debjani bagchi | Maharaja Sayajirao University of Baroda (original) (raw)

Papers by debjani bagchi

BioNanoScience, Jun 15, 2024

Environmental science and pollution research international, Jul 9, 2024

The European physical journal. Special topics, May 31, 2024

arXiv (Cornell University), Sep 20, 2010

Small angle X-ray scattering (SAXS) studies in poly[2-methoxy-5-(2 '-ethyl-hexyloxy)-1,4-phenylen... more Small angle X-ray scattering (SAXS) studies in poly[2-methoxy-5-(2 '-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV) with varying conjugation, and polyethylene dioxythiophene complexed with polystyrene sulfonate (PEDOT-PSS) in different solvents have shown the important role of -electron conjugation and solvent-chain interactions in controlling the chain conformation and assembly. In MEH-PPV, by increasing the extent of conjugation from 30 to 100 %, the persistence length (l p) increases from 20 to 66 Å. Moreover, a pronounced second peak in the pair distribution function has been observed in fully conjugated chain, at larger length scales. This feature indicates that the chain segments tend to self-assemble as the conjugation along the chain increases. In case of PEDOT-PSS, the chains undergo solvent induced expansion and enhanced chain organization. The clusters formed by chains are better correlated in dimethyl sulfoxide (DMSO) solution than water, as observed in the scattered intensity profiles. The values of radius of gyration and the exponent (water: 2.6, DMSO: 2.31

arXiv (Cornell University), Jul 5, 2020

Effect of microstructures and interactions on segmental dynamics in polyethylene glycol (PEG) sol... more Effect of microstructures and interactions on segmental dynamics in polyethylene glycol (PEG) solution in water is probed with macro-scale oscillatory rheology and micro-scale diffusion of a fluorescent probe. PEG solution fluorescence recovery after photobleaching (FRAP) curves have immobile fractions which increase with PEG concentration, for PEG volume fraction (c) > 0.2, indicating structuring. PEG solution micro-scale diffusion coefficients follow Rouse scaling ~− 0.54 for c < 0.8 (c*=0.03), resembling unentangled neutral polymers in good solvent. Small amount (0.01-1 wt%) nanoclay bentonite (B) in PEG matrix slows down probe diffusion 3-7 times, with heterogeneous dynamics. With 0.01-1 wt% carboxymethyl cellulose (CMC) in PEG matrix, probe diffusion is homogeneous with ~10% enhancement in diffusion time. The macroscale storage modulii (G') for PEG, PEG+B, and PEG + CMC solutions scale as viscous fluid-like power law ω α with α=2 for < −1 , with the terminal relaxation time, followed by short elastic plateau for −1 ≤ ≤ −1. For the regime > −1 , the scaling is a concentration-dependent power law ω α , with α greater than the Rouse scaling of 0.5 for 0.1<c<0.2 PEG solutions. We identify a time scale due to intermolecular interactions in PEG, such that for > −1 , Rouse scaling is recovered. Addition of CMC to PEG restores Rouse scaling. Addition of B gives contributions from both polymer matrix and network of B particles, leading to departure from pure Rouse behaviour. Static microtructural studies reveal clay aggregation due to depletion interactions on increasing the concentration of clay particles in PEG matrix, which leads to a non-monotonic concentration dependence of G' with c at 1 wt% B.

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy

Methods in molecular biology, 2021

The ability of magnetic tweezers to apply forces and measure molecular displacements has resulted... more The ability of magnetic tweezers to apply forces and measure molecular displacements has resulted in its extensive use to study the activity of enzymes involved in various aspects of nucleic acid metabolism. These studies have led to the discovery of key aspects of protein-protein and protein-nucleic acid interaction, uncovering dynamic heterogeneities that are lost to ensemble averaging in bulk experiments. The versatility of magnetic tweezers lies in the possibility and ease of tracking multiple parallel single-molecule events to yield statistically relevant single-molecule data. Moreover, they allow tracking both fast millisecond dynamics and slow processes (spanning several hours). In this chapter, we present the protocols used to study the interaction between E. coli SSB, single-stranded DNA (ssDNA), and E. coli RecQ helicase using magnetic tweezers. In particular, we propose constant force and force modulation assays to investigate SSB binding to DNA, as well as to characteriz...

Nucleic Acids Research, 2019

DEAD-box helicases are involved in all steps of RNA metabolism. They are ATP-dependent RNA bindin... more DEAD-box helicases are involved in all steps of RNA metabolism. They are ATP-dependent RNA binding proteins and RNA-dependent ATPases. They can displace short duplexes, but they lack processivity. Their mechanism and functioning are not clearly understood; classical or bulk biochemical assays are not sufficient to answer these questions. Singlemolecule techniques provide useful tools, but they are limited in cases where the proteins are nonprocessive and give weak signals. We present here a new, magnetic-tweezers-based, single-molecule assay that is simple and that can sensitively measure the displacement time of a small, hybridized, RNA oligonucleotide. Tens of molecules can be analyzed at the same time. Comparing the displacement times with and without a helicase gives insights into the enzymatic activity of the protein. We used this assay to study yeast Ded1, which is orthologous to human DDX3. Although Ded1 acts on a variety of substrates, we find that Ded1 requires an RNA substrate for its ATP-dependent unwinding activity and that ATP hydrolysis is needed to see this activity. Further, we find that only intramolecular single-stranded RNA extensions enhance this activity. We propose a model where ATP-bound Ded1 stabilizes partially unwound duplexes and where multiple binding events may be needed to see displacement.

Nucleic Acids Research, 2018

Most RecQ DNA helicases share a conserved domain arrangement that mediates their activities in ge... more Most RecQ DNA helicases share a conserved domain arrangement that mediates their activities in genomic stability. This arrangement comprises a helicase motor domain, a RecQ C-terminal (RecQ-C) region including a winged-helix (WH) domain, and a 'Helicase and RNase D C-terminal' (HRDC) domain. Singlemolecule real-time translocation and DNA unwinding by full-length Escherichia coli RecQ and variants lacking either the HRDC or both the WH and HRDC domains was analyzed. RecQ operated under two interconvertible kinetic modes, 'slow' and 'normal', as it unwound duplex DNA and translocated on single-stranded (ss) DNA. Consistent with a crystal structure of bacterial RecQ bound to ssDNA by base stacking, abasic sites blocked RecQ unwinding. Removal of the HRDC domain eliminates the slow mode while preserving the normal mode of activity. Unexpectedly, a RecQ variant lacking both the WH and HRDC domains retains weak helicase activity. The inclusion of E. coli ssDNA-binding protein (SSB) induces a third 'fast' unwinding mode four times faster than the normal RecQ mode and enhances the overall helicase activity (affinity, rate, and processivity). SSB stimulation was, furthermore, observed in the RecQ deletion variants, including the variant missing the WH domain. Our results support a model in which RecQ and SSB have multiple interacting modes.

Advanced Materials Research, 2016

Using a fractal analysis approach to study plant leaf venation and stem sections, we find that pl... more Using a fractal analysis approach to study plant leaf venation and stem sections, we find that plants use very intelligent scaffolding strategies to tune mechanical strength of leaves and stems. Within plant organs, specialized types of tissues with different mechanical properties have evolved. Ideally, the biopolymers cellulose, hemicelluloses and lignin present in plant cell walls confer mechanical rigidity to plant tissues, but our studies reveal that the manner these biopolymers are distributed in the tissue matrix hold the key to the mechanical rigidity of the tissues. We have developed an algorithm to determine fractal dimension of the scaffolding matrix and the well-known box counting algorithm to calculate fractal dimensions of leaf venation in high resolution images of reticulate–veined leaves and optical microscope image of cellulose, hemicellulose, and lignin-stained cross sections of Turbina corymbosa. We found that in leaves with reticulate venation, veins form a scaffolding matrix imparting mechanical rigidity to leaves, and have a fractal dimension close to 1.0 for leaves which have less bending resistance, compared to fractal dimensions close to 1.7 for leaves which have higher bending resistance. Deriving this idea from plants, we use evaporation instability to develop scaffolding matrix with fractal dimensions higher than 1.5 in polymer films. This can form the basis of an efficient strategy to devise thin, stand-alone polymer films with tunable bending stiffness.

Nature Communications, 2015

RNA helicases are implicated in most cellular RNA-dependent events. In eukaryotes however, only f... more RNA helicases are implicated in most cellular RNA-dependent events. In eukaryotes however, only few have been functionally characterized. Upf1 is a RNA helicase essential for nonsense-mediated mRNA decay (NMD). Here, using magnetic tweezers and bulk assays, we observe that human Upf1 is able to translocate slowly over long single-stranded nucleic acids with a processivity >10 kb. Upf1 efficiently translocates through double-stranded structures and protein-bound sequences, demonstrating that Upf1 is an efficient ribonucleoprotein complex remodeler. Our observation of processive unwinding by an eukaryotic RNA helicase reveals that Upf1, once recruited onto NMD mRNA targets, can scan the entire transcript to irreversibly remodel the mRNP, facilitating its degradation by the NMD machinery.

Biophysical Journal, 2015

Physica A: Statistical Mechanics and its Applications, 2003

The light scattering measurements that yield the osmotic susceptibility (χT) in a ternary liquid ... more The light scattering measurements that yield the osmotic susceptibility (χT) in a ternary liquid mixture of 3-methylpyridine+water+sodiumbromide are presented. The measurements have been performed in the one-phase region near the lower consolute points TL's of samples with different concentrations (X) of NaBr. The data analysis has been performed by incorporating both one and two correction-to-scaling terms. Results indicate that for

Physica A: Statistical Mechanics and its Applications, 2007

We demonstrate with the aid of visual investigations that multiply reentrant liquid–liquid transi... more We demonstrate with the aid of visual investigations that multiply reentrant liquid–liquid transitions can be obtained in ethyl alcohol (E)–water (W) mixtures, by the addition of ions. Multiplicity of reentrance can be tuned by changing the concentration, size, or the structure forming ability of the ions added. This is a route to the realization of various thermodynamic states, such as special critical points (SCPs), in the vanishing limit of reentrance. We show that in E+W+ ion systems, one can achieve a plait point, a critical double point, a double critical point, and a critical inflection point, in addition to a line of critical points. We adduce evidence for the presence of supramolecular structures and the associated nanoscopic length scale in these systems, by small angle X-ray scattering experiments. Structuring gives rise to the intriguing phase behavior and renders these systems potentially significant to study the role of supramolecular structuring on the approach to asymptotic Ising criticality near SCPs.

Journal of Physics: Condensed Matter, 2009

Small angle X-ray scattering (SAXS) in poly[2-methoxy-5-(2 '-ethyl-hexyloxy)-1,4phenylene vinylen... more Small angle X-ray scattering (SAXS) in poly[2-methoxy-5-(2 '-ethyl-hexyloxy)-1,4phenylene vinylene] (MEH-PPV) solution has shown the important role of -electron conjugation in controlling the chain conformation and assembly. By increasing the extent of conjugation from 30 to 100 %, the persistence length (l p) increases from 20 to 66 Å. Moreover, a pronounced second peak in the pair distribution function has been observed in fully conjugated chain, at larger length scales. This feature indicates that the chain segments tend to self-assemble as the conjugation along the chain increases. Xylene enhances the rigidity of PPV backbone to yield extended structures, while tetrahydrofuran solvates the side groups to form compact coils in which the l p is much shorter.