spectroscopy, and cyclic voltammetry in the presence and absence of β-cyclodextrin (β-CD) acting as capping agent. Molecular modelling was used to optimise the study of 6MF-β-CD and 6MF-DNA interactions. Enhancement in the fluorescence intensity of 6MF was observed due to the formation of 1 : 1 complex with β-CD. In the presence and absence of DNA, 6MF showed different characteristics such as hyperchromic effect, red shift of absorption spectra and fluorescence quenching of 6MF due to binding between 6MF and ctDNA. The nature of the binding group was found to be different for the 6MF-ctDNA and 6MF-ctDNA-β-CD systems. An increase in fluorescence intensity was observed for the 6MF-ctDNA system while varying the concentration of β-CD due to encapsulation of a part of 6MF in cyclodextrin. The results are compatible with the possibility of the interaction of dihydrobenzopyran-4-one moiety of 6MF with ctDNA as well as with β-CD. Cyclic voltammetric studies confirmed the binding interaction between 6MF and ctDNA in the absence and presence of β-CD and molecular modelling explains the site of the interaction of 6MF with cyclodextrin and ctDNA.

C-hexylpyrogallol[4]arene and β-cyclodextrin as directors of the mode of binding of Coumarin 153 with DNA

The supramolecular interaction between calf thymus DNA (ctDNA) and Coumarin 153 in the presence of β-cyclodextrin (β-CD) or C-hexylpyrogallol[4]arene (C-HPA) was studied. Inclusion complexes of Coumarin 153 with β-CD and C-HPA were characterised by infrared spectroscopy, proton nuclear magnetic resonance spectroscopy and two-dimensional rotating-frame nuclear overhauser effect spectroscopy. The inclusion complexation was further followed by steady-state and time-resolved fluorescence measurements. The influence of β-CD or C-HPA in the binding strength and binding model of C153 with ctDNA was studied by UV–visible, fluorescence and molecular modelling technique. The possible group of interaction of Coumarin 153 with DNA, β-CD and C-HPA was shown by molecular modelling technique.

Chromenone-conjugated magnetic iron oxide nanoparticles. Toward conveyable DNA binders.

Magnetic nanoparticles can transport drug and possibly target cancer. DNA-binding of ligands loaded in dextran coated magnetic nanoparticles, could aid their better target-specific binding. In this work, we report the loading of chromenones onto aminoethylamino-modified dextran coated iron oxide nanoparticles, their loading efficiency, and openness for binding to DNA. The magnetic behavior, the size, and the morphology of the nanoparticles are analyzed. The crystallite size of the magnetic nanoparticles is around 40 nm. The chromenones are present on the surface of the dextran shell, as revealed by their cyclodextrin-binding characteristics, which is a new approach in comprehending the accessibility of the surface-bound molecules by macromolecules. The mode of binding of the chromenones to DNA is not altered on surface loading on dextran shell, although the binding strength is generally diminished, compared to the strength of binding of the free chromenones to DNA.

Loading of chromenones on superparamagnetic iron oxide-modified dextran core–shell nanoparticles: openness to bind to β-cyclodextrin and DNA

This paper presents the loading of chromenones, viz., flavanone, hesperetin, naringenin, coumarin 6 and coumarin 7 onto aminoethylamino-modified dextran-coated superparamagnetic iron oxide core–shell nanoparticles. The chemically modified iron oxide core–shell nanoparticles retain their superparamagnetic behaviour even upon chromenone loading. The accessibility of loaded chromenones to DNA for binding is analysed using UV-visible absorption and fluorescence spectroscopy. β-Cyclodextrin is used as an aid to detect whether the chromenones are buried inside the aminoethylamino-modified dextran-coated superparamagnetic iron oxide core–shell nanoparticle shell or available on the surface to readily bind to the macromolecular target. The stoichiometry of the loaded chromenones with the β-cyclodextrin inclusion complex is 1 : 1 in all cases, except with naringenin which binds to two β-cyclodextrin molecules. Coumarin 7 shows a fluorescence quenching upon binding to calf thymus DNA. This study could improve the understanding of the mode of binding of small molecules loaded on magnetic nanoparticles to DNA.

Chemico-biological interaction of Etravirine and its β-Cyclodextrin complex with macromolecular targets

The interaction of etravirine with β-cyclodextrin is analyzed by UV–visible absorption, infrared, fluorescence, nuclear magnetic resonance, two-dimensional rotational frame nuclear Overhauser effect spectroscopy, and molecular modeling studies. The 4-hydroxy-3, 5-dimethylbenzonitrile moiety is found to take part in the binding. The stoichiometry of the inclusion complex of ET with β-CD is 1:1 with the binding constant of 2.03 × 103 mol−1 dm3. The binding of ET with calf thymus DNA (ctDNA) and bovine serum albumin (BSA) protein is investigated in the presence and the absence of β-CD. Fluorescence enhancement is observed during the binding of ET with ctDNA in the absence of β-CD, whereas in the presence of β-CD, fluorescence quenching is observed. The binding constants of the binding of ET and ET–β-CD to ctDNA are 7.84 × 104 and 4.38 × 104 mol−1 dm3, respectively. The binding constant of the binding of ET and ET–β-CD to BSA are 3.14 × 104 and 1.6396 × 104 mol−1 dm3, respectively. The apparent binding constants between ET–β-CD complex and ctDNA or BSA protein decreases significantly. The numbers of binding sites of interaction of ET with BSA protein and the binding distance between BSA protein and ET the absence and the presence of β-CD differ. β-CD modulates the binding of ET with the macromolecular targets. Graphical abstract β-Cyclodextrin act as carrier of etravirine for the binding with DNA and Protein targets.