Publications by authors named "Apurba L Koner"

37 Publications

Strategic engineering of alkyl spacer length for a pH-tolerant lysosome marker and dual organelle localization.

Chem Sci 2021 Jul 14;12(28):9630-9644. Epub 2021 Jun 14.

Bionanotechnology Lab, Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal Madhya Pradesh India

Long-term visualization of lysosomal properties is extremely crucial to evaluate diseases related to their dysfunction. However, many of the reported lysotrackers are less conducive to imaging lysosomes precisely because they suffer from fluorescence quenching and other inherent drawbacks such as pH-sensitivity, polarity insensitivity, water insolubility, slow diffusibility, and poor photostability. To overcome these limitations, we have utilized an alkyl chain length engineering strategy and synthesized a series of lysosome targeting fluorescent derivatives namely by attaching a morpholine moiety at the position of the 1,8-naphthalimide (NI) ring through varying alkyl spacers between morpholine and 1,8-naphthalimide. The structural and optical properties of the synthesized were explored by H-NMR, single-crystal X-ray diffraction, UV-Vis, and fluorescence spectroscopy. Afterward, optical spectroscopic measurements were carefully performed to identify a pH-tolerant, polarity sensitive, and highly photostable fluoroprobes for further live-cell imaging applications. displayed excellent pH-tolerant and polarity-sensitive properties. Consequently, all were employed in kidney fibroblast cells (BHK-21) to investigate their applicability for lysosome targeting and probing lysosomal micropolarity. Interestingly, a switching of localization from lysosomes to the endoplasmic reticulum (ER) was also achieved by controlling the linker length and this phenomenon was subsequently applied in determining ER micropolarity. Additionally, the selected probe was also employed in BHK-21 cells for 3-D spheroid imaging and in () for imaging, to evaluate its efficacy for imaging animal models.
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http://dx.doi.org/10.1039/d1sc00542aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8293980PMC
July 2021

Supramolecular Encapsulation of a Neurotransmitter Serotonin by Cucurbit[7]uril.

Front Chem 2020 23;8:582757. Epub 2020 Oct 23.

Bionanotechnology Laboratory, Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, India.

pH-dependent host-guest complexation of a monoamine neurotransmitter, Serotonin, with cucurbit[7]uril has been thoroughly investigated. The binding phenomena were explored using steady-state and time-resolved fluorescence spectroscopy at different pH values. At lower pH, i.e., protonated Serotonin, the binding affinity with cucurbit[7]uril was significantly higher compared to higher pH. Furthermore, detailed NMR titration experiments depicted the solution structure of the host-guest complex through the complexation induced chemical shift values. A competitive binding assay with cesium ions at pD 2.8 was subsequently performed for the further manifestation of the binding. Finally, the molecular docking studies provided well-documented proof of the 1:1 inclusion complex and the geometry of the complex. We believe that understanding from such studies can be important for pH-controlled delivery of serotonin for biological applications.
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http://dx.doi.org/10.3389/fchem.2020.582757DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7645158PMC
October 2020

Cellular metabolic activity marker via selective turn-ON detection of transporter protein using nitrobenzoxadiazole-based fluorescent reporter.

Sci Rep 2020 03 5;10(1):4166. Epub 2020 Mar 5.

Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, (MP), India.

A nitrobenzoxadiazole-based fluoroprobe (NBD-Bu) is designed to probe cellular metabolic activity in cancer and normal cells. NBD-Bu shows a significant fluorescence enhancement upon selective binding to the transport protein serum albumin in PBS buffer at ambient conditions. Encouraged by this finding, the site- specificity of NBD-Bu has been explored through a competitive displacement assay in the presence of site-specific markers such as warfarin and ibuprofen. Notably, even at micromolar concentrations, the probe possesses the ability to displace the site marker drug ibuprofen, efficiently. Subsequently, high-resolution fluorescence imaging results consolidated the potential of NBD-Bu for detection of abnormal cellular metabolic activity.
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http://dx.doi.org/10.1038/s41598-020-60954-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7058046PMC
March 2020

Synthesis of Two-Photon Active Tricomponent Fluorescent Probe for Distinguishment of Biotin Receptor Positive and Negative Cells and Imaging 3D-Spheroid.

Org Lett 2018 10 8;20(20):6425-6429. Epub 2018 Oct 8.

Department of Chemistry , Indian Institute of Science Education and Research Bhopal , Bhopal Bypass Road , Bhauri, Bhopal - 462066 , India.

A fluorescence microscopy-based distinguishment between biotin receptor (BiR) positive and negative cell lines via receptor-mediated endocytosis has been demonstrated. A water-soluble, three-component, two-photon (2P) active solvatofluorochromic probe has been designed and synthesized. The applicability of the probe for 2P microscopy and 3D-spheroid was also assessed.
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http://dx.doi.org/10.1021/acs.orglett.8b02748DOI Listing
October 2018

Encapsulation and modulation of protolytic equilibrium of β-carboline-based norharmane drug by cucurbit[7]uril and micellar environments for enhanced cellular uptake.

Colloids Surf B Biointerfaces 2018 Nov 31;171:530-537. Epub 2018 Jul 31.

Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462 066, Madhya Pradesh, India. Electronic address:

The effect of supramolecular nanocavity on photophysical and acid-dissociation properties of Norharmane (NHM), a physiologically important, anxiety control and memory-enhancing β-carboline-based drug, has been investigated using steady-state absorption and fluorescence spectroscopy. Self-assembled organization derived from surfactants and rigid water-soluble macrocyclic host Cucurbit[7]uril (CB7) have been selected for this investigation. The confined-space offered by the supramolecular assemblies modulates the pK value of NHM (up to 3 units) as it can exist in two protolytic forms at near neutral pH. Therefore, the pH-dependent binding properties, modulation of pK value and its consequences on the photophysical, chemical and solubility properties are investigated in detail. This investigation shows a large shift in the protolytic equilibrium which in turn causes ca. 15 times solubility-enhancement at near neutral pH. Moreover, the effect of enhanced solubility has been further investigated by the augmentation in the cellular uptake of NHM entrapped inside CB7. Thus, the modulation of the acid-base properties and solubility of β-carboline-based drugs will have immense potential for their formulation, cellular uptake and bioavailability.
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http://dx.doi.org/10.1016/j.colsurfb.2018.07.061DOI Listing
November 2018

Large Stokes-shifted NIR-emission from nanospace-induced aggregation of perylenemonoimide-doped polymer nanoparticles: imaging of folate receptor expression.

Chem Commun (Camb) 2018 Jan;54(5):523-526

Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal, MP 462066, India.

The development of a water-soluble, perylenemonoimide (PMI) dye-doped polymer nanoparticle (PNP) with NIR emission for live-cell imaging is demonstrated. The large Stokes-shifted NIR emission is due to confined nanospace-induced aggregation offered by the polymer matrix. Later, folic acid functionalised PNP (PNP-FA) is successfully employed to differentiate folate receptor positive and negative cancer cells.
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http://dx.doi.org/10.1039/c7cc08404hDOI Listing
January 2018

A rapid, naked-eye detection of hypochlorite and bisulfite using a robust and highly-photostable indicator dye Quinaldine Red in aqueous medium.

Spectrochim Acta A Mol Biomol Spectrosc 2018 Feb 12;191:217-220. Epub 2017 Oct 12.

Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462 066, Madhya Pradesh, India. Electronic address:

A "naked-eye" detection of health hazardous bisulfite (HSO) and hypochlorite (ClO) using an indicator dye (Quinaldine Red, QR) in a wide range of pH is demonstrated. The molecule contains a quinoline moiety linked to an N,N-dimethylaniline moiety with a conjugated double bond. Treatment of QR with HSO and ClO, in aqueous solution at near-neutral pH, resulted in a colorless product with high selectivity and sensitivity. The detection limit was 47.8μM and 0.2μM for HSO and ClO respectively. However, ClO was 50 times more sensitive and with 2 times faster response compared to HSO. The detail characterization and related analysis demonstrate the potential of QR for a rapid, robust and highly efficient colorimetric sensor for the practical applications to detect hypochlorite in water samples.
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http://dx.doi.org/10.1016/j.saa.2017.10.037DOI Listing
February 2018

Differentiation of Folate-Receptor-Positive and -Negative Cells Using a Substrate-Mimicking Fluorescent Probe.

Chemistry 2017 Oct 6;23(60):15008-15011. Epub 2017 Oct 6.

Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road Bhauri, Bhopal (MP)-, 462066, India.

Diagnosis and therapy exploiting overexpressed receptors on the cell surface is one important strategy in medicine. Determination of the over expression level of a particular receptor is prerequisite for it to be of clinical use. Differentiation between FR-positive (FR=folate receptor) and -negative cells via fluorescence microscopy using a substrate mimetic fluorophore is presented in this work. The strategy adopted here is not the classical FA-conjugated (FA=folic acid) fluorescent probe but a small and environment-sensitive pterin-based (pterin is part of folate, i.e., vitamin B9) fluorescent probe. Electronically diverse pterin-based fluorescent probes have been designed and synthesized to understand the effect of the binding environment on the receptor-substrate interactions. By utilizing steady-state UV/Vis and fluorescence along with time-resolved fluorescence spectroscopy, the effects on the electronic and acid-base properties of the substrate were investigated. Evidently, one synthesized probe showed FA-mimicking behavior with strong binding interaction with FR.
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http://dx.doi.org/10.1002/chem.201703305DOI Listing
October 2017

Long-Lived Polypyridyl Based Mononuclear Ruthenium Complexes: Synthesis, Structure, and Azo Dye Decomposition.

Inorg Chem 2017 Jun 16;56(11):6489-6498. Epub 2017 May 16.

School of Basic Sciences, Indian Institute of Technology Bhubaneswar , Argul 752050, India.

Two mononuclear ruthenium complexes [(bpy)RuL/L](ClO) ([1]/[2]) (bpy-2,2' bipyridine, L = 2,3-di(pyridin-2-yl)pyrazino[2,3-f][1,10]phenanthroline) and L = 2,3-di(thiophen-2-yl)pyrazino[2,3-f][1,10]phenanthroline have been synthesized. The complexes have been characterized using various analytical techniques. The complex [1] has further been characterized by its single crystal X-ray structure suggesting ruthenium is coordinating through the N donors of phenanthroline end. Theoretical investigation suggests that the HOMOs of both complexes are composed of pyridine and pyrazine unit of ligands L and L whereas the LUMOs are formed by the contribution of bipyridine units. The low energy bands at ∼480 nm of the complexes can be assigned as MLCT with partial contribution from ligand transitions, whereas the rest are ligand centered. The complexes have shown Ru/Ru oxidation couples at E at 1.26 (70 mV) V and 1.28 (62 mV) V for [1] and [2] vs Ag/AgCl, respectively, suggesting no significant role of distal thiophene or pyridine units of the ligands. The complexes are emissive and display solvent dependent emission properties. Both complexes have shown highest emission quantum yield and lifetime in DMSO (ϕ = 0.05 and τ = 460 ns and λ at 620 nm for [1]; ϕ = 0.043 and τ = 425 ns and λ at 635 nm for [2]). Further, the long luminescent lifetime of these complexes has been utilized to generate reactive oxygen species for efficient azo dye decomposition.
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http://dx.doi.org/10.1021/acs.inorgchem.7b00536DOI Listing
June 2017

Customized tuning of aggregation-induced emission of a napthalimide dye by surfactants and cyclodextrin.

J Colloid Interface Sci 2017 Aug 23;499:46-53. Epub 2017 Mar 23.

Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, India. Electronic address:

The aggregation-induced emission behaviour of an environment sensitive 2,3-substituted napthalimide dye has been investigated at neutral pH in presence of three different surfactants i.e., cationic, anionic, and neutral. The changes observed in the excitation spectrum of the dye compared to its absorption spectra in water in presence of the surfactants above their micellar concentration reveals the transformation of the H-aggregates of the dye to the monomeric form. The alteration of the dye aggregates to its monomeric form and its consequence on emission properties has been utilized to estimate the surfactant concentration parameter for pre-micellar to micellar transformation. The aggregation of the dye molecules has been made reversible by removal of the surfactant molecules from the system upon host-guest complexation with α-cyclodextrin. This switchable aggregation-deaggregation phenomenon of DMN-Bu by employing surfactants and α-cyclodextrin at neutral pH in water is utilized for determining their critical micellar concentration.
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http://dx.doi.org/10.1016/j.jcis.2017.03.097DOI Listing
August 2017

Spectroscopic investigation of bio-mimetic solvolysis of 6-(N,N-dimethylamino)-2,3-naphthalic anhydride in confined nanocavities.

Phys Chem Chem Phys 2017 Feb;19(6):4337-4344

Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal-462066, India.

Enzymes are biological catalysts that can vastly accelerate the reaction rate of a substrate by accommodating it within the active site. The local environment provided by the active site of a natural catalyst causes a significant rate-enhancement of the reaction as compared to that without catalyst. The solvolysis reaction of a 6-(N,N-dimethylamino)-2,3-naphthalic anhydride probe is investigated using UV-Vis and fluorescence spectroscopy in pure alcohols and in bio-mimetic nano-sized environments like surfactants, macrocyclic hosts and protein nanocavities. The solvolysis rate in alcohols is found to be regulated directly by the alkyl chain length and follows Arrhenius dependence. The hydrolysis rate of the probe in water under physiological conditions (pH 7.4, at 25 °C) is very slow. However, under identical conditions, the rate can be accelerated significantly by protein and supramolecular nanocavities. Therefore, such fundamental kinetic analysis of the understanding of this bio-mimetic solvolysis will allow us to design a novel probe-drug conjugate with efficient controlled-release and function.
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http://dx.doi.org/10.1039/c6cp08009jDOI Listing
February 2017

Investigation of the effect of cucurbit[7]uril complexation on the photophysical and acid-base properties of the antimalarial drug quinine.

Phys Chem Chem Phys 2016 Nov;18(44):30520-30529

Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal-462066, India.

Host-guest complexation of mono and dicationic quinine with cucurbit[7]uril (CB7), a water-soluble macrocyclic host molecule, has been investigated. Job's plot, time-resolved anisotropy as well as concentration dependent NMR titration confirm the binding of two CB7 macrocycles with one quinine molecule. The binding affinity of dicationic quinine with CB7 is one order of magnitude higher than the binding constant of mono-cationic quinine. Such preferential binding results in one unit pK shift in the ground-state of the quinoline ring. However, using fluorescence spectroscopy we have obtained two acid-dissociation constants, one for quinoline ring nitrogen and the other for the nitrogen of the quinuclidine moiety. In the excited state, CB7 complexation causes one unit pK shift for the quinoline ring and 1.9 unit shift for the quinuclidine moiety. Interestingly, a large enhancement of fluorescence lifetime and anisotropy of quinine at pH 2.7 and pH 9.0 upon CB7 complexation was observed due to the restriction of conformational flexibility. Moreover, at pH 3.0, a large fluorescence enhancement of quinine due to CB7 complexation was observed and it was quite significant as compared to that of quinine in 0.1 (M) HCl without CB7. We believe that this study of quinine complexation with CB7 will reduce phototoxicity, increase bioavailability and offer an alternative standard for quantum yield measurements in an amiable condition.
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http://dx.doi.org/10.1039/c6cp04931aDOI Listing
November 2016

Supramolecular guest relay using host-protein nanocavities: an application of host-induced guest protonation.

Mol Biosyst 2016 08;12(9):2859-66

Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, India.

Small drug molecules and other important metabolites are delivered via a suitable carrier protein-mediated transport through a specific receptor. The process is highly coordinated and associated with complexation induced properties of deliverable molecules. To get a molecular insight, in this report, we tried to mimic the delivery process to know how the carrier protein relocates the drug molecule from the macrocyclic host cavity to its binding pocket and how the electronic and the chemical properties of the guest get altered. Bovine and human serum albumin (BSA and HSA) were used as the model carrier proteins which can snatch out 6-propanoyl-2-(N,N-dimethylamino)naphthalene (PRO), dye used as a drug model (known to bind at the drug-binding pocket of the carrier protein), from the cucurbit[7]uril (CB7) cavity, a potential drug delivery carrier. Prior to performing the fluorescence-based bio-supramolecular relocation assay using BSA and HSA, CB7 and PRO, we have investigated the effect of CB7 encapsulation and protonation on the fluorescence properties of PRO. A significant shift in the pKa value from 3.4 to 6.6 (ca. 3.2 logarithmic units) of PRO was observed upon encapsulation with CB7, which causes a huge fluorescence quenching even at neutral pH. The binding affinity of protonated and neutral PRO for CB7 also confirms a 3.2 unit shift in the acid-dissociation constant. A displacement assay using a strong CB7 binder, viz., 1,6-diaminohexane, confirms encapsulation of PRO in the CB7 cavity. Encapsulation of neutral PRO by CB7 shows a significant fluorescence enhancement accompanied by a ∼35 nm blue shift in the emission maxima.
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http://dx.doi.org/10.1039/c6mb00423gDOI Listing
August 2016

Iridium Complexes as a Roadblock for DNA Polymerase during Amplification.

ChemMedChem 2016 07 31;11(13):1410-4. Epub 2016 May 31.

Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By Pass Road, Bhauri, 462066, Bhopal, India.

Iridium-based metal complexes containing polypyridyl-pyrazine ligands show properties of DNA intercalation. They serve as roadblocks to DNA polymerase activity, thereby inhibiting the polymerization process. Upon the addition of increasing concentrations of these iridium complexes, a rapid polymerase chain reaction (PCR)-based assay reveals the selective inhibition of the DNA polymerization process. This label-free approach to study the inhibition of fundamental cellular processes via physical roadblock can offer an alternative route toward cancer therapy.
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http://dx.doi.org/10.1002/cmdc.201600101DOI Listing
July 2016

Probing microenvironment of micelle and albumin using diethyl 6-(dimethylamino)naphthalene-2,3-dicarboxylate: An electroneutral solvatochromic fluorescent probe.

J Colloid Interface Sci 2016 Apr 30;467:81-89. Epub 2015 Dec 30.

Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, India. Electronic address:

Synthesis, single-crystal X-ray characterization, and spectroscopic investigation of small, non-charged diethyl 6-(dimethylamino)naphthalene-2,3-dicarboxylate (DMNDC) by UV-Visible, steady-state, and time-resolved fluorescence reveal a series of interesting photophysical properties originating from the intrinsic intramolecular charge transfer (ICT) state, leading to diverse applications. Stokes shift, lifetime, and emission maxima of DMNDC show a very good correlation with ET(30) solvent polarity scale for a series of different polarity solvents, confirms that it has very good environment sensitivity. Furthermore, this dye has been found to be an exceptionally suitable probe for determining Critical Micelle Concentration (CMC) and probing self-organization processes of five different type of surfactant with structural diversity. A 20-60nm blue shift in emission maxima accompanied by a large fluorescence lifetime enhancement (ca. 23ns) was observed upon relocation of DMNDC into a hydrophobic microenvironment. Along with this, the small size, electroneutrality, pH stability, and excellent solvatochromic fluorescent properties are employed for deciphering the number of hydrophobic binding pockets with strong affinity and their local microenvironment present in Bovine Serum Albumin (BSA).
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http://dx.doi.org/10.1016/j.jcis.2015.12.022DOI Listing
April 2016

A ratiometric fluorescent probe for detection of biogenic primary amines with nanomolar sensitivity.

Analyst 2016 Feb 6;141(3):827-31. Epub 2016 Jan 6.

Department of Chemistry, Indian Institute of Science Education and Research (IISER), Bhopal By-pass Road, Bhauri, Bhopal-462066, Madhya Pradesh, India.

An ultrasensitive ratiometric fluorescent sensor made of an N,N-dimethylaminonaphthalene anhydride moiety for detection of aliphatic primary amines is reported. Biogenic amines at nanomolar concentration is detected with the additional ability to discriminate between primary, secondary and tertiary amines by using both UV-Visible and fluorescence spectroscopy.
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http://dx.doi.org/10.1039/c5an01911gDOI Listing
February 2016

Complexation induced fluorescence and acid-base properties of dapoxyl dye with γ-cyclodextrin: a drug-binding application using displacement assays.

Phys Chem Chem Phys 2015 Jun 1;17(24):16015-22. Epub 2015 Jun 1.

Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, India.

Host-guest complexation of dapoxyl sodium sulphonate (DSS), an intramolecular charge transfer dye with water-soluble and non-toxic macrocycle γ-cyclodextrin (γ-CD), has been investigated in a wide pH range. Steady-state absorption, fluorescence and time-resolved fluorescence measurements confirm the positioning of DSS into the hydrophobic cavity of γ-CD. A large fluorescence enhancement ca. 30 times, due to 1 : 2 complex formation and host-assisted guest-protonation have been utilised for developing a method for the utilisation of CD based drug-delivery applications. A simple fluorescence-displacement based approach is implemented at physiological pH for the assessment of binding strength of pharmaceutically useful small drug molecules (ibuprofen, paracetamol, methyl salicylate, salicylic acid, aspirin, and piroxicam) and six important antibiotic drugs (resazurin, thiamphenicol, chloramphenicol, ampicillin, kanamycin, and sorbic acid) with γ-CD.
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http://dx.doi.org/10.1039/c5cp01696gDOI Listing
June 2015

Hydroxy-terminated conjugated polymer nanoparticles have near-unity bright fraction and reveal cholesterol-dependence of IGF1R nanodomains.

ACS Nano 2013 Feb 30;7(2):1137-44. Epub 2013 Jan 30.

Department of Biochemistry, Oxford University, South Parks Road, OX1 3QU, United Kingdom.

Fluorescent nanoparticles have enabled many discoveries regarding how molecular machines function. Quantum dots have been the dominant class of fluorescent nanoparticles but suffer from blinking and from a substantial dark fraction--particles where the fluorescence is never seen--complicating any analysis of biological function. Nanoparticles composed of conjugated fluorescent polymers (Pdots) have recently been shown to have high brightness and no blinking. Here we develop a robust and efficient means to measure the dark fraction of Pdots, conjugating Atto dyes to the nanoparticles and testing fluorescence colocalization of dye and Pdot puncta. This established that the Pdots we generated had minimal dark fraction: ∼3%. The application of nanoparticles in biological environments is highly sensitive to surface functionalization. For Pdots we found that passivation with uncharged hydroxy-terminated polyethylene glycol caused a dramatic reduction in nonspecific cell binding and aggregation compared to a charged coating. Using carbonyl di-imidazole the hydroxy-Pdots were functionalized efficiently with streptavidin for high stability targeting, allowing specific labeling of mammalian cells. Type I insulin-like growth factor receptor (IGF1R) regulates cell survival and development, with roles in aging, heart disease, and cancer. We used hydroxy-Pdots to track the dynamics of IGF1R on a breast cancer cell-line, determining the diffusion characteristics and showing cholesterol-containing membrane nanodomains were important for receptor mobility at the plasma membrane. The near-unity bright fraction and low nonspecific binding of hydroxy-Pdots, combined with Pdot photostability and lack of blinking, provides many advantages for investigations at the single molecule level.
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http://dx.doi.org/10.1021/nn3042122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584654PMC
February 2013

Mechanisms for size-dependent protein segregation at immune synapses assessed with molecular rulers.

Biophys J 2011 Jun;100(12):2865-74

Sir Alexander Fleming Building, Division of Cell and Molecular Biology, Imperial College London, London, UK.

Immunological synapses are specialized intercellular contacts formed by several types of immune cells in contact with target cells or antigen-presenting cells. A late-stage immune synapse is commonly a bulls-eye pattern of immune cell receptor-ligand pairs surrounded by integrin complexes. Based on crystal structures, the intermembrane distance would be ∼15 nm for many immune cell receptor-ligand pairs, but ∼40 nm for integrin-ligand pairs. Close proximity of these two classes of intermembrane bonds would require significant membrane bending and such proteins can segregate according to their size, which may be key for receptor triggering. However, tools available to evaluate the intermembrane organization of the synapse are limited. Here, we present what we believe to be a novel approach to test the importance of size in the intercellular organization of proteins, using live-cell microscopy of a size-series of fluorescently-labeled molecules and quantum dots to act as molecular rulers. Small particles readily colocalized at the synapse with MHC class I bound to its cognate natural killer cell receptor, whereas particles larger than 15 nm were increasingly segregated from this interaction. Combined with modeling of the partitioning of the particles by scaled-particle adsorption theory, these molecular rulers show how membrane-bending elasticity can drive size-dependent exclusion of proteins within immune synapses.
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http://dx.doi.org/10.1016/j.bpj.2011.05.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123984PMC
June 2011

How the biotin-streptavidin interaction was made even stronger: investigation via crystallography and a chimaeric tetramer.

Biochem J 2011 Apr;435(1):55-63

Department of Biochemistry, Oxford University, South Parks Road, Oxford OX1 3QU, UK.

The interaction between SA (streptavidin) and biotin is one of the strongest non-covalent interactions in Nature. SA is a widely used tool and a paradigm for protein-ligand interactions. We previously developed a SA mutant, termed Tr (traptavidin), possessing a 10-fold lower off-rate for biotin, with increased mechanical and thermal stability. In the present study, we determined the crystal structures of apo-Tr and biotin-Tr at 1.5 Å resolution. In apo-SA the loop (L3/4), near biotin's valeryl tail, is typically disordered and open, but closes upon biotin binding. In contrast, L3/4 was shut in both apo-Tr and biotin-Tr. The reduced flexibility of L3/4 and decreased conformational change on biotin binding provide an explanation for Tr's reduced biotin off- and on-rates. L3/4 includes Ser45, which forms a hydrogen bond to biotin consistently in Tr, but erratically in SA. Reduced breakage of the biotin-Ser45 hydrogen bond in Tr is likely to inhibit the initiating event in biotin's dissociation pathway. We generated a Tr with a single biotin-binding site rather than four, which showed a simi-larly low off-rate, demonstrating that Tr's low off-rate was governed by intrasubunit effects. Understanding the structural features of this tenacious interaction may assist the design of even stronger affinity tags and inhibitors.
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http://dx.doi.org/10.1042/BJ20101593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062853PMC
April 2011

Transition-metal-promoted chemoselective photoreactions at the cucurbituril rim.

Angew Chem Int Ed Engl 2011 Jan;50(2):545-8

School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.

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http://dx.doi.org/10.1002/anie.201005317DOI Listing
January 2011

Modulation of spectrokinetic properties of o-quinonoid reactive intermediates by electronic factors: time-resolved laser flash and steady-state photolysis investigations of photochromic 6- and 7-arylchromenes.

Chemistry 2009 ;15(17):4289-300

Department of Chemistry, Indian Institute of Technology, Kanpur 208 016, India.

A ready synthetic accessibility of a series of 6- and 7-arylchromenes via Pd(0)-catalyzed Suzuki coupling protocol has permitted a comprehensive investigation of the thermal decay behavior of a broad set of photogenerated o-quinonoid reactive intermediates. It is shown that substantial mesomeric effect between the benzopyran nucleus and the aryl ring at C6 or C7 position of the former renders significant absorption beyond 350 nm such that they are readily photoactivated to yield colored o-quinonoid intermediates. The absorption spectra of the latter are found to be strongly influenced by the substituents on C2-, C6- and C7-aryl rings; indeed the colored absorptions can be conveniently tuned by appropriate choice of substituents. The thermal decay (bleaching phenomenon), which is important from the point of view of their application in ophthalmic lenses, was investigated in each case by micros-ms as well as real-time absorption spectroscopy. By careful experimentation, we have extracted the decay rate constants for Z,E and E,E o-quinonoid isomers of all 6- and 7-arylchromenes in an attempt to establish a correlation between the electronic attributes with their thermokinetic behavior. From a combined analysis of micros-ms (laser flash) and real-time kinetic data, it is shown that the colored o-quinonoid intermediates decay faster when the C2-aryl and C6-/C7-aryl rings contain electron-donating and electron-accepting groups, respectively. In the same vein, the decay was found to occur slowly for the reversed scenario, while intermediate decay rates are observed when both substituents are electron-donating. Thus, any substituent on the C2-aryl ring that contributes mesomerically to the development of charge on the quinonoid oxygen, and any substituent on the C6-/C7-aryl ring that exerts -I effect appear to expedite thermal decay. Furthermore, evidence is obtained for the first time from mus time-resolved laser-flash spectroscopy for the formation and characterization of the trans,cis (E,Z) o-quinonoid isomer, which has heretofore eluded spectral characterization in the photochromic phenomena of pyrans.
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http://dx.doi.org/10.1002/chem.200801925DOI Listing
June 2009

Intramolecular O-H...O hydrogen-bond-mediated reversal in the partitioning of conformationally restricted triplet 1,4-biradicals and amplification of diastereodifferentiation in their lifetimes.

J Am Chem Soc 2008 Oct 17;130(41):13608-17. Epub 2008 Sep 17.

Department of Chemistry, Indian Institute of Technology, Kanpur 208 016, India.

The photoreactivity and nanosecond transient phenomena have been investigated for a rationally designed set of ketones 4-9 in order to gain comprehensive insights concerning the influence of intramolecular hydrogen bonding on (i) the lifetimes of triplet 1,4-biradicals and (ii) the partitioning of the latter between cyclization and elimination. Comparisons of the photochemical results and lifetime data for the biradicals of ketones 6 versus 8 and 7 versus 9 revealed a remarkable influence of hydrogen bonding when superimposed upon steric factors: while 6 and 7 yielded cyclobutanols in poor yields, cyclization was found to be overwhelmingly predominant for 8-anti and moderately so for 9-anti, with a high stereoselectivity in the formation of cyclobutanols (>95% for 8-anti). The diastereochemistry in the case of 8 permitted the occurrence of fragmentation or cyclization almost exclusively (>90% cyclization for 8-anti and >75% elimination for 8-syn). Significantly, the intramolecular hydrogen bonding in the biradicals of 8 and 9 was found to reverse their partitioning between cyclization and elimination compared with the behavior of the biradicals of ketones 3; the ketones 8-anti and 9-anti underwent cyclization in benzene, predominantly leading to cyclobutanols with syn stereochemistry between the C2 and C3 substituents. In accordance with photoproduct profiles, an unprecedented approximately 2-fold difference in the lifetimes of the intermediate diastereomeric triplet biradicals of ketones 8 in nonpolar solvents (e.g., tau(syn) = 123 ns and tau(anti) = 235 ns in cyclohexane) was observed via nanosecond laser flash photolysis, while no such difference in lifetimes was found for the triplet biradicals of acetoxy ketones 9. The intriguing diastereodifferentiation in the lifetimes of the diastereomeric triplet 1,4-biradicals of 8 and the product profiles of ketones 6, 7, and 9 are best reconciled via a unified mechanistic picture in which superposition of steric factors over varying magnitudes of O-H...O hydrogen bonding selectively facilitates a particular pathway. In particular, the diastereodifferentiation in the photochemical outcomes for the diastereomers of ketone 8 and in the lifetimes of their triplet biradicals can be understood on the basis of rapid deactivation of the 8-syn triplet biradical via fragmentation and slow cyclization of the 8-anti triplet biradical from chair- and twist-boat-like hydrogen-bonded conformations, respectively. The photolysis in polar aprotic solvents such as DMSO and pyridine was found to reverse the chemoselectivity, yielding reactivity paralleling that of ketones 3, for which the steric factors between the C2 and C3 substituents control the photochemical outcome.
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http://dx.doi.org/10.1021/ja8032179DOI Listing
October 2008

Activation and stabilization of drugs by supramolecular pKa shifts: drug-delivery applications tailored for cucurbiturils.

Angew Chem Int Ed Engl 2008 ;47(29):5398-401

Department of Chemistry, College of Science, Yarmouk University, 21163 Irbid, Jordan.

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http://dx.doi.org/10.1002/anie.200801054DOI Listing
August 2008

Kinetic solvent effects on hydrogen abstraction reactions.

Org Lett 2007 Jul 20;9(15):2899-902. Epub 2007 Jun 20.

School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany.

Kinetic solvent effects on hydrogen abstractions, namely, acceleration in nonpolar solvents, have been presumed to be restricted to O-H hydrogen donors. We demonstrate that also abstractions from C-H and even Sn-H bonds by cumyloxyl radicals and n,pi*-excited 2,3-diazabicyclo[2.2.2]oct-2-ene are fastest in the gas phase and nonpolar solvents but slowest in acetonitrile. Accordingly, solvent effects on hydrogen abstractions are more general, presumably due to stabilization of the reactive oxygen or nitrogen species in polar solvents.
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http://dx.doi.org/10.1021/ol071165gDOI Listing
July 2007

Selective sensing of citrate by a supramolecular 1,8-naphthalimide/calix[4]arene assembly via complexation-modulated pKa shifts in a ternary complex.

J Org Chem 2007 May 14;72(10):3889-95. Epub 2007 Apr 14.

School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany.

A water-soluble supramolecular sensing assembly, composed of an imidazolium-substituted calix[4]arene and a fluorescent aminodiacetate derivative of 1,8-naphthalimide, was studied. Addition of citrate led to a large fluorescence enhancement, while tartrate, acetate, as well as selected inorganic anions gave smaller effects. The sensing principle and selectivity for citrate rely on the formation of a ternary fluorophore-host-anion complex and complexation-induced pKa shifts of an amino group attached to the fluorophore. The complexation of citrate induces a protonation of the amino group, which switches off intramolecular photoinduced electron transfer as the fluorescence quenching pathway, leading to an enhancement of the optical output signal. The intricate sensor principle was corroborated by pH titrations, binding constants, and structural information as obtained by 1H NMR spectroscopy.
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http://dx.doi.org/10.1021/jo070268+DOI Listing
May 2007

Dynamically self-assembling metalloenzyme models based on calixarenes.

Angew Chem Int Ed Engl 2006 Nov;45(44):7400-4

School of Engineering and Science, International University Bremen, Campus Ring 1, 28759 Bremen, Germany.

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http://dx.doi.org/10.1002/anie.200602999DOI Listing
November 2006

Diastereomeric discrimination in the lifetimes of Norrish Type II triplet 1,4-biradicals and stereocontrolled partitioning of their reactivity (Yang cyclization versus Type II fragmentation).

Chemistry 2006 Nov;12(34):8744-9

Department of Chemistry, Indian Institute of Technology, Kanpur 208 016, India.

The stereochemistry at C2 and C3 carbons controls the partitioning of triplet 1,4-biradicals of ketones 2 among various pathways. Differences in the major reaction pathways, for example, cyclization (syn) and fragmentation (anti), adopted by the diastereomeric 1,4-radicals of ketones 2 have permitted unprecedented diastereomeric discrimination in their lifetimes to be observed by nanosecond laser flash photolysis. From quantum yield measurements and transient lifetime data, the absolute rate constants for cyclization and fragmentation of a pair of diastereomeric triplet 1,4-biradicals have been determined for the first time.
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http://dx.doi.org/10.1002/chem.200600880DOI Listing
November 2006

ESPT of 2-(2'-pyridyl)benzimidazole at the Micelle-Water interface: selective enhancement and slow dynamics with sodium dodecyl sulfate.

J Phys Chem B 2005 Jun;109(25):12567-73

Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India.

The effect of micellar environment on the excited state proton transfer (ESPT) of 2-(2'-pyridyl)benzimidazole (2PBI) has been investigated by steady state and time resolved fluorescence spectroscopy. The ESPT, which occurs to a rather small extent at pH 7, is found to be enhanced remarkably at the interface of sodium dodecyl sulfate (SDS) micelles and water. Such an enhancement is not observed for the cationic cetyl trimethyl ammonium bromide (CTAB) or neutral Triton X-100 micelles. This selective enhancement is explained in the light of a modification of pK(a) and a more acidic local pH in the micelle-water interface. A rise time of about 890 ps is observed in the region of tautomer emission. The origin of this rise time is explored, considering three factors, namely, diffusion controlled protonation of the normal form of 2PBI, slow and possibly incomplete solvation of the transition state, leading to a slowing down of the proton transfer process and a similar slow dynamics of the tautomeric excited state.
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http://dx.doi.org/10.1021/jp051574zDOI Listing
June 2005

Analysis of host-assisted guest protonation exemplified for p-sulfonatocalix[4]arene--towards enzyme-mimetic pKa shifts.

Chemistry 2006 Jun;12(18):4799-807

School of Engineering and Science, International University Bremen, Campus Ring 1, 28759 Bremen, Germany.

The pD dependence of the complexation of p-sulfonatocalix[4]arene (CX4) with the azoalkanes 2,3-diazabicyclo[2.2.1]hept-2-ene (1), 2,3-diazabicyclo[2.2.2]oct-2-ene (2), 2,3-diazabicyclo[2.2.3]non-2-ene (3), and 1-methyl-4-isopropyl-2,3-diazabicyclo[2.2.2]oct-2-ene (4) in D(2)O has been studied. The pD-dependent binding constants, determined by (1)H NMR spectroscopy, were analyzed according to a seven-state model, which included the CX4 tetra- and penta-anions, the protonated and unprotonated forms of the azoalkanes, the corresponding complexes, as well as the complex formed between CX4 and the deuteriated hydronium ion. The variation of the UV absorption spectra, namely the hypsochromic shift in the near-UV band of the azo chromophore upon protonation, was analyzed according to a four-state model. Measurements by independent methods demonstrated that complexation by CX4 shifts the pK(a) values of the guest molecules by around 2 units, thereby establishing a case of host-assisted guest protonation. The pK(a) shift can be translated into improved binding (factor of 100) of the protonated guest relative to its unprotonated form as a result of the cation-receptor properties of CX4. The results are discussed in the context of supramolecular catalytic activity and the pK(a) shifts induced by different types of macrocyclic hosts are compared.
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http://dx.doi.org/10.1002/chem.200501479DOI Listing
June 2006
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