Assessing the Suitability of a Dicationic Ionic Liquid as a Stabilizing Material for the Storage of DNA in Aqueous Medium.

The present study has been undertaken with an objective to find out a suitable medium for the long-term stability and storage of the ct-DNA structure in aqueous solution. For this purpose, the potential of a pyrrolidinium-based dicationic ionic liquid (DIL) in stabilizing ct-DNA structure has been investigated by following the DNA-DIL interaction. Additionally, in order to understand the fundamental aspects regarding the DNA-DIL interaction in a comprehensive manner, studies are also done by employing structurally similar monocationic ionic liquids (MILs). The investigations have been carried out both at ensemble-average and single molecular level by using various spectroscopic techniques. The molecular docking study has also been performed to throw more light into the experimental observations. The combined steady-state and time-resolved fluorescence, fluorescence correlation spectroscopy, and circular dichroism measurements have demonstrated that DILs can effectively be used as better storage media for ct-DNA as compared to MILs. Investigations have also shown that the extra electrostatic interaction between the cationic head group of DIL and the phosphate backbone of DNA is primarily responsible for providing better stabilization to ct-DNA, retaining its native structure in aqueous medium. The outcomes of the present study are also expected to provide valuable insights in designing new polycationic IL systems that can be used in nucleic acid-based applications.

Conformational changes of GDNF-derived peptide induced by heparin, heparan sulfate, and sulfated hyaluronic acid - Analysis by circular dichroism spectroscopy and molecular dynamics simulation.

Glial-cell-line-derived neurotrophic factor (GDNF) is a protein that has therapeutic potential in the treatment of Parkinson's disease and other neurodegenerative diseases. The activity of GDNF is highly dependent on the interaction with sulfated glycans which bind at the N-terminus consisting of 19 residues. Herein, we studied the influence of different glycosaminoglycan (i.e., glycan; GAG) molecules on the conformation of a GDNF-derived peptide (GAG binding motif, sixteen amino acid residues at the N-terminus) using both experimental and theoretical studies. The GAG molecules employed in this study are heparin, heparan sulfate, hyaluronic acid, and sulfated hyaluronic acid. Circular dichroism spectroscopy was employed to detect conformational changes induced by the GAG molecules; molecular dynamics simulation studies were performed to support the experimental results. Our results revealed that the sulfated GAG molecules bind strongly with GDNF peptide and induce alpha-helical structure in the peptide to some extent.

Molecular interactions of MnO2@RGO (manganese dioxide-reduced graphene oxide) nanocomposites with bovine serum albumin.

Graphene based materials have attracted global attention due to their excellent properties. GO-metal oxide nanocomposites have been conjugated with biomolecules for the development of novel materials and potentially used as biomarkers. Herein, a detailed study on the interaction of Bovine serum albumin (BSA) with MnO2@RGO (manganese dioxide-reduced graphene oxide) nanocomposites (NC) has been carried out. MnO2@RGO nanocomposites were prepared through a template/surfactant free hydrothermal route at 180 °C for 12 h by varying the graphene oxide (GO) concentration. Different biophysical experiments have been carried out to evaluate molecular interactions between BSA and NCs. Intrinsic fluorescence has been used to quantify the quenching efficiency of NCs and the binding association of BSA-NC complexes. NCs effectively quenched the intrinsic fluorescence of BSA via static and dynamic mechanism. Further, the results indicate that the molecular interactions of NC with BSA are dependent on the GO percentage in NC. Circular dichroism results demonstrate nominal changes in the secondary structure of BSA in presence of NCs. Also, the esterase-like activity of BSA was marginally affected after adsorption upon NCs. In addition, the FESEM micrographs reveal that the protein-NC complexes consist of nanorod and sheet-like morphologies are forming aggregates of different sizes. We hope that this study will provide a basis for the design of novel graphene based and other related nanomaterials for several biological applications.Communicated by Ramaswamy H. Sarma.

Insights into the binding interaction between copper ferrite nanoparticles and bovine serum albumin: An effect on protein conformation and activity.

The binding affinity between bovine serum albumin (BSA) and copper ferrite (CuFe2 O4 ) nanoparticles in terms of conformation, stability and activity of protein was studied using various spectroscopic methods. The quenching involved in BSA-CuFe2 O4 NP interaction was static quenching as analysed by different techniques (steady-state and time-resolved fluorescence along with temperature-dependent fluorescence measurements). Among all types of possible interactions, it was revealed that the major binding forces were van der Waals interaction and hydrogen bonding, which were explored from negative values of enthalpy change (∆H = -193.85 kJ mol-1 ) and entropy change (∆S = -588.88 J mol-1  K-1 ). Additionally, synchronous, circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopy measurements confirmed the conformational changes in BSA upon the addition of CuFe2 O4 NP. Furthermore, thermal denaturation observations were consistent with the circular dichroism results. The interaction of CuFe2 O4 NP with BSA decreased the esterase activity in the BSA assay, revealing the affinity of copper ferrite towards the active site of BSA.

Exploring the effect of 5-Fluorouracil on conformation, stability and activity of lysozyme by combined approach of spectroscopic and theoretical studies.

In this present work, a detailed investigation of the effect of an anticancer drug, 5-Fluorouracil (5-FU), on conformation, stability and activity of lysozyme (Lyz) was reported. The interaction between Lyz and 5-FU was reflected in terms of intrinsic fluorescence quenching and change in secondary structure of Lyz. The mode of quenching mechanism involved was evaluated by the steady-state and time-resolved fluorescence measurements. Synchronous and Circular Dichroism (CD) results revealed the conformational changes induced in Lyz upon complexation with 5-FU. Additionally, the effect of temperature and chemical denaturant on the stability of Lyz-5FU complex was carried out. As well as the activity of Lyz in the absence and presence of 5-FU were measured using Micrococcus luteus strain. To support our experimental findings, in vitro interaction between Lyz and 5-FU was done by theoretical studies. The current study will provide a better understanding on the nature of the interactions possible between proteins and drug molecules, which might create a bench mark in medical science in terms of the toxic effect or biological benefits of drug molecules on protein structure and conformation.

Molecular level insight into the effect of triethyloctylammonium bromide on the structure, thermal stability, and activity of Bovine serum albumin.

Understanding the interactions between protein and ionic liquids (IL) is vital in order to avail the ILs in biological applications. In this study, we have investigated the influence of triethyloctylammonium bromide on the structure, stability, and activity of Bovine Serum Albumin (BSA) using different spectroscopic methods Fluorescence and circular dichroism measurements revealed that BSA appears to be in a non-native compact structure in the presence of IL (up to concentration 0.02M). But beyond that limit (0.02M), the protein was found to be in an unfolded state. The results are supported by dynamic light scattering (DLS) measurements and also esterase-like activity test proves non-native or unfolded form of protein at a higher concentration of IL. In addition, molecular docking study is carried out to find the possible binding sites of IL with BSA.

A Spectroscopic and Molecular Simulation Approach toward the Binding Affinity between Lysozyme and Phenazinium Dyes: An Effect on Protein Conformation.

A comparative study of binding interaction between Safranin O (SO) and Neutral Red (NR) with lysozyme (Lyz) has been reported using several spectroscopic methods along with computational approaches. Steady-state fluorescence measurements revealed static quenching as the major quenching mechanism in Lyz-SO and Lyz-NR interaction, which is further supported by time-resolved fluorescence and UV-vis measurements. Additionally, binding and thermodynamic parameters of these interactions are calculated from temperature dependent fluorescence data. Moreover, conformational changes of protein upon binding with SO and NR are provided by synchronous and circular dichroism (CD) measurements. Molecular docking study provided the exact binding location of SO and NR in lysozyme. Along with this study, molecular dynamics simulation is carried out to measure the stability of Lyz, Lyz-SO, and Lyz-NR complex. The present study revealed the strong binding affinity of dyes with lysozyme, and this study would be helpful toward medical and environmental science.

Spectroscopic insight into the interaction of bovine serum albumin with imidazolium-based ionic liquids in aqueous solution.

The study of protein-ionic liquid interactions is very important because of the widespread use of ionic liquids as protein stabilizer in the recent years. In this work, the interaction of bovine serum albumin (BSA) with different imidazolium-based ionic liquids (ILs) such as [1-ethyl-3-methyl-imidazolium ethyl sulfate (EmimESO4 ), 1-ethyl-3-methyl-imidazolium chloride (EmimCl) and 1-butyl-3-methyl-imidazolium chloride (BmimCl)] has been investigated using different spectroscopic techniques. The intrinsic fluorescence of BSA is quenched by ILs by the dynamic mechanism. The thermodynamic analysis demonstrates that very weak interactions exist between BSA and ILs. 8-Anilino-1-naphthalenesulfonic acid (ANS) fluorescence and lifetime measurements reveal the formation of the compact structure of BSA in IL medium. The conformational changes of BSA were monitored by CD analysis. Temperature-dependent ultraviolet (UV) measurements were done to study the thermal stability of BSA. The thermal stability of BSA in the presence of ILs follows the trend EmimESO4  > EmimCl > BmimCl and in the presence of more hydrophobic IL, destabilization increases rapidly as a function of concentration.

Interaction of Lysozyme with Rhodamine B: A combined analysis of spectroscopic & molecular docking.

The interaction of Rhodamine B (RB) with Lysozyme (Lys) was investigated by different optical spectroscopic techniques such as absorption, fluorescence, and circular-dichroism (CD), along with molecular docking studies. The fluorescence results (including steady-state and time-resolved mode) revealed that the addition of RB effectively causes strong quenching of intrinsic fluorescence in Lysozyme and mostly, by the static quenching mechanism. Different binding and thermodynamic parameters were calculated at different temperatures and the binding constant value was found to be 2963.54Lmol(-1) at 25°C. The average distance (r0) was found to be 3.31nm according to Förster's theory of non-radiative energy transfer between Lysozyme and RB. The conformational change in Lysozyme during interaction with RB was confirmed from absorbance, synchronous fluorescence, and circular dichroism measurements. Finally, molecular docking studies were done to confirm that the dye binds with Lysozyme.