TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

January 16, 2017 at 4.00 pm in AG-69

Title :

RNA Editing by Adenosine Deaminases

Abstract :

ADARs (adenosine deaminases acting on RNA) are editing enzymes that convert adenosine (A) to inosine (I) in duplex RNA, a modification that has wide-ranging consequences on RNA function including altering miRNA recognition sites, redirecting RNA splicing and changing the meaning of specific codons in mRNA. Recent work has demonstrated a causal link between altered RNA editing and human disease. However, our understanding of the ADAR reaction mechanism, origin of editing site selectivity and the effect of disease-causing mutations was limited by the lack of high-resolution structural data for complexes of ADARs bound to RNA. This presentation will describe the combined chemical biology/structural biology approach used to solve this problem wherein we used RNA bearing a nucleoside analog to trap the reaction intermediate allowing for crystallization of the complexes. Solving the structures of the complexes uncovered ADARs’ use of a unique base-flipping mechanism well-suited for modifying duplex RNA, revealed an ADAR-specific RNA-binding loop near the enzyme active site and explained flanking sequence preferences. In addition, our results provide a structural framework for understanding the effects of ADAR mutations associated with human disease.

January 5, 2017 at 2.30 pm in AG-80

Title :

Design and Application of Sensors for Bioimaging

Abstract :

Over the last two decades, the development and applications of optical chemical sensors and bio-imaging agents have been pursued with great interest by many researchers. There is a tremendous potential for employing such methods in diverse areas, such as the determination of pollutants in the environment or that of bioactive small molecules in living systems. This talk attempts to address three key problems. Firstly, to detect the real time distribution of toxic heavy metals i.e. Hg2+; secondly, to design and synthesise carbon dot-based probes for toxic quinone derivatives; and finally to visualize and quantify monoamine neurotransmitter (MNT) like serotonin (5-HT) and dopamine (DA) in live cells and in living organisms  (e.g. zebrafish). I will talk about how tools of organic synthesis, fluorescence correlation spectroscopy (in solution) and optical imaging methods help us tease out the critical roles of the respective analytes in these model systems. 

January 3, 2017 at 2.30 pm in AG-69

Title :

Electron Transport in Molecular Circuits

Abstract :

The idea of building electronic devices using single molecule as active component was first proposed by Aviram and Ratner in the early seventies. Indeed, molecules are of great interest for application in electronic devices because of their small size, their recognition properties, their ability of self-organization and their possibility of chemical modification and customisation. Thus, the ability to measure and control charge transport across metal/molecule/metal junction is of considerable fundamental interest and represents a key step towards the development of molecular electronic devices.

 

In the first part of my presentation, I will introduce working principle our measurement techniques (i.e STM break junctions (STM-BJ), mechanically controllable break junction (MCBJ) and Conducting probe AFM (CP-AFM) technique).1,2 Using the results from several case studies, I will try to demonstrate a frame work for building a molecular circuit theory based on metal/molecule/metal junctions at single molecular level.2,3,4,5 In the later part of my presentation, I will discuss the results mainly focusing on bottom up fabrication of smart surfaces and exploiting the functionality of these smart surfaces for different applications ranging from molecular electronics to catalysis and energy storage/conversion.5,6 

 

References: 

1. Hong, W.J et al., Beilstein J. Nanotechnol. 2011. 2, 699-713. 

2. Kaliginedi et al., Journal of American chemical society. 2012, 134 (11), 5262–5275. 

3. Seth, C., Kaliginedi et al., Chemical Science. 2016, Accepted (DOI: 10.1039/C6SC03204D). 

4. Moreno-Garcia et al., Journal of American chemical society. 2013, 135(33), 12228−12240. 

5. Kaliginedi et al., Nanoscale. 2015, 7 (42), 17685-17692. 

6. Kaliginedi et al., Science Advances. 2016, under revision.

 

December 13, 2016 at 2.30 pm in AG-69

Title :

Mononuclear copper(II) complexes with the residues in the metal ion binding peptide loop of the CuA center of cytochrome oxidase

 

December 5, 2016 at 4.00 pm in AG-69

Title :

What XAFS can answer for nano-structure? 

Abstract :

X-ray Absorption Fine Structure (XAFS) is unique local structural tool - particularly useful for disordered systems where long-range-order is absent and diffraction/ HRTEM fail to extract details beyond a certain limit. The talk will present characterization and quantification of structural configurations/ defects / oxidation states for wide-ranged nano-systems (bimetallic and semiconductor-metal composite catalysts, semiconductor biosensors, drugs, spintronics, multiferroics, molecular magnetic switches, metallic glass) and their correlation with respective properties of scientific interest. Technical, analytical and sample considerations for the suitability of XAFS for a certain scientific problem and the scope of XAFS at INDUS-2 synchrotron facility (RRCAT) will be addressed. 

November 28, 2016 at 2.30 pm in B-333 (DBS Seminar R00m)

Title :

Probing the Fate of Excitons in Organic Semiconductors

November 21, 2016 at 4.00 pm in AG-69

Title :

Probing Photoinduced Charge Generation in Organic-inorganic Hybrid Perovskites Using Ultrafast Spectroscopy

November 16, 2016 at 2.30 pm in B-333 (DBS Seminar R00m)

Title :

Supramolecular Chemistry: A Tale of a Container  Novel Proposed Materials for Biomedical and Material Applications

Abstract :

Supramolecular chemistry has evolved from the molecular chemistry over the years as the science of “chemistry beyond the molecule”. Molecules are held-together by intermolecular non-covalent interactions in a supramolecular assembly. In this seminar, I will talk about a new water-soluble synthetic supramolecular host named as "octa acid" (OA) as a reaction cavity for manipulating photochemical and photophysical properties of organic molecules. Most of the guest molecules are enclosed within a capsule made of two OA molecules. The interior of OA capsule is benzene-like nonpolar despite the complex being present in water. Additionally, the confined guests are not isolated but can communicate with molecules present in solution. This part will be discussed with photoinduced electron transfer from the donor incarcerated within OA-capsule to the acceptor free in solution as well as to TiO2 semiconductor. 

In the second part, I will propose a novel “support-free iterative” strategy to build a new class of functionally-controlled architecturally diverse macromolecules. With this strategy, I will discuss how we, as chemists, can create functional materials in a rapid, scalable and economic way for diverse biomedical and material applications. In addition, design of a unique supramolecule-based functional devise will be proposed for advanced applications.  

 

November 15, 2016 at 2.30 pm in B-333 (DBS Seminar Room)

Title :

A Novel Class of Sequence-Defined Polymers: Design, Synthesis and Applications

Abstract :

Sequence control is a crucial parameter for tuning the structure, property, and function of synthetic macromolecules. However, achieving precise control of monomer sequence with fast reaction kinetics has been the key hurdle. Herein, I will demonstrate an effort to circumvent this difficulty via a de novo approach for the synthesis of a novel class of sequence-defined polymers, named as oligothioetheramides (oligoTEAs). The oligoTEAs look like the biopolymers in our body, but are instead created with synthetic molecules designed in the lab. This unique approach is based on the strategic design of ‘allyl acrylamide monomer’ with orthogonal reactive sites and a liquid-phase fluorous support. Key strengths of our approach include fast solution kinetics, step-wise characterization via common spectroscopic techniques, and a large structural diversity due to the ease of monomer synthesis. 

By creating these synthetic polymers from the bottom up in an iterative and controlled manner, we can precisely tune their size, composition and properties. We further advanced our synthetic strategy by designing monomers that can afford oligoTEA macrocycles via a one-pot acid catalyzed cascade reaction. With an eye towards biological applications, various bioactive side chains were introduced into the primary sequence. The effects of these side chain and backbone groups on the chemical properties and biological function will be discussed. 

 

November 7, 2016 at 4.00 pm in AG-69

Title :

Form, Function, and Phase Behavior of Intrinsically Disordered Proteins

November 4, 2016 at 2.30 pm in AG-66

Title :

Proteins as Polymers

October 21, 2016 at 2.30 pm. in AG-66

Title :

Design and Synthesis of Polymeric Materials: Structure-Property Relationship via Self-assembly and Biomedical Applications

Abstract :

Design and validation of pericyclic reactions for sensing conformational stretching in polymer materials.

The naphthalene and anthraquinone based fluorescent reporter molecules were synthesized in multistep for monitoring pericyclic reactions in polymers. These reporter molecules were incorporated into polymer backbones by click reactions. The reaction was monitored optically and optimized using organic chemistry characterization techniques. The mechanical force felicitate to bonds to come into proper orientation for claisen reaction to occur. The overall goal of the research is to design, implement, and validate functional groups designed to react specifically within stressed polymer materials to signal the onset of mechanical failure.

 

Design and synthesis of Novel Alternating sulfone copolymers for biomedical applications

Interest in stimulus-responsive polymers and materials has been increasing in recent years. In particular, efforts to apply these polymers for biomedical applications have focused on changing the structure of assemblies and particles in response to both endogenous molecules and externally-applied energy sources to release drugs, activate contrast agents, or initiate fluorescent signal. Sulfur dioxide has been shown to copolymerize with certain vinyl monomers in a specifically alternating manner, provided that the vinyl group is immediately adjacent to an electron-donating group; examples include vinyl acetate, vinyl carbonate, and olefins. The resulting copolymer possesses a low ceiling temperature. The depolymerisation of poly(vinyl acetate-alt- sulfur dioxide) as initiated by chemical stimuli such as reactive oxygen species (ROS) and mechanical stimuli was studied as a proof of concept. Then, a novel class of hydrolytically depolymerizable macromolecules, poly(O-vinyl carbamate-alt-sulfones), were synthesized via free radical polymerization with excellent functional group tolerance. The polymers were then found to form nanoparticles capable of encapsulating both Rhodamine B and Alexa Fluor 488, and the resulting particles were labile at pH > 6. Finally, these particles were found to retain their contents in mucus at pH 5 but release it at pH 8, resulting in an increase in diffusivity of encapsulated fluorophores from very small to matching that of free dye. Current efforts are focused on adapting the polymers and their particles for mucosal drug delivery.

 

During doctoral studies, my research focussed on the self assembling behavior of various pyrene labeled polymers having different architecture like homopolymers, block, and random copolymers, where the pyrene labeling was varied from 1-100%. The photophysical properties were studied using various fluorescence techniques like steady-state and life time decay analysis as well as time resolved emission spectra (TRES). The applicative aspect of the pyrene labeled polymers was also shown by rhodamine dye encapsulation and release studies as a function of temperature and its temperature triggered release was also used as a handle to understand the microstructural changes inside the polymer microcapsule.

 

Thus, the thesis analyses the following important aspects:

 

1.    Exploration of fundamental aspects of the self assembly of different pyrene labelled polymers like block, random or homopolymers by the detailed photophysical analyses

 

2.    Applicative aspects of the pyrene labeled polymers: probed by rhodamine B encapsulation and release.

 

3.    Self assembly behavior in H-bonded versus non-H-bonded polymers at very dilute concentrations: differences and similarities.

 

 4.       Architectural differences among the polymers: probed by TRES and temperature dependent fluorescence.

October 17, 2016 at 4.00 pm in AG-69

Title :

Design and development of optical probes for imaging signal mediating phospholipids

October 3, 2016 at 4.00 pm in AG-69

Title :

 An energy landscape perspective of biomolecular structure and dynamics

 Abstract :

 During the last decade, the concept of energy landscapes has emerged as a unifying theme in seemingly disparate disciplines, such as biomolecular folding and aggregation, self-assembly, and glassy dynamics, and have provided fundamental insight into the thermodynamics and kinetics of complex systems. For many practical applications, it is often sufficient to consider a coarse-grained description of the landscape, in terms of stationary points (energy minima and transition states). This coarse-graining eliminates the need for dynamical sampling, and stationary points on the underlying landscape can be located in a time-independent fashion, exploiting tools of geometry optimisation. This approach offers several key advantages over conventional rare event sampling techniques, particularly for complex landscapes featuring broken ergodicity, and characterised by multiple relaxation time scales. My talk will discuss the methodological aspects of the computational energy landscape framework, and highlight some recent applications to the study of biophysical problems of contemporary interest, such as RNA folding, conformational switching between alternative folds in DNA and peptides, and structural heterogeneity in intrinsically disordered proteins.

September 20, 2016 at 2.30 pm in AG-69

Title :

Nano-bioconjugation of Mutant Cytochrome P450cam for Biocatalysis