sanjoy singh - Academia.edu (original) (raw)
Papers by sanjoy singh
European Journal of Chemistry, 2010
Fluorescence behavior of intramolecular charge transfer probe trans-ethyl-p-(dimethylamino) cinna... more Fluorescence behavior of intramolecular charge transfer probe trans-ethyl-p-(dimethylamino) cinnamate (EDAC) is extremely sensitive to the local environment. This study explores the interaction of EDAC with several Igepal, Brij and Tween series of non-ionic surfactants by steady state and picoseconds time-resolved fluorescence spectroscopy. The physico-chemical properties, like critical micelle concentration and micropolarity of the micellar media surrounding the probe were determined. In most of the cases, the observed values were in good agreement with the data reported in the literature. Results obtained from time-resolved fluorescence experiments show a substantial reduction in total nonradiative decay rate of the probe in micellar medium compared to that in aqueous phase. This indicates preferential association of the probe inside the micellar core. The association constant of the probe-micelle interaction was also evaluated in different cases. Fluorescence Non-ionic surfactants Intramolecular charge transfer CMC Micropolarity Association constant
Biochemistry, 2012
In this study, we employed a combination of steady-state and time-resolved fluorescence spectrosc... more In this study, we employed a combination of steady-state and time-resolved fluorescence spectroscopy and studied the site-specific dynamics in a GTP aptamer using 2-aminopurine as a fluorescent probe. We compared the dynamics of the GTP-bound aptamer with that of the free aptamer as well as when it is denatured. GTP binding leads to an overall compaction of structure in the aptamer. The general pattern of fluorescence lifetimes and correlation times scanned across several locations in the aptamer does not seem to change following GTP binding. However, a remarkable narrowing of the lifetime distribution of the aptamer ensues following its compaction by GTP binding. Interestingly, such a "conformational narrowing" is evident from the lifetime readouts of the nucleotide belonging to the stem as well as the "bulge" part of the aptamer, independent of whether it is directly interacting with GTP. Taken together, these results underscore the importance of an overall intrinsic structure associated with the free aptamer that is further modulated following GTP binding. This work provides strong support for the "conformational selection" hypothesis of ligand binding. RNA aptamers are RNA oligonucleotides that can bind specifically to a wide range of target molecules such as small molecules, cofactors, amino acids, etc., with high affinity. 1−3 Aptamers are selected from a combinatorial library through an artificial evolution procedure called systematic evolution of ligands by exponential enrichment (SELEX). 4,5 There has been an exponentially growing number of applications of aptamers, namely, as biosensors, 6,7 as a tool for metabolite sensing, 8 as diagnostics or biomedical applications, 9 and as drug delivery tools. 10 One of the main attractive properties of aptamers is the in vitro selection procedure that can provide an aptamer against virtually any target of choice and with a predefined affinity. The structural flexibility of oligonucleotides allows for adaptation of the aptamer to various structures. 1,11−20 The recognition and binding of a small molecule ligand by nucleic acids are thought to be based mainly on stacking interactions and hydrogen bonding. 18,21,22 These types of interactions are crucial for RNA function in nature as well as in the context of RNA as a drug target. 23,24 RNA aptamers are ideal systems for detailed studies of these interactions. 25 Several structures of aptamer (both artificial and natural)−ligand complexes have been determined using X-ray crystallography 26−30 and nuclear magnetic resonance (NMR) spectroscopy. 14−23,31−37 The structures of complexes of aptamers with ATP, biotin, or FMN, among others, demonstrated that specificity is most often achieved by specific hydrogen bonding patterns and stacking of aromatic ring systems in the ligand with bases in the RNA. 21,31,38 Another characteristic feature of these complexes, especially those with artificially selected aptamers, is the fact that the RNA binding pocket in its ligand free form is largely unstructured and folding occurs simultaneously with ligand binding, a process that has been termed conformational selection or adaptive binding. 19,22,39,40 Artificially selected RNA aptamers are quite small in size, very similar to the aptamer domain of RNA switches. 28−37,41,42 In RNA switches, structural changes in the aptamer domain caused by ligand binding led to the switching action. Understanding the intricacies of ligand-induced changes in
![Research paper thumbnail of Photophysical properties and excited state intramolecular proton transfer in 2-hydroxy-5-[(E)-(4-methoxyphenyl)diazenyl]benzoic acid in homogeneous solvents and micro-heterogeneous environments](https://a.academia-assets.com/images/blank-paper.jpg)
](Journal of Luminescence, 2014
ABSTRACT A systematic study on the photophysical properties and excited state intramolecular prot... more ABSTRACT A systematic study on the photophysical properties and excited state intramolecular proton transfer (ESIPT) behavior of 2-hydroxy-5-[(E)-(4-methoxyphenyl)diazenyl]benzoic acid, is reported using steady-state and time-resolved fluorescence spectroscopy in homogeneous solvents as well as in different micro-heterogeneous environments. Depending on the nature of intramolecular hydrogen bond (IHB), the salicylic acid derivative may exist in two different ground state conformers (I and II). Structure I having IHB between the carbonyl oxygen and phenolic hydrogen can undergo ESIPT upon excitation as evidenced by largely Stokes-shifted fluorescence at ~455 nm; whereas, normal fluorescence in the blue side of the spectrum (~410 nm) is due to the spontaneous emission from conformer II. The results in homogeneous solvents were compared with those in bio-mimicking environments of β-cyclodextrin (CD) and surfactants. The intensity of the ESIPT fluorescence increases substantially upon encapsulation of the probe into the cyclodextrin as well as micellar nano-cavities. Detailed analysis of the spectroscopic data indicates that the probe forms 1:1 complex with CD in aqueous medium. Binding constant of the probe with the micelles as well as critical micelle concentration was obtained from the variation of fluorescence intensity on increasing concentration of different surfactants in aqueous medium.
European Journal of Chemistry, 2010
Fluorescence behavior of intramolecular charge transfer probe trans-ethyl-p-(dimethylamino) cinna... more Fluorescence behavior of intramolecular charge transfer probe trans-ethyl-p-(dimethylamino) cinnamate (EDAC) is extremely sensitive to the local environment. This study explores the interaction of EDAC with several Igepal, Brij and Tween series of non-ionic surfactants by steady state and picoseconds time-resolved fluorescence spectroscopy. The physico-chemical properties, like critical micelle concentration and micropolarity of the micellar media surrounding the probe were determined. In most of the cases, the observed values were in good agreement with the data reported in the literature. Results obtained from time-resolved fluorescence experiments show a substantial reduction in total nonradiative decay rate of the probe in micellar medium compared to that in aqueous phase. This indicates preferential association of the probe inside the micellar core. The association constant of the probe-micelle interaction was also evaluated in different cases. Fluorescence Non-ionic surfactants Intramolecular charge transfer CMC Micropolarity Association constant
Biochemistry, 2012
In this study, we employed a combination of steady-state and time-resolved fluorescence spectrosc... more In this study, we employed a combination of steady-state and time-resolved fluorescence spectroscopy and studied the site-specific dynamics in a GTP aptamer using 2-aminopurine as a fluorescent probe. We compared the dynamics of the GTP-bound aptamer with that of the free aptamer as well as when it is denatured. GTP binding leads to an overall compaction of structure in the aptamer. The general pattern of fluorescence lifetimes and correlation times scanned across several locations in the aptamer does not seem to change following GTP binding. However, a remarkable narrowing of the lifetime distribution of the aptamer ensues following its compaction by GTP binding. Interestingly, such a "conformational narrowing" is evident from the lifetime readouts of the nucleotide belonging to the stem as well as the "bulge" part of the aptamer, independent of whether it is directly interacting with GTP. Taken together, these results underscore the importance of an overall intrinsic structure associated with the free aptamer that is further modulated following GTP binding. This work provides strong support for the "conformational selection" hypothesis of ligand binding. RNA aptamers are RNA oligonucleotides that can bind specifically to a wide range of target molecules such as small molecules, cofactors, amino acids, etc., with high affinity. 1−3 Aptamers are selected from a combinatorial library through an artificial evolution procedure called systematic evolution of ligands by exponential enrichment (SELEX). 4,5 There has been an exponentially growing number of applications of aptamers, namely, as biosensors, 6,7 as a tool for metabolite sensing, 8 as diagnostics or biomedical applications, 9 and as drug delivery tools. 10 One of the main attractive properties of aptamers is the in vitro selection procedure that can provide an aptamer against virtually any target of choice and with a predefined affinity. The structural flexibility of oligonucleotides allows for adaptation of the aptamer to various structures. 1,11−20 The recognition and binding of a small molecule ligand by nucleic acids are thought to be based mainly on stacking interactions and hydrogen bonding. 18,21,22 These types of interactions are crucial for RNA function in nature as well as in the context of RNA as a drug target. 23,24 RNA aptamers are ideal systems for detailed studies of these interactions. 25 Several structures of aptamer (both artificial and natural)−ligand complexes have been determined using X-ray crystallography 26−30 and nuclear magnetic resonance (NMR) spectroscopy. 14−23,31−37 The structures of complexes of aptamers with ATP, biotin, or FMN, among others, demonstrated that specificity is most often achieved by specific hydrogen bonding patterns and stacking of aromatic ring systems in the ligand with bases in the RNA. 21,31,38 Another characteristic feature of these complexes, especially those with artificially selected aptamers, is the fact that the RNA binding pocket in its ligand free form is largely unstructured and folding occurs simultaneously with ligand binding, a process that has been termed conformational selection or adaptive binding. 19,22,39,40 Artificially selected RNA aptamers are quite small in size, very similar to the aptamer domain of RNA switches. 28−37,41,42 In RNA switches, structural changes in the aptamer domain caused by ligand binding led to the switching action. Understanding the intricacies of ligand-induced changes in
Journal of Luminescence, 2014
ABSTRACT A systematic study on the photophysical properties and excited state intramolecular prot... more ABSTRACT A systematic study on the photophysical properties and excited state intramolecular proton transfer (ESIPT) behavior of 2-hydroxy-5-[(E)-(4-methoxyphenyl)diazenyl]benzoic acid, is reported using steady-state and time-resolved fluorescence spectroscopy in homogeneous solvents as well as in different micro-heterogeneous environments. Depending on the nature of intramolecular hydrogen bond (IHB), the salicylic acid derivative may exist in two different ground state conformers (I and II). Structure I having IHB between the carbonyl oxygen and phenolic hydrogen can undergo ESIPT upon excitation as evidenced by largely Stokes-shifted fluorescence at ~455 nm; whereas, normal fluorescence in the blue side of the spectrum (~410 nm) is due to the spontaneous emission from conformer II. The results in homogeneous solvents were compared with those in bio-mimicking environments of β-cyclodextrin (CD) and surfactants. The intensity of the ESIPT fluorescence increases substantially upon encapsulation of the probe into the cyclodextrin as well as micellar nano-cavities. Detailed analysis of the spectroscopic data indicates that the probe forms 1:1 complex with CD in aqueous medium. Binding constant of the probe with the micelles as well as critical micelle concentration was obtained from the variation of fluorescence intensity on increasing concentration of different surfactants in aqueous medium.