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List of publications...

A BODIPY based probe for the reversible "turn on" detection of Au(III) ions

Abstract: A new “turn on” fluorescent probe for the rapid and selective detection of Au3+ ions over other metal ions was developed. T he probe design was constructed on a BODIPY-2-aminopyridine skeleton showing a weak fluorescence emission signal which increased substantially after the coordination of Au3+ ions. The probe displayed remarkable sensing performances such as a low limit of detection (17 nM), a short response time (<1 min), and ability in a wide range of pH’s (6–11). The designed probe was found to have 2:1 coordination stoichiometry according to Job’s plot analysis and most importantly to interact reversibly with Au3+ ions.

2022

Author(s): Muhammed Ucuncu

Journal:  Turkish Journal of Chemistry

Rapid detection of major Gram-positive pathogens in ocular specimens using a novel fluorescent vancomycin-based probe

Abstract: Bacterial infections of the eye are significant causes of morbidity that can lead to permanent visual loss without rapid and adequate treatment, with Gram-positive bacteria causing the majority of ocular infections. Here we report a novel probe, based on the reductive amination of vancomycin with a 4-nitrobenzoxadiazole (NBD)-based aldehyde, that rapidly and specifically detects Gram positive infections from ocular samples

2022

Author(s): Richa Sharma, Harinee Rajagopalan, Maxime Klausen, Mani Vimalin Jeyalatha, Muhammed Üçüncü, Seshasailam Venkateswaran, Appakkudal R Anand, Mark Bradley

Journal:  Sensors & Diagnostics

Light-controlled, living radical polymerisation mediated by fluorophore-conjugated RAFT agents

Abstract: Photoinduced electron transfer-reversible addition−fragmentation chain-transfer (PET-RAFT) polymerisation allows the controlled synthesis of polymers and provides an alternative to transition metal-based photoinitiators. Here, fluorophore-conjugated RAFT agents, containing either 5-carboxyfluorescein or a “boron-dipyrromethene” (BODIPY) moiety attached to a thiocarbonylthio group, were synthesised.

2021

Author(s): Shuo Zhang, Yichuan Zhang, Muhammed Üçüncü, Annamaria Lilienkampf, Jin Geng, Mark Bradley

Journal:  Polymer

Molecular detection of Gram-positive bacteria in the human lung through an optical fiber–based endoscope

Abstract: The relentless rise in antimicrobial resistance is a major societal challenge and requires, as part of its solution, a better understanding of bacterial colonization and infection. To facilitate this, we developed a highly efficient no-wash red optical molecular imaging agent that enables the rapid, selective, and specific visualization of Gram-positive bacteria through a bespoke optical fiber–based delivery/imaging endoscopic device.

2021

Author(s):  Bethany Mills ,..., Muhammed Ucuncu, James M Stone

Journal:  European Journal of Nuclear Medicine and Molecular Imaging

BODIPY–vinyl dibromides as triplet sensitisers for photodynamic therapy and triplet–triplet annihilation upconversion

Abstract: We devised a new generation of halogen-based triplet sensitisers comprising geminal dibromides at the vinyl backbone of a BODIPY fluorophore. Incorporating geminal dibromides into the π-conjugation of BODIPY enhanced intersystem crossing due to the heavy atom effect, which in turn improved the extent of excited triplet states.

2021

Author(s): Suay Dartar, Muhammed Ucuncu, Erman Karakus, Yuqi Hou, Jianzhang Zhao, Mustafa Emrullahoglu

Journal:  Chemical Communications

Dyeing fungi: amphotericin B based fluorescent probes for multiplexed imaging

Abstract: The clinically used antifungal polyene amphotericin B was conjugated, via the mycosamine and the aglycon moieties, to fluorophores. The Cy5 conjugated probe showed selective labelling of fungi in the presence of bacteria, allowing multiplexed imaging and identification of microbial species in a co-culture of fungi and Gram-positive and Gram-negative bacteria.

2021

Author(s): Assel Baibek, Muhammed Üçüncü, Bryn Short, Gordon Ramage, Annamaria Lilienkampf, Mark Bradley

Journal:  Chemical Communications

Wash‐free, peptide‐based fluorogenic probes for microbial imaging

Abstract: Peptides with pan‐antimicrobial affinity were synthesized and decorated with environmentally sensitive fluorophores nitrobenzoxadiazole (green) and merocyanine (red). The labeling efficacies against a range of clinically relevant fungal and Gram‐negative and positive bacterial species (Candida albicans, Escherichia coli, and Staphylococcus aureus) were explored.

2021

Author(s): Assel Baibek, Muhammed Üçüncü, Elizabeth A Blackburn, Mark Bradley, Annamaria Lilienkampf

Journal:  Peptide Science

Bioorthogonal swarming: In situ generation of dendrimer

Abstract: With the aid of bioorthogonal chemistry, we demonstrate the fabrication of synthetic dendrimers in situ around living cells. Using tetrazine dienophile and aminooxyl/hydrazide aldehyde chemistries, the density of functional groups on the dendrimers exponentially amplified intensities of fluorescent markers in antibody-targeted live cell imaging. This novel “swarming” approach highlights the power of bioorthogonal chemistry and provides a route to non-natural chemical structures on cells, paving the way for the generation of various artificial cellular nanostructures and scaffolds.

2020

Author(s): Yichuan Zhang, Muhammed Üçüncü, Alessia Gambardella,..., Mark Bradley, Annamaria Lilienkampf

Journal: Journal of the American Chemical Society

A new fluorescent ‘turn on’probe for rapid detection of biothiols

Abstract: We designed and synthesised a novel molecular probe exhibiting high selectivity and sensitivity towards reactive sulphur species (RSS) over other amino acids and biologically relevant species, as well as scrutinised its spectroscopic behaviours under physiological conditions and in living milieu.We used an electrophilic cyanate group as a masking agent to block the excited state intramolecular proton transfer process of 2-(2-cyanato-3-methoxyphenyl)benzo[d]thiazole (HMBT-OCN), which readily hydrolyses to the highly fluorescent structure, 2-(2ʹ-Hydroxy-3ʹ-methoxyphenyl)benzothiazole (HMBT-OH), in the presence of reactive sulphur species

2020

Author(s): Muhammed Üçüncü, Hüseyin Zeybek, Erman Karakuş, Canan Üçüncü, Mustafa Emrullahoğlu

Journal: Supramolecular Chemistry

Design of photosensitizing agents for targeted antimicrobial photodynamic therapy

Abstract: Photodynamic inactivation of microorganisms has gained substantial attention due to its unique mode of action, in which pathogens are unable to generate resistance, and due to the fact that it can be applied in a minimally invasive manner. In photodynamic therapy (PDT), a non-toxic photosensitizer (PS) is activated by a specific wavelength of light and generates highly cytotoxic reactive oxygen species (ROS) such as superoxide (O2−, type-I mechanism) or singlet oxygen (1O2*, type-II mechanism).

2020

Author(s): Maxime Klausen, Muhammed Ucuncu, Mark Bradley

Journal:  Molecules

Time-resolved spectroscopy of fluorescence quenching in optical fibre-based pH sensors

Abstract: Numerous optodes, with fluorophores as the chemical sensing element and optical fibres for light delivery and collection, have been fabricated for minimally invasive endoscopic measurements of key physiological parameters such as pH. These flexible miniaturised optodes have typically attempted to maximize signal-to-noise through the application of high concentrations of fluorophores. We show that high-density attachment of carboxyfluorescein onto silica microspheres, the sensing elements, results in fluorescence energy transfer, manifesting as reduced fluorescence intensity and lifetime in addition to spectral changes.

2020

Author(s): Katjana Ehrlich, Tushar R Choudhary, Muhammed Ucuncu, ..., Mark Bradley, Michael G Tanner

Journal:  Sensors

Multifunctional, histidine-tagged polymers: antibody conjugation and signal amplification

Abstract: A polymer scaffold, with multiple reactive centres, was synthesised by RAFT polymerisation and conjugated to the antibody herceptin. A hexahistidine RAFT agent enabled the rapid and simple purification of polymer–protein conjugates, while the tetrazine conjugation strategy allows myriad cargos to be attached and amplified.

2020

Author(s):Yichuan Zhang, Alessia Gambardella, Muhammed Üçüncü, Jin Geng, Jessica Clavadetscher, Mark Bradley, Annamaria Lilienkampf

Journal:  Chemical Communications

For more papers, please check the list below!

*Mills, B.,* Megia-Fernandez, A., Norberg, D., Duncan, S., Marshall, A., Akram, A. R., Quinn, T., Young, I., Bruce, A. M., Scholefield, E., Williams, G. O. S., Krstajić, N., Choudhary, T. R., Parker, H. E., Tanner, M. G., Harrington, K., Wood, H. A. C., Birks, T. A., Knight, J. C., Haslett, C., Dhaliwal, K., Bradley, M.* Ucuncu, M.* and Stone, J. M. “Molecular Detection of Gram-positive Bacteria in the human lung through an optical fiber–based endoscope” 2020, Eur. J. Nucl. Med. Mol. Imaging., doi:10.1007/s00259-020-05021-4. (*Corresponding author)


*Ucuncu, M.;+ Mills, B.;+ Duncan, S.; Staderini, M.; Dhaliwal, K. and Bradley M. “Polymyxin-Based Photosensitizer for the Potent and Selective Killing of Gram-Negative Bacteria” Chem. Comm. 2020, 56, 3757-3760. (+equal contribution)


*Choudhary, T., Tanner, M., Megia-Fernandez, A., Harrington, K., Wood, H.A., Marshall, A., Zhu, P., Chankeshwara, S.V., Choudhury, D., Monro, G., Ucuncu, M., Yu, F., Duncan, R., Thomson, R., Dhaliwal, K. and Bradley, M. “High Fidelity Fibre-Based Physiological Sensing Deep In Tissue” Sci. Rep. 2019, 9, 7713.


*Üçüncü, M., Karakuş, E., Demirci, E.K., Sayar, M., Dartar, S. and Emrullahoğlu, M. “BODIPY−Au(I): A Photosensitizer for Singlet Oxygen Generation and Photodynamic Therapy” Org. Lett. 2017, 19, 2522−2525.


*Bor, G., Üçüncü, M., Emrullahoğlu, M., Tomak, A. and Şanlı-Mohamed, G.” BODIPY-conjugated chitosan nanoparticles as a fluorescent probe” Drug Chem Toxicol., 2017, 40, 375–382.


*Akdogan, Y., Emrullahoglu, M., Tatlidil, D., Ucuncu M. and Cakan-Akdogan, G. “EPR Studies of Intermolecular Interactions and Competitive Binding of Drugs In A Drug–BSA Binding Model” Phys. Chem. Chem. Phys., 2016, 18, 22531-22539.


*Üçüncü, M., Cantürk, C., Karakuş, E., Zeybek, H., Bozkaya, U., Soydaş, E., Şahin, E. and Emrullahoğlu, M. “A Rare γ-Pyranopyrazole Skeleton: Design, One-Pot Synthesis and Computational study” Org. Biomol.Chem., 2016, 14, 7490-7494.


*Üçüncü, M., Karakuş, E. and Emrullahoğlu, M. “A BODIPY-Based Fluorescent Probe for Ratiometric Detection of Gold Ions: Utilization of Z-Enynol as The Reactive Unit” Chem. Commun., 2016, 52, 8247-8250.


*Çetintaş, C., Karakuş, E., Üçüncü M. and Emrullahoğlu M. “A Fluorescein-Based Chemodosimeter for Selective Gold(III) Ion Monitoring in Aqueous Media and Living Systems” Sensors Actuat B-Chem., 2016, 234, 109-114.


*Horzum, N., Mete, D., Karakuş E., Üçüncü, M., Emrullahoğlu, M. and Demir. M. M. “Rhodamine-Immobilized Electrospun Chitosan Nanofibrous Mat as A Fluorescence Turn-On Hg2+ Sensor” ChemistrySelect, 2016, 5, 896–900.


*Karakuş, E., Üçüncü M. and Emrullahoğlu M. “An Electrophilic Cyanate as A Recognition Motif for Reactive Sulphur Species: Selective Fluorescence Detection of H2S” Anal. Chem., 2016, 88, 1039–1043.


*Tatlıdil, D., Üçüncü, M. and Akdoğan, Y. “Physiological Concentrations of Albumin Favor Drug Binding” Phys. Chem. Chem. Phys., 2015, 17, 22678-22685.


*Üçüncü, M., Karakuş, E. and Emrullahoğlu, M. “A BODIPY/Pyridine Conjugate for Reversible Fluorescence


Detection of Gold(III) Ions” New J. Chem., 2015, 39, 8337-8341.
*Üçüncü, M., Karakuş, E. and Emrullahoğlu, M. “A Ratiometric Fluorescent Probe for Gold and Mercury Ions” Chem. Eur. J., 2015, 21, 13201–13205.


*Cantürk, C., Üçüncü, M. and Emrullahoğlu, M. “A BODIPY-Based Fluorescent Probe for The Differential Recognition of Hg(II) and Au(III) Ions” RSC Adv., 2015, 5, 30522-30525. (Citations: 27) (impact factor:3.049)


*Kurtulus I., Yilmaz G., Ucuncu M., Emrullahoglu M., Becer C.R. and Bulmus V. “A New Proton Sponge Polymer Synthesized by RAFT Polymerization for Intracellular Delivery of Biotherapeutics” Polym. Chem., 2014, 5, 1593-1604.


*Üçüncü, M. and Emrullahoğlu, M. “A BODIPY-Based Reactive Probe for The Detection of Au(III) Species and Its Application to Cell Imaging” Chem. Commun., 2014, 50, 5884-5886.


*Karakuş, E.+ Üçüncü, M.+ and Emrullahoğlu, M. "A Rhodamine/BODIPY- Based Fluorescent Probe for The Differential Detection of Hg(II) and Au(III)" Chem. Commun., 2014, 50, 1119-1121. (+equal contribution)


*Karakuş, E., Üçüncü M., Eanes, R. and Emrullahoğlu, M. “The Utilization of pH Sensitive Spirocyclic Rhodamine Dyes for Monitoring D-Fructose Consumption During A Fermentation Process” New J. Chem., 2013, 2632-2635.


*Emrullahoğlu, M., Üçüncü, M. and Karakuş, E. “A BODIPY Aldoxime-Based Chemodosimeter for Highly Selective and Rapid Detection of Hypochlorous Acid” Chem. Commun., 2013, 49, 7836-7838. (Top 10 most
accessed articles July-September 2013)


*Emrullahoğlu, M., Karakuş, E. and Üçüncü, M. “A Rhodamine Based “Turn-on” Chemodosimeter for Monitoring Gold Ions In Synthetic Samples and Living Cells” Analyst, 2013, 138, 3638–3641.


*Akpınar, G.E., Kuş, M., Üçüncü, M., Karakuş, E. and Artok, L. “Palladium-Catalyzed Alkoxycarbonylation of (Z)-2-En-4-yn Carbonates Leading to 2,3,5-Trienoates” Org. Lett., 2011, 13, 748–751.


* Üçüncü, M., Karakuş, E., Kuş, M., Akpınar, G.E., Aksın-Artok, Ö., Krause, N., Karaca, S., Elmacı, N. and Artok,L. “Rhodium- and Palladium-Catalyzed 1,5-Substitution Reactions of 2-En-4-yne Acetates and Carbonates with Organoboronic Acids” J. Org. Chem., 2011, 76 (15), 5959–5971.

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