Research

1) Fluorescent molecular probes for bioimaging

This was my primary research direction since PhD thesis. In particular, I worked on dyes undergoing proton and charge transfer (3-hydroxychromones, Nile Red, push-pullfluorene, etc), which change their color and intensity in response to environment polarity. Using these probes I developed a number of probes for lipid membranes, proteins and nucleic acids, which have already been tested in >100 laboratories worldwide. Among them, a probe for apoptosis detection (F2N12S) is currently on the market.

Currently, we focus on fluorogenic and solvatochromic probes for: (1) Biological membranes, notably lipid rafts and exosomes; (2) Membrane receptors, notably GPCRs; (3) Nucleic acids inside the cells based on dye-aptamer recognition concept (“Spinach”-like).

This direction is supported by ANR BrightRiboProbes (2017-2020) and ANR Fluoropep (2017-2020). 

2) Fluorescent nanoparticles based on lipids and polymers

This direction I established in 2010 with the idea to find organic alternative to quantum dots. Our building blocks for nanoparticles are lipids or polymers loaded with specially designed dyes. To ensure high brightness of nanoparticles, I introduced concept of bulky counterions that prevent dyes self-quenching inside the polymer/lipid core. This approach in combination with our unique nanoprecipitation methodology gives 30-40 nm nanoparticles that are >10-fold brighter than quantum dots. Moreover, we described unprecedented ON-OFF switching behavior of up to 500 dyes inside nanoparticles.

Our current research with nanoparticles includes: (1) Ultra-small and super-bright nanoparticles; (2) Fluorogenic and chromogenic nanoparticles for detection of membrane receptors and RNA; (3) Nanoparticles for multi-color long-term cell tracking; (4) Near-infrared in vivo imaging of nanoparticles for cancer theranostics.

This direction is supported by ERC Consolidator grant BrightSens (2015-2020).

 

Education/Career

I born in Kherson, Ukraine, in 1976. I started my research with chemistry and photophysics of new fluorescent dyes, which was a subject of my PhD degree from Kiev National University in 2003. Then, I worked in the University of Strasbourg in a group of Yves Mely, where I could combine synthesis of new dyes with their bioimaging applications. In 2005, in order to extend my expertise towards supramolecular chemistry and nanotechnology, I moved to Catholic University of Leuven, group of Steven de Feyter. Then, I joined CNRS in 2006, received CNRS Bronze Medal in 2010 and was promoted to Director of Research in 2014. In 2015, I obtained ERC consolidator grant BrightSens to work on fluorescent nanoparticles for ultrasensitive detection of cancer markers.

Selected Publications

(>140 per-reviewed articles in total)

Collot, M.; Ashokkumar, P.; Anton, H.; Boutant, E.; Faklaris, O.; Galli, T.; Mely, Y.; Danglot, L.; Klymchenko, A. S.: MemBright: A Family of Fluorescent Membrane Probes for Advanced Cellular Imaging and Neuroscience. Cell Chem. Biol., 2019.

Melnychuk, N.; Klymchenko, A.S.: DNA-Functionalized Dye-Loaded Polymeric Nanoparticles: Ultrabright FRET Platform for Amplified Detection of Nucleic Acids, J. Am. Chem. Soc. 2018, 140, 10856.

Trofymchuk, K.; Reisch, A.; Didier, P.; Fras, F.; Gilliot, P.; Mely, Y.; Klymchenko, A. S.: Giant light-harvesting nanoantenna for single-molecule detection in ambient light. Nature Photonics 2017, 11, 657.

Klymchenko, A. S.: Solvatochromic and Fluorogenic Dyes as Environment-Sensitive Probes: Design and Biological Applications, Acc. Chem Res. 2017, 50, 366.

Bouchaala, R.; Mercier, L.; Andreiuk, B.; Mély, Y.; Vandamme, T.; Anton, N.; Goetz, J.G. Klymchenko, A.S.:Integrity of lipid nanocarriers in bloodstream and tumor quantified by near-infrared ratiometric FRET imaging in living mice. J. Controlled Release 2016, 236, 57.

Reisch, A.; Klymchenko, A.S.: Fluorescent Polymer Nanoparticles Based on Dyes: Seeking Brighter Tools for Bioimaging. Small 2016, 12, 1968.

Shulov, I.; Rodik, R. V.; Arntz, Y.; Reisch, A.; Kalchenko, V. I.; Klymchenko, A. S.: Protein-Sized Bright Fluorogenic Nanoparticles Based on Cross-Linked Calixarene Micelles with Cyanine Corona. Angew. Chem.Int. Ed. 2016, 55, 15884-15888.

Niko, Y.; Didier, P.; Mely, Y.; Konishi, G.; Klymchenko, A. S.: Bright and photostable push-pull pyrene dye visualizes lipid order variation between plasma and intracellular membranes. Sci. Rep. 2016, 6, 18870.

Karpenko, I. A.; Niko, Y.; Yakubovskyi, V. P.; Gerasov, A. O.; Bonnet, D.; Kovtun, Y. P.;Klymchenko, A. S.: Push-pull dioxaborine as fluorescent molecular rotor: far-red fluorogenic probe for ligand-receptor interactions. J. Mater. Chem. C 2016, 4, 3002-3009.

Reisch A, Runser A, Arntz Y, Mély Y, Klymchenko A.S.: Charge-controlled nanoprecipitation as a modular approach to ultrasmall polymer nanocarriers: making bright and stable nanoparticles. ACS Nano 2015, 9, 5104.

Shulov, I.; Oncul, S.; Reisch, A.; Arntz, Y.; Collot, M.; Mely, Y.; Klymchenko, A. S.: Fluorinated counterion-enhanced emission of rhodamine aggregates: ultrabright nanoparticles for bioimaging and light-harvesting. Nanoscale 2015, 7, 18198-18210.

Collot, M.; Kreder, R.; Tatarets, A. L.; Patsenker, L. D.; Mely, Y.; Klymchenko, A. S.: Bright fluorogenic squaraines with tuned cell entry for selective imaging of plasma membrane vs. endoplasmic reticulum. Chem. Commun. 2015, 51, 17136-17139.

Kreder, R.; Pyrshev, K. A.; Darwich, Z.; Kucherak, O. A.; Mely, Y.; Klymchenko, A. S.: Solvatochromic Nile Red Probes with FRET Quencher Reveal Lipid Order Heterogeneity in Living and Apoptotic Cells. Acs Chemical Biology 2015, 10, 1435-1442.

Karpenko, I. A.; Collot, M.; Richert, L.; Valencia, C.; Villa, P.; Mely, Y.; Hibert, M.; Bonnet, D.; Klymchenko, A. S.: Fluorogenic Squaraine Dimers with Polarity-Sensitive Folding As Bright Far-Red Probes for Background-Free Bioimaging. J. Am. Chem. Soc. 2015, 137, 405-412.

Reisch, A.; Didier, P.; Richert, L.; Oncul, S.; Arntz, Y.; Mély, Y.; Klymchenko, A. S.: Collective fluorescence switching of counterion-assembled dyes in polymer nanoparticles. Nature Commun. 2014, 5, 4089.

Y. Niko, Y. Arntz, Y. Mely, G.-I. Konishi, A. S. Klymchenko: Disassembly-driven fluorescence turn-on of polymerized micelles by reductive stimuli in living cells. Chem. Eur. J. 2014, 20, 16473–16477.

Trofymchuk, K., Reisch, A.; Shulov, I.; Mély, Y.; Klymchenko, A. S.: Tuning color and photostability of perylene diimides inside polymer nanoparticles: towards biodegradable substitutes of quantum dots. Nanoscale, 2014, 6, 12934 – 12942.

Kilin, V. N.; Anton, H.; Anton, N.; Steed, E.; Vermot, J.; Vandamme, T. F.; Mely, Y.;Klymchenko, A. S.: Counterion-enhanced cyanine dye loading into lipid nano-droplets for single particle tracking in zebrafish. Biomaterials 2014, 35, 4950.

Klymchenko, A. S.; Kreder, R.: Fluorescent probes for lipid rafts: from model membranes to living cells, Chem. Biol., 2014, 21, 97-113.

Strizhak, A.V.; Postupalenko, V.Y. Shvadchak, V.V.; Morellet, N. Guittet, E. Pivovarenko, V.G.Klymchenko, A.S.; Mély, Y.: Two-color fluorescent L-amino acid mimic of tryptophan for probing peptide-nucleic acid complexes. Bioconjugate Chem. 2012, 23, 2434−2443.

Klymchenko, A.S.; Roger, E.; Anton, N.; Anton, H.; Shulov, I.; Vermot, J.; Mely, Y.;Vandamme, T.F.:  Highly lipophilic fluorescent dyes in nano-emulsions: towards bright non-leaking nano-droplets. RSC Advances, 2012, 2, 11876-11886.

Rodik, R, V.; Klymchenko, A. S.; Jain, N.; Miroshnichenko, S. I.; Richert, L.; Kalchenko, V. I.;Mély, Y. Virus-sized DNA nanoparticles for gene delivery based on micelles of cationic calixarenes. Chem. Eur. J. 2011, 17, 5526-5538.

Kucherak, O.; Oncul, S.; Darwich, Z.; Yushchenko, D. A.; Arntz, Y.; Didier, P.; Mély, Y.;Klymchenko, A. S.: Switchable Nile Red-based probe for cholesterol and lipid order at the outer leaflet of biomembranes. J. Am. Chem. Soc. 2010, 132, 4907–4916.

Kucherak, O.A.; Didier, P.; Mély, Y.; Klymchenko, A.S. Fluorene analogues of Prodan with superior fluorescence brightness and solvatochromism. J. Phys. Chem. Lett. 2010, 1, 616-620.

Shynkar, V. V., Klymchenko, A. S., Kunzelmann, C.; Duportail, G.; Muller, C. D.; Demchenko, A. P.; Freyssinet J.-M.; Mely, Y.: Fluorescent Biomembrane Probe for Ratiometric Detection of Apoptosis. J. Am. Chem. Soc. 2007, 129, 2187-2193.

Klymchenko, A. S.; Demchenko, A. P.: Multiparametric Probing of Intermolecular Interactions with Fluorescent Dye Exhibiting Excited State Intramolecular Proton Transfer. Phys Chem Chem Phys 2003, 5, 461-468.

Klymchenko, A. S.; Duportail, G.; Ozturk, T.; Pivovarenko, V. G.; Mély, Y.; Demchenko, A. S. Novel two-band ratiometric fluorescence probes with different location and orientation in phospholipid membranes. Chem. Biol. 2002, 9, 1199-1208.

Klymchenko, A. S.; Demchenko, A. P.: Electrochromic Modulation of Excited-State Intramolecular Proton Transfer: the New Principle in Design of Fluorescence Sensors J. Am. Chem. Soc. 2002, 124, 12372-12379.