Publications

Macchia, K. Björkström, A. Tewari,V. Eskonen, A. Luukkonen, A. Ghafari, L. Sarcina, M. Caputo, N. Tong-Ochoa, K. Kopra, F. Pettersson, Z. Gounani, L. Torsi, H. Härmä, R. Österbacka Label-free electronic detection of peptide post-translational modification with functional enzyme-driven assay at the physical limit. Cell Reports Physical Science, 2024

Gooran, K. Kopra. Fluorescence-Based Protein Stability Monitoring. Review. International Journal of Molecular Sciences 2024, 25, 1764.

Togo, T. Linh, L.G. Denton, X. ElHilali-Pollard, J. Gu, J. Jiang, C. Liu, H. Liu, Y. Zhao,Y. Zhao,Y. Zheng,Y. Zheng,J. Yang,P. Fan,M.R. Arkin, H. Härmä,D. Sun,S.S. Canan,S.E. Wheeler,A.R. Renslo. Systematic Study of Heteroarene Stacking Using a Congeneric Set of Molecular Glues for Procaspase-6. Journal of Medicinal Chemistry. 2023, 14, 9784-9796.

Mahran, N. Vello, A. Komulainen, M. Malakoutikhah, H. Härmä, K. Kopra. Isothermal chemical denaturation assay for monitoring protein stability and inhibitor interactions. Scientific Reports.2023, 13, 20066.

Kopra, R. Mahran, T. Yli-Hollo, S. Tabata, E. Vuorinen, Y. Fujii, I. Vuorinen, A. Ogawa-Iio, A. Hirayama, T. Soga, A. Sasaki, H. Härmä. Homogeneous luminescent quantitation of cellular guanosine and adenosine triphosphates (GTP and ATP) using QT-Luc^GTP&ATP assay. Analytical and bioanalytical chemistry. 2023, 415, 6689-6700.

Mahran, N. Vello, A. Komulainen, H. Härmä, K. Kopra. Isothermal chemical KRAS denaturation assay for monitoring stability and inhibitors interactions. ESMO Open 2023, 8, 100922.

M.Malakoutikhah, R. Mahran, N. Gooran, A. Masoumi, K. Lundell, A. Liljeblad, Guiley, S. Dai, Q. Zheng, L. Zhu, K.M. Shokat, K. Kopra, H. Härmä. Nanomolar Protein Thermal Profiling with Modified Cyanine Dyes. Analytical Chemistry. 2023, 95, 18344-18351.

Kopra, S. Valtonen, R. Mahran, J.N. Kapp, N. Hassan, W. Gillette, B. Dennis, L. Li, K.D. Westover, A. Plückthun, H. Härmä. Thermal Shift Assay for Small GTPase Stability Screening: Evaluation and Suitability. International journal of molecular sciences. 2022,23, 7095.

Kopra, N. Hassan, E. Vuorinen, S. Valtonen, R. Mahran, H. Habib, P. Jalkanen, P. Susi, V. Hytönen, M. Hankaniemi, S. Ylä-Herttuala, L. Kakkola, M. Peurla, H. Härmä. Rapid high-throughput compatible label-free virus particle quantification method based on time-resolved luminescence. Analytical and Bioanalytical Chemistry. 2022, 414, 4509-4518.

H. Ecke, M. Scislowski, N. Hassan, M. Saura, S. Hallmann, S. Koch, S. Vuolle,M.Malakoutikhah, K. Kopra, H. Härmä. Luminophore Chemistry for Detection of Urinary Bladder Cancer–Comparison to Cytology and Urinary Rapid Tests (BTA stat®, NMP22® BladderChek® and UBC® Rapid Test). Anticancer Research. 2022, 42, 5249-5256.

Vuorinen, S. Valtonen, N. Hassan, R. Mahran, H. Habib, M. Malakoutikhah, K. Kopra, H.Härmä. Protease Substrate-Independent Universal Assay for Monitoring Digestion of Native Unmodified Proteins. International Journal of Molecular Sciences.2021, 22, 6362.

Valtonen, E. Vuorinen, V. Eskonen, M. Malakoutikhah, K. Kopra, H.Härmä. Sensitive, homogeneous, and label-free protein-probe assay for antibody aggregation and thermal stability studies. mAbs. 2021, 13, e1955810.

Kopra, H. Härmä. Methods to Monitor Ras Activation State. In Methods in Molecular Biology, Ras activity and signaling. Eds. I. Rubio and I. Prior, Humana Press, 2021, p. 137

Valtonen, E. Vuorinen, T. Kariniemi, V. Eskonen, J. Le Quesne, M. Bushell, H. Härmä, Kari Kopra. Nanomolar Protein−Protein Interaction Monitoring with a Label-Free Protein-Probe Technique. Analytical Chemistry. 2020, 92, 15781.

Vuorinen, S. Valtonen, V. Eskonen, K. Kopra, H. Härmä. Sensitive thermal stability assay for protein denaturation and protein-ligand interaction studies. Analytical Chemistry. 2020, 92, 3512.

Kopra, E. Vuorinen, M. Abreus-Blanco, Qi Wang, V. Eskonen, W. Gillette, A.T. Pulliainen, M. Holderfield, H. Härmä. Homogeneous Dual-Parametric-Coupled Assay for Simultaneous Nucleotide Exchange and KRAS/RAF-RBD Interaction Monitoring. Analytical Chemistry. 2020, 92, 4971.

Eskonen, N. Tong-Ochoa, L. Mattsson, M. Miettinen, M. Lastusaari, A.T. Pulliainen, K. Kopra, H. Härmä. Single-Peptide TR-FRET Detection Platform for Cysteine-Specific Post-Translational Modifications. Analytical Chemistry. 2020, 92, 19, 13202.

Kopra, I. Sharina, E. Martin, H. Härmä. Homogeneous single-label cGMP detection platform for the functional study of nitric oxide-sensitive (soluble) guanylyl cyclases and cGMP-specific phosphodiesterases. Scientific Reports. 2020, 10, 17469.

G. Manoharan, K. Kopra, H. Härmä, D. Abankwa. High-throughput amenable fluorescence-assays to screen for calmodulin-inhibitors as K-Ras stemness-signaling disruptors. Analytical Biochemistry. 2019, 572, 25.

K. Kopra, N. Tong Ochoa, M. Laine, V. Eskonen, P. J. Koskinen, H. Härmä. Homogeneous peptide-break assay for luminescent detection of enzymatic protein post-translational modification activity utilizing charged peptides. Analytica Chimica Acta. 2019, 1055, 126.

K. Kopra, V. Eskonen, T. Seppälä, J. Jakovleva, H. Härmä. Luminescent peptide-break ‘’signal-on’’ and ‘’signal-off’’ assays for the detection of protein post-translational modifications. ACS Omega. 2019, 4, 4269.

V. Eskonen, N. Tong-Ochoa, S. Valtonen, K. Kopra, H. Härmä. Thermal Dissociation Assay for Time-Resolved Fluorescence Detection of Protein Post-Translational Modifications. ACS Omega. 2019, 4, 16501.

M. Syrjänpää, E. Vuorinen, Q. Wang, H. Härmä, K. Kopra. QTR-FRET: Efficient background reduction technology in time-resolved fluorescence resonance energy transfer assays. Analytica Chimica Acta. 2019, 1092, 93.

P. Grönroos, N.E. Habiba, K. Salminen, M. Nissinen, T. Tuomaala, K. Miikki, Q. Zhang, N. Wei, E. Kauppinen, J. Eskola, H. Härmä, S. Kulmala. Immunoassays Based on Hot Electron-Induced Electrochemiluminescence at Disposable Cell Chips with Printed Electrodes. Sensors. 2019, 19, 2751.

H. Härmä, N. Tong-Ochoa, A.J. van Adrichem, I. Jelesarov, K. Wennerberg, K. Kopra. Toward universal protein post-translational modification detection in high throughput format. Chemical Communications 2018, 54, 2910.

K. Salminen, P. Grönroos, H. Härmä, S. Kulmala. Hot electron-induced electrochemiluminescence of calcein and calcein-Tb(III) complex at disposable oxide-covered aluminum and polyvinyl butyral-carbon black/metal composite electrodes in aqueous solutions. Electrochimica Acta 2018, 266, 212.

K. Kopra, A.J. van Adrichem, O.M.H. Salo-Ahen, J. Peltonen, K. Wennerberg, H. Härmä. High-Throughput Dual Screening method for Ras Activities and Inhibitor.
Analytical Chemistry. 2017, 89, 4508.

Norrbo, J.M. Carvalho, P. Laukkanen, J. Mäkelä, F. Mamedov, M. Peurla, H. Helminen, S. Pihlasalo, H. Härmä, J. Sinkkonen, M. Lastusaari. Lanthanide and Heavy Metal Free Long White Persistent Luminescence from Ti Doped Li–Hackmanite: A Versatile, Low-Cost Material. Advance Functional Materials. 2017, 27, 1606547.

S. Pihlasalo,T. Deguchi, M. Virtamo, J. Jacobino, K. Chary, F.R. Lopez-Picon, G. Brunhofer-Bolzer, R. Huttunen, A. Fallarero, P. Vuorela, H. Härmä. Luminometric nanoparticle-based assay for high sensitivity detection of β-amyloid aggregation.
Analytical Chemistry, 2017, 89, 2398.

M. Högmander, C.J. Paul, S. Chan, E. Hokkanen, V. Eskonen, T. Pahikkala, S. Pihlasalo. Luminometric Label Array for Counting and Differentiation of Bacteria. Analytical Chemistry, 2017, 89, 3208.

S. Pihlasalo, T. Deguchi, M. Virtamo, J. Jacobino, K. Chary, F.R. López-Picón, G. Brunhofer-Bolzer, R. Huttunen, A. Fallarero, P. Vuorela, H. Härmä. Luminometric Nanoparticle-Based Assay for High Sensitivity Detection of β-Amyloid Aggregation. Analytical Chemistry, 2017, 89, 2398.

P. Naula, A. Airola, S. Pihlasalo, I. Montoya Perez, T. Salakoski, T. Pahikkala. Assessment of metal ion concentration in water with structured feature selection. Chemosphere, 2017, 185, 1063.

J. Terävä, E. Hokkanen, S. Pihlasalo. Nonspecific luminometric assay for monitoring protein adsorption efficiency and coverage on nanoparticles. Nanoscale. 2017, 9, 2232.

S. Pihlasalo, L. Mariani, H. Härmä. Quantitative and discriminative analysis of nucleic acid samples using luminometric nonspecific nanoparticle methods. Nanoscale, 2016, 8, 5902.

S. Pihlasalo, I. Montoya Perez, N. Hollo, E. Hokkanen, T. Pahikkala, H. Härmä. Luminometric Label Array for Quantification and Identification of Metal Ions. Analytical Chemistry, 2016, 88, 5271.

R. Huttunen, T. Näreoja, L. Mariani, H. Härmä. Residual nanoparticle label immunosensor for wash-free C-reactive protein detection in blood. Biosensors and Bioelectronics, 2016, 83, 54.

H. Härmä, R. Peltomaa, S. Pihlasalo. Lanthanide Label Array Method for Identification and Adulteration of Foodstuff. Analytical Chemistry, 2015, 87, 6451.

K. Kopra, A. Rozwandowicz-Jansen, M. Syrjänpää, O. Blaževitš, A. Ligabue, S. Veltel, U. Lamminmäki, D. Abankwa, H. Härmä. A GTP-specific Fab fragment based GTPase activity assay. Analytical Chemistry 2015, 87, 3527.

M. Solman, A. Ligabue, O. Blazevits, A. Jaiswal, Y. Zhou, H. Liang, K. Kopra, C. Guzman, H. Härmä, J.F. Hancock, T. Aittokallio. Cancer associated mutations in the switch III-region of Ras increase tumorigenicity by nanocluster augmentation. eLIFE, 2015, 4, e08905.

S. Pihlasalo, P. Hänninen H. Härmä. Method for Determination of Polyethylene Glycol Molecular Weight. Analytical Chemistry. 2015, 87, 3981.

N. Tong Ochoa, K. Kopra, M. Syrjänpää, H. Härmä. EGFR-mediated peptide-phosphorylation monitoring using pTyr-ab and QRET technique. Analytica Chimica Acta, 2015, 897, 96.

K. Kopra, H. Härmä. Quenching resonance energy transfer (QRET): a single-label technique for inhibitor screening and interaction. New Biotechnology. 2015, 32, 575.

K. Kopra, A. Rozwandowicz-Jansen, A. Ligabue, M. Syrjänpää, O. Blaževitš, S. Veltel, P. Hänninen, D. Abankwa, U. Lamminmäki, H. Härmä. GTP-specific antibody for monitoring Ras GTPases activation cycle through GTP hydrolysis. Analytical Chemistry. 2015, 87, 3527.

S. Pihlasalo, M. Virtamo, N. Legrand, P. Hänninen, H. Härmä. Simple nanoparticle-based luminometric method for molecular weight determination of polymeric compounds. Analytical Chemistry, 2014, 86, 1038.

K. Kopra, M. Syrjänpää, P. Hänninen, H. Härmä. Non-Competitive Aptamer-Based Quenching Resonance Energy Transfer Assay for Homogeneous Growth Factor Quantification. Analyst. 2014, 139, 2016.

K. Kopra, A. Ligabue, Q. Wang, M. Syrjänpää, O. Blaževitš, S. Veltel, A.J. van Adrichem, P. Hänninen, D. Abankwa, H. Härmä. A homogeneous quenching resonance energy transfer assay for kinetic analysis of the GTPase nucleotide exchange reaction. Analytical Bioanalytical Chemistry 2014, 406, 4147.

T. Näreoja, A. Ebner, H.J. Gruber, B. Taskinen, F. Kienberger, P. Hänninen, V.P. Hytönen, P. Hinterdorfer, H. Härmä. Kinetics of bioconjugate nanoparticle label binding in a sandwich-type immunoassay. Analytical Bioanalytical Chemistry 2014, 406, 493.

J. Siivonen, S. Tiittanen, M. Lehmusto, P. Lehtonen, P. Hänninen, H. Härmä. Novel nonspecific liquid fingerprint technology for wine analysis: A feasibility study. Australian Journal of Grape and Wine Research, 2014, 20, 172.

P. Hänninen, J. Siivonen, P. Väisänen, S. Tiittanen, M. Lehmusto, T. Teimonen, N. Törnkvist, M. Sandell, A. Knaapila, P. Mundill, H. Härmä. Fuzzy liquid analysis by an array of non-specifically interacting reagents – the taste of fluorescence. JACS 2013, 135, 7422.

S. Pihlasalo, A. Engbert, E. Martikkala, P. Ylander, P. Hänninen, H. Härmä. Particle-Based Method with Two-Photon Excitation Detection for Sensitive Quantification of Proteins and Counting of Cells. Analytical Chemistry, 2013, 85, 2689.

P. Ihalainen, H. Majumdar, T. Viitala, B. Törngren, T. Närjeoja, A. Määttänen, J. Sarfraz, H. Härmä, M. Yliperttula, R. Österbacka, J. Peltonen. Application of paper-supported printed gold electrodes for impedimetric immunosensor development. Biosensors 2013, 3, 1.

K. Kopra, Shweta, E. Martikkala, P. Hänninen, U. Petäjä-Repo, H. Härmä. A homogeneous single-label quenching resonance energy transfer assay for a δ-opioid receptor-ligand using intact cells. Analyst, 2013, 138, 4907.

Q. Wang, K. Nchimi Nono, M. Syrjänpää, L.J. Charbonniére, J. Hovinen, P. Hänninen, H. Härmä. Stable and highly fluorescent europium(III) chelates for time-resolved immunoassays. Inorganic Chemistry, 2013, 5, 8461.

H. Härmä, S. Pihlasalo, P.J. Cywinski, P. Mikkonen, T. Hammann, H.-G. Löhmannsröben, P. Hänninen. Protein Quantificatin Using Resonance Energy Transfer between Donor Nanoparticles and Acceptor Quantum Dots. Analytical Chemistry, 2013, 85, 2921.

S. Pihlasalo, J. Granberg, P. Hänninen, H. Härmä. Luminescence stability improvement in liposome based homgeneous luminescence resonance energy transfer. Analytical Biochemistry, 2013, 440, 6.

T. Stenholm, A.J. Hakanen, E. Hakanen, H. Härmä, M. Osterblad,. J. Vuopio, P.E. Hänninen, P. Huovinen, K. Rankakokko-Jalava, P. Kotilainen. High-throughput screening of colonization samples for methicillin-resistant Staphylococcus aureus. Scandinavian Journal of Infectious Diseases. 2013, 45, 922.

S. Pihlasalo, L. Auranen, P. Hänninen, H. Härmä. Method for estimation of protein isoelectric point. Analytical Chemistry, 2012, 84, 8253.

S. Pihlasalo, P. Puumala, P. Hänninen, H. Härmä. Sensitive method for the determination of protein and cell concentration based on competitive adsorption to nanoparticle and time-resolved luminescence resonance energy transfer between labeled proteins. Analytical Chemistry, 2012, 84, 4950.

S. Pihlasalo, A. Kulmala, A. Rozwandowicz-Jansen, P. Hänninen, H. Härmä. Sensitive Luminometric Method for Quantification of Proteins Based on Particle Adsorption and Dissociation of Chelated Europium. Analytical Chemistry. 2012, 84, 1386-93.

E. Martikkala, S. Veltel, J. Kirjavainen, A. Rozwandowicz-Jansen, U. Lamminmäki, P. Hänninen, H. Härmä. A Homogeneous Single-Label Biochemical Ras Activation Assay using Time-Resolved Luminescence. Analytical Chemistry, 2011, 83, 9230.

S. Pihlasalo, P. Hänninen, H. Härmä. A Simple High Sensitivity Luminescence Nanoparticle Assay for the Detection of Protein Aggregation. Analytical Chemistry, 2011, 83, 1163.

H. Härmä, J. Toivonen, J. Soini, P. Hänninen, W. Parak. Manipulation of long-lived luminescence in CdTe quantum dots and time-resolved fluorescence immunoassay of C-reactive protein using CdTe quantum dots. Sensors, 2011, 11, 11335.

P. Hänninen, H. Härmä, Lanthanide Luminescence: Photophysical, Analytical and Biological Aspects, Springer Series on Fluorescence, Springer, Vol. 7, 2011.

T. Soukka, H. Härmä. Lanthanide nanoparticules as photoluminescent reporters. Eds. Hänninen, Härmä. In Lanthanide Luminescence: Photophysical, Analytical and Biological Aspects, Springer Series on Fluorescence, Springer, Vol. 7, 2011, 89-114.

R. Huttunen, J. Soini, P. Härkönen, P. Hänninen, H. Härmä. Multiparametric luminescence method for quantitative cell surface protein expression analysis and imaging. Journal of Immunological Methods, 2011, 367, 40.

E. Martikkala, A. Rozwandowicz-Jansen, H. Frang, I. Hemmilä, P. Hänninen, H. Härmä. Sensitive cell-based homogeneous cAMP assay using QRET technique. Journal of Biomolecular Screening, 2011, 16, 356.

R. Huttunen, Shweta, E. Martikkala, M. Lahdenranta, P. Virta, P. Hänninen, H. Härmä. Single-label time-resolved luminescence assay for estrogen receptor-ligand binding. Analytical Biochemistry, 2011, 415, 27.

A. Chaudhary, H. Härmä, P. Hänninen, M.J. McShane, R. Srivastava. Glucose response of near-infrared alginate-based microsphere sensors under dynamic reversible conditions. Diabetes Technology & Therapeutics, 2011, 13, 827.

T. Stenholm, A.J. Hakanen, S. Salmenlinna, S. Pihlasalo, H. Härmä, P.E. Hänninen, P. Huovinen, J. Vuopio, P. Kotilainen. Evaluation of the TPX MRSA assay for the detection of methicillin-resistant Staphylococcus aureus. European journal of clinical microbiology & infectious diseases, 2011, 30, 1237.

H. Härmä, S. Laakso, S. Pihlasalo, P. Hänninen, Bertrand Faure, Subhasis Rana, L. Bergström,. Rapid detection of trace amounts of surfactants using nanoparticles in fluorometric assays. Nanoscale, 2010, 2, 69.

A. Rozwandowicz-Jansen, J. Laurila, E. Martikkala, H. Frang, I. Hemmilä, M. Scheinin, P. Hänninen, H. Härmä. Homogeneous GTP binding assay for activation of G-protein coupled receptor. Journal of Biomolecular Screening, 2010, 15, 261.

H. Härmä, S. Laakso, S. Pihlasalo, P. Hänninen. A fluorometric fullerenol sensor for rapid detection of ionic and non-ionic surfactants. Tenside Surfactants Detergents, 2010, 1, 40.

S. Pihlasalo, L. Pellonperä, P. Hänninen, H. Härmä. Sensitive fluorometric nanoparticle assays for cell counting and viability. Analytical Chemistry, 2010, 82, 9282.

H. Härmä, G. Sarrail, J. Kirjavainen, E. Martikkala, I. Hemmilä, P. Hänninen. Comparison of homogeneous single-label fluorometric binding assays: Fluorescence polarization and multiparameter QRET technique. Analytical Chemistry, 2010, 82, 892.

S. Tang, J. Zhao, A. Wang, R. Viswanath, H. Härmä, R.F. Little, R. Yarchoan, S.L. Stramer, S. Lee, O. Wood, E.Y. Wong, X. Wang, I.K. Hewlett. Characterization of immune responses to capsid protein (p24) of human immunodeficiency virus type 1: Implications for detection. Clinical Vaccine Immunology, 2010, doi:10.1128/CVI.00066-10.

M. Aaltonen, M. Waris, T. Hyypiä, H. Härmä. Emergence and Immergence of viruses.
Emergence: Complexity & Organization Journal, 2010, 12, 1.

S. Pihlasalo, J. Kirjavainen, P. Hänninen, H. Härmä. Ultrasensitive protein concentration measurement based on particle adsorption and fluorescence quenching.
Analytical chemistry 2009, 81, 4995.

H. Härmä, A. Rozwandowicz-Jansen, E. Martikala, H. Frang, M. Perälä, P. Hänninen. A new simple cell-based homogeneous time-resolved fluorescence QRET technique for receptor-ligand interaction screening. Journal of Biomolecular Screening, 2009, 14, 936.

S. Tang, M. Moayeri, Z. Chen, H. Härmä, J. Zhao, R.H. Purcell, S.H. Leppla, I.K. Hewlett. Detection of Anthrax Toxin by an Ultrasensitive Immunoassay Using Europium Nanoparticles. Clinical and Vaccine Immunology, 2009, 16, 408.

A. Valanne, J. Suojanen, J. Peltonen, T. Soukka, P. Hänninen, H. Härmä. Size effect of europium(III) donor particles in a FRET-based assay utilizing adsorption of acceptor-labelled protein. Analyst, 2009, 134, 980.

S. Pihlasalo, M. Hara, P. Hänninen, J.P. Slotte, J. Peltonen, H. Härmä. Liposome Based Homogeneous Luminescence Resonance Energy Transfer, Analytical Biochemistry, 2009, 384, 231.

T. Näreoja, M. Vehniäinen, U. Lamminmäki, P. Hänninen, H. Härmä. Study on nonspecificity of an immuoassay using nanoparticle labels, Journal of Immunological Methods, 2009, 345, 80.

H. Härmä, R. Suhonen, T. Kololuoma, A. Kärkkäinen, M. Hara, P. Hänninen. Thin Solid Europium(III) Dye Layers as Donors in Time-Resolved Fluorescence Resonance Energy Transfer Assays, Applied Surface Science, 2009, 255, 6529.

E. Martikkala, M. Lehmusto, M. Lilja, A. Rozwandowicz, J. Lunden, P. Hänninen, U. Petäjä-Repo, H. Härmä. Cell-based 2-adrenergic receptor ligand-binding assay using synthesized europium-labeled ligands and time-resolved fluorescence. Analytical Biochemistry, 2009, 392, 103.

T. Näreoja, A. Määttänen, J. Peltonen, P. Hänninen, H. Härmä. Does surface defects and denaturation of capture surface proteins lead to nonspecific binding in immunoassays using antibody-coated polystyrene nanoparticle labels. Journal of immunological methods, 2009, 347, 24.

A. Chaudhary, M. Raina, H. Härmä, P. Hänninen, M. McShane, R. Srivastava. Evaluation of glucose sensing affinity binding assay entrapped in fluorescent dissolved-core alginate microspheres. Biotechnology and Bioengineering, 2009, 104, 1075.

Ville Eskonen, 2020

Peptide-Based Drug Discovery Tools for Protein Post-Translational Modifications

Natalia Tong-Ochoa, 2019

The Peptide-Break Technology: A Novel Approach for Protein Post-translational Modification Assays in Drug Discovery