Jiri Homola

• Prof. PhD, DSc.
• Managing Director at Institute of Photonics and Electronics (IPE)

Nanomedicines, including polymer nanocarriers with controlled drug release, are considered next-generation therapeutics with advanced therapeutic properties and reduced side effects. To develop safe and efficient nanomedicines, it is crucial to precisely determine the drug release kinetics. Herein, we present application of analytical methods, i.e....

Aberrant glycosylation of glycoproteins has been linked with various pathologies. Therefore, understanding the relationship between aberrant glycosylation patterns and the onset and progression of the disease is an important research goal that may provide insights into cancer diagnosis and new therapy development. In this study, we use a surface pl...

Antifouling polymer brushes are widely utilized in biomedical applications to prevent non-specific interactions with biological fluids. They consist of surface-tethered polymer chains and are commonly formed when the chains are “grafted to” (GT) a surface by chemisorption or “grafted from” (GF) a surface in a surface-initiated polymerization. Altho...

Here we study the analytical performance of label-free optical biosensors with respect to analyte-induced refractive index changes that can be measured by a biosensor (refractive index resolution). We present an analytical model that interrelates the refractive index resolution and the parameters of the optical platform of a biosensor. We demonstra...

Nanophotonic devices, which control light in subwavelength volumes and enhance light–matter interactions, have opened up exciting prospects for biosensing. Numerous nanophotonic biosensors have emerged to address the limitations of the current bioanalytical methods in terms of sensitivity, throughput, ease-of-use and miniaturization. In this Review...

Base excision repair is one of the important DNA repair mechanisms in cells. The fundamental role in this complex process is played by DNA glycosylases. Here, we present a novel approach for the real-time measurement of uracil DNA glycosylase activity, which employs selected oligonucleotides immobilized on the surface of magnetic nanoparticles and...

Microribonucleic acids (miRNAs) are short noncoding ribonucleic acids that have been linked with a multitude of human diseases including lung, breast, and hematological cancers. In this work, we present a novel, extremely sensitive assay for the label-free optical biosensor-based detection of miRNAs, which is based on the oligonucleotide-triggered...

We present a new optical biosensor based on surface plasmons excited on an array of gold nanostripes via attenuated total reflection. We investigate performance of the biosensor using a theoretical model that considers both optical and mass transport aspects. The analysis of optical aspects employs two different approaches: a complex model incorpor...

Functional materials employing organic coatings on inorganic substrates are perceived as potential platforms for applications in a variety of fields. Therefore, the investigation of interactions of such systems with the microenvironment has become an important direction in surface science. Herein, we study the interaction of one of the buffers most...

In early stages of Alzheimer’s disease (AD), amyloid beta (Aβ) accumulates in the mitochondrial matrix and interacts with mitochondrial proteins, such as cyclophilin D (cypD) and 17β-hydroxysteroid dehydrogenase 10 (17β-HSD10). Multiple processes associated with AD such as increased production or oligomerization of Aβ affect these interactions and...

Progressive mitochondrial dysfunction due to the accumulation of amyloid beta (Aβ) peptide within the mitochondrial matrix represents one of the key characteristics of Alzheimer’s disease (AD) and appears already in its early stages. Inside the mitochondria, Aβ interacts with a number of biomolecules, including cyclophilin D (cypD) and 17β-hydroxys...

We report on new approach to rapidly actuate plasmonic characteristics of thin gold film perforated with nanohole arrays that are coupled with arrays of gold nanoparticles. The near-field interaction between localized and propagating surface plasmon modes supported by the structure is actively modulated by changing the distance between nanoholes an...

The nucleus-encoded 17β-hydroxysteroid dehydrogenase type 10 (17β-HSD10) regulates cyclophilin D (cypD) in the mitochondrial matrix. CypD regulates opening of mitochondrial permeability transition pores. Both mechanisms may be affected by amyloid β peptides accumulated in mitochondria in Alzheimer's disease (AD). In order to clarify changes occurri...

The development of methods advancing the understanding of molecular processes related to Alzheimer`s disease (AD) and detection of biomarkers of AD presents an important research goal. We present a new biosensor-based method for the detection of a prospective biomarker of AD, the complex of tau protein and amyloid β (Aβ). The detection method combi...

In early stages of Alzheimer’s disease (AD), amyloid-β (Aβ) accumulates in neuronal mitochondria where it interacts with a number of biomolecules including 17beta-hydroxysteroide dehydrogenase 10 (17β-HSD10) and cyclophilin D (cypD). It has been hypothesized that 17β-HSD10 interacts with cypD preventing it from opening mitochondrial permeability tr...

The study of optical affinity biosensors based on plasmonic nanostructures has received significant attention in recent years. The sensing surfaces of these biosensors have complex architectures, often composed of localized regions of high sensitivity (electromagnetic hot spots) dispersed along a dielectric substrate having little to no sensitivity...

The onset and progression of numerous serious diseases (e.g. various types of malignancies, neurodegenerative diseases, and cardiac diseases) are, on a molecular level, associated with protein modifications and misfolding. Current methods for the detection of misfolded proteins are not able to detect the whole misfolded subproteome and, moreover, a...

Myelodysplastic syndromes (MDS) are a heterogeneous group of hematological malignancies with a high risk of transformation to acute myeloid leukemia (AML). MDS are associated with posttranslational modifications of proteins and variations in the protein expression levels. In this work, we present a novel interactomic diagnostic method based on both...

Bisphenol A (BpA) is a chemical that is extensively used in common plastic products, such as food and drink containers. It can leach from the plastics and penetrate into the human body, where it acts as an endocrine disruptor with significant risks to human health. In order to minimize the exposure of human populations to BpA, methods for the detec...

Surface plasmon resonance microscopy and imaging are optical methods that enable observation and quantification of interactions of nano- and microscale objects near a metal surface in a temporally and spatially resolved manner. This review describes the principles of surface plasmon resonance microscopy and imaging and discusses recent advances in...

We introduce a new approach to plasmonic biosensing with superior biosensing properties based on spectroscopy of an electromagnetic mode guided by a monolayer of sparsely distributed colloidal plasmonic nanoparticles. The theoretical prediction of optical and sensing performance is confirmed by an experimental study in which adsorption of biomolecu...

Nanoparticles functionalized with specific biological recognition molecules play a major role for sensor response enhancement in surface plasmon resonance (SPR) based biosensors. The functionalization procedure of such nanoparticles is crucial, since it influences their interactions with the environment and determines their applicability to biomole...

Surface plasmon resonance (SPR) biosensors have become an important label-free optical biomolecular sensing technology and a “gold standard” for retrieving information on the kinetics of biomolecular interactions. Even though biomolecules typically contain an abundance of easily ionizable chemical groups, there is a gap in understanding of whether...

Unraveling the details of how supported lipid bilayers (SLBs) are coupled to oxide surfaces is experimentally challenging, and there is an outstanding need to develop highly surface-sensitive measurement strategies to determine SLB separation distances. Indeed, subtle variations in separation distance can be associated with significant differences...

There has recently been a growing use of surface bound nanorods within electrochemical and optical sensing applications. Predictions of the microfluidic rate of analyte transport to such nanorods (either individual or to an array) remains important for sensor design and data analysis; however, such predictions are difficult, as nanorod aspect ratio...

Surface-plasmon resonance (SPR) sensors represent a formidable technology for molecular biology and bioanalytics applications. Here, we devise a new interrogation architecture that transforms a standard SPR chip into an optical-heterodyne clock detector comparable with the best SPR instruments. The key ingredients are (i) the conversion of refracti...

Optical biosensors based on plasmonic nanostructures present a promising alternative to conventional biosensing methods and provide unmatched possibilities for miniaturization and high-throughput analysis. Previous works on the topic, however, have been overwhelmingly directed towards elucidating the optical performance of such sensors, with little...

Background: Pregnancy-associated plasma protein A (PAPP-A) is associated with adverse outcome of long-term hemodialysis patients (HD). The aim of the study was to test whether its homolog pregnancy-associated plasma protein A2 (PAPP-A2) can be detected in serum of HD patients and to define its significance. Methods: The studied group consisted o...

There remains a need for the multiplexed detection of biomolecules at extremely low concentrations in fields of medical diagnostics, food safety, and security. Surface plasmon resonance imaging is an established biosensing approach in which the measurement of the intensity of light across a sensor chip is correlated with the amount of target biomol...

Functional gold nanoparticles (AuNPs) are commonly used to enhance the response of optical affinity biosensors. In this work, we investigated the effect of preparation conditions on functional properties of AuNPs functionalized with antibody (Ab-AuNPs), specifically AuNPs with antibody against carcinoembryonic antigen (CEA) covalently attached via...

Fouling from complex biological fluids such as blood plasma to biorecognition element (BRE)-functionalized coatings hampers the use of affinity biosensor technologies in medical diagnostics. Here we report the effects the molecular mechanisms involved in functionalization of low-fouling carboxy-functional coatings have on the BRE capacity and resis...

Introduction Myelodysplastic syndromes are clonal hematopoetic stem cell disorders characterized by refractory cytopenias with displasia as a result of ineffective hematopoiesis. Approximately 30 percent of MDS cases progress to acute myeloid leukemia. Excess blasts are the strongest predictors for poor outcome and are associated with disease progr...

Introduction Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal stem cell disorders characterized by a high risk of evolution into acute myeloid leukemia (AML). Different processes are involved in its pathogenesis, such as (epi)genetic alterations and immunological dysfunctions. Till now, in plasma several protein markers for MDS w...

This paper reviews fundamentals of optical affinity biosensors based on plasmonic nanostructures and discusses recent advances in the development of this technology, including plasmonic nanostructures and surface plasmon phenomena, advances in sensor instrumentation, and functional coatings. Examples of applications for both the detection of chemic...

There has recently been an extensive amount of work regarding the development of optical, electrical, and mechanical (bio)sensors employing planar arrays of surface bound nanoparticles. The sensor output for these systems is dependent on the rate at which analyte is transported to, and interacts with, each nanoparticle in the array. However, there...

The scavenger receptor cysteine-rich (SRCR) family comprises a group of membrane-attached or secreted proteins that contain one or more modules/domains structurally similar to the membrane distal domain of type I macrophage scavenger receptor. Although no all-inclusive biological function has been ascribed to the SRCR family, some of these receptor...

The electromagnetic enhancement in surface-enhanced Raman scattering (SERS) caused by localized surface plasmon resonance is a near-field effect, often limiting the practicality of SERS in many applications. However, no attempts have been made to investigate field extension through symmetrical refractive index modulation in a SERS-based system. Her...

Proteins purified and used in SPR assays. (A) Coomassie-staining of sCD5, sCD6, and Spα proteins purified from TCS with Ni-NTA resin and imidazole elution. Gels of sCD6 and sCD5 (12%) and Spα (10%) were run under reducing conditions. Identity of the proteins was confirmed by immunoblotting (not shown). (B) Anionic chromatography of N-SSc5D recovere...

sCD6 binds to cells expressing its ligand, CD166. Panel of cells screened using recombinant sCD6 tetramers for binding to CD166. Cells were incubated with streptavidin-PE as an isotype control (red), sCD6 tetramers (blue), and sCD58 tetramers (green). (A) Jurkat and K562 cells do not express CD166, and therefore sCD6 tetramers showed no binding. sC...

Functional polymer coatings that combine the ability to resist non-specific fouling from complex media with high biorecogni-tion element (BRE) immobilization capacity represent an emerging class of new functional materials for a number of bioanalyti-cal and biosensor technologies for medical diagnostics, security, and food safety. Here we report on...

Gold nanoplasmonic substrates with high sensitivity and spectral reproducibility are key components of molecular sensors based on surface-enhanced Raman scattering (SERS). In this work, we used a confocal Raman microscope and several types of gold nanostructures (arrays of nanodiscs, nanocones and nanodisc dimers) prepared by hole-mask colloidal li...

A novel method enabling rapid fabrication of 2D periodic arrays of plasmonic nanoparticles across large areas is presented. This method is based on the interference of multiple coherent beams originating from diffraction of large-diameter collimated beam on a transmission phase mask. Mutual orientation of the interfering beams is determined by para...

Pregnancy associated plasma protein A2 (PAPP-A2) is a metalloproteinase that plays multiple roles in fetal development and post-natal growth. Here we present a novel surface plasmon resonance (SPR) biosensor for the rapid and quantitative detection of PAPP-A2 in blood samples. This biosensor uses a single surface referencing approach and a sandwich...

A nanoplasmonic ruler method is presented in order to measure the deformation of adsorbed, nm-scale lipid vesicles on solid supports. It is demonstrated that single adsorbed vesicles undergo greater deformation on silicon oxide over titanium oxide, offering direct experimental evidence to support membrane tension-based theoretical models of support...

We investigate selected periodic arrays of nanostructures inspired by metasurfaces originally used in metamaterial structures and evaluate their potential for surface plasmon resonance applicable in sensing. Building blocks including rectangles, cut wires, crosses, fishnets, split ring resonators were ordered on suitable substrates and their reflec...

In this study we examine the experimental use of the staggered herringbone mixer (SHM) for the signal enhancement of a microfluidic surface plasmon resonance imaging (SPRi) affinity-based biosensor. We define the signal enhancement (Emix) as the ratio of the time-dependent slope of the sensor response of a SHM-based microfluidic channel and that of...

In this study we examine the use of the staggered herringbone mixer (SHM) to increase the efficiency of analyte delivery to a planar biosensor surface. Although there has been an extensive amount of research regarding the optimization of the SHM for mixing purposes, there has been very little work regarding the use of said micromixers for sensing p...

This review focuses on recent advances in the development of functionalizable antifouling coatings and their applications in label-free optical biosensors. Approaches to the development of antifouling coatings, ranging from self-assembled monolayers and PEG derivatives to ultra-low-fouling polymer brushes, are reviewed. Methods of preparation and c...

Over the last 20 years, optical methods have been increasingly used in analytical and bioanalytical applications. These methods have been applied in two rather broad ways: for direct and for indirect detection. Whereas direct-detection approaches typically enable the detection of an analyte in a single step, indirect approaches usually require the...

The process of DNA transposition involves the binding, cleavage, and recombination of specific DNA segments (transposable elements, TE) and is catalyzed by special enzymes encoded by the TE transposases. REP-associated tyrosine transposases (RAYTs) are a class of Y1 nucleases related to the IS200/IS605 transposases associated with a bacterial TE kn...

Introduction MicroRNAs (miRNAs) are involved in the control of hematopoiesis, their deregulation also appears to play role in the pathogenesis of several hematopoietic diseases. Multiple miRNAs have been reported to be abnormally expressed in hematologic cancers; moreover, specific miRNA expression profiles have been proposed as diagnostic and prog...

Introduction The protein microarrays are becoming the leading technology in proteomic research area. They enable to implement both features of proteins that can be altered in disease as quantitative proteomics (levels in biological samples) as well as functional proteomics (determination of their selective interactions with other biomolecules). Pro...

New composite layer architecture of 3D hydrogel polymer network that is loaded with mole­cularly imprinted polymer nanoparticles (nanoMIP) is reported for direct optical detection of low‐molecular‐weight compounds. This composite layer is attached to the metallic surface of a surface plasmon resonance (SPR) sensor in order to simultaneously serve a...

We study how the size of spherical gold nanoparticles (AuNPs) influences their ability to enhance the response of optical biosensors based on surface plasmon resonance (SPR). We present a theoretical model that relates the enhancement generated by the AuNPs with their composition, size, and concentration, thus allowing for accurate predictions rega...

We investigate the optical response to refractive index changes of a Fano resonance occurring in a random array of gold nanoparticles supported on a glass substrate. The Fano resonance results from the interference between localized surface plasmon on a gold nanoparticle and the light reflected at the boundary of the glass substrate. We demonstrate...

Surface plasmons (SPs) excited on microscopic areas are desired in a variety of applications, including SP microscopy and (bio)sensing. We present an optical method of excitation of SPs using a dry, medium-magnification microscope objective and a diffraction grating. SPs are excited by focusing laser light into a diffraction-limited spot on the gra...

A novel nanofabrication technique based on 4-beam interference lithography is presented that enables the preparation of large macroscopic areas (>50 mm²) of perfectly periodic and defect-free two-dimensional plasmonic arrays of nanoparticles as small as 100 nm. The technique is based on a special interferometer, composed of two mirrors and a sample...

The low-fouling and functionalizable surface platforms were investigated in terms of functionalization effect on fouling resistance from undiluted media (blood plasma, food extracts), surface capacities, and biorecognition capabilities. The platforms included hydroxy- and carboxyfunctional polymer brushes and standard OEG-based alkanethiolate chemi...

Engineered combinatorial libraries derived from small protein scaffolds represent a powerful tool for generating novel binders with high affinity, required specificity and designed inhibitory function. This work was aimed to generate a collection of recombinant binders of human interleukin-23 receptor (IL-23R), which is a key element of proinflamma...

Several oligothymidylates containing various ratios of phosphodiester and isopolar 5′-hydroxyphosphonate, 5′-O-methylphosphonate and 3′-O-methylphosphonate internucleotide linkages were examined with respect to their hybridization properties with oligoriboadenylates and their ability to induce RNA cleavage by ribonuclease H (RNase H). The results d...

We investigate the performance of a surface-plasmon-resonance refractive-index (RI) sensor based on an optical resonator. The resonator transforms RI changes of liquid samples, interacting with the surface plasmon excited by near-infrared light, into a variation of the intra-cavity optical loss. Cavity ring-down measurements are provided as a proof...

The combination of microarray technologies with microfluidic sample delivery and real-time detection methods has the capability to simultaneously monitor 10-1000s of biomolecular interactions in a single experiment. Despite the benefits that microfluidic systems provide, they typically operate in the laminar flow regime under mass transfer limitati...

Theoretical study of sensing properties of lattice resonances supported by arrays of gold nanoparticles expressed in terms of the figure of merit (FOM) is reported. Analytical expressions for the FOM for surface and bulk refractive index changes are derived to establish the relationship between the sensing performance and design parameters and to a...

Nanopatterned 2-dimensional Au nanocluster arrays with controlled configuration are fabricated onto reconstructed nanoporous poly(styrene-block-vinylpyridine) inverse micelle monolayer films. Near-field coupling of localized surface plasmons is studied and compared for disordered and ordered core-centered Au NC arrays. Differences in evolution of t...

Plasmonic nanoantennas provide new routes for efficiently detecting, analyzing, and monitoring single biomolecules via fluorescence, Raman, and infrared absorption spectroscopies. The development of efficient biosensors for multispectral spectroscopy remains nevertheless limited by the narrowband responses of plasmonic devices, as they are generall...

It is suggested that intracellular tau protein (τ), when released extracellularly upon neuron degeneration, could evoke direct toxic effects on the cholinergic neurotransmitter system through muscarinic receptors and thus contribute to the pathogenesis of Alzheimer's disease. In this study, we evaluated the in vitro effects of six naturally occurri...

We report on a method for surface plasmon resonance (SPR) refractive index sensing based on direct time-domain measurements. An optical resonator is built around an SPR sensor, and its photon lifetime is measured as a function of loss induced by refractive index variations. The method does not rely on any spectroscopic analysis or direct intensity...

We present a novel approach to reference-compensated label-free affinity biosensing in complex media. Unlike conventional approaches that employ surfaces with different biological functionalities in the detection and reference channels to produce a reference-compensated sensor response, the new approach (referred as to single surface referencing -...

We report a system, which combines electrochemical and surface plasmon resonance (SPR) techniques on the same sensing chip. Each channel of a four-channel laboratory SPR sensor is supplemented with two planar gold electrodes (the reference and the counter electrodes), whereas the gold layer of SPR chip is used as the working electrode. A custom ele...

A new concept of compact biochip for surface plasmon-enhanced fluorescence assays is reported. It takes advantage of the amplification of fluorescence signal through the coupling of fluorophore labels with confined and strongly enhanced field intensity of surface plasmons. In order to efficiently excite and collect the emitted fluorescence light vi...

Affinity-based biosensing systems have become an important analytical tool for the detection and study of numerous biomolecules. The merging of these sensing technologies with microfluidic flow cells allows for faster detection times, increased sensitivities, and lower required sample volumes. In order to obtain a higher degree of performance from...

Multifunctional mitochondrial enzyme 17β-hydroxysteroid dehydrogenase type 10 plays a role in the development of Alzheimer's disease. However, changes in its expression in the brain or cerebrospinal fluid are not fully specific for this type of dementia. Our previous study revealed that complexes of the enzyme and amyloid β in cerebrospinal fluid c...

Optical antennas represent an enabling technology for enhancing the detection of molecular vibrational signatures at low concentrations and probing the chemical composition of a sample in order to identify target molecules. However, efficiently detecting different vibrational modes to determine the presence (or the absence) of a molecular species r...

A finite element method based on the full-vectorial H -field formulation has been employed to achieve the maximum field penetration in the sensing medium of the slot-waveguide-based ring resonator biosensor. The use of nanometer scale guiding structure where optical mode is confined in a low-index region permits a very compact sensor with high opti...

Human interferon gamma (hIFNγ) is an important inflammatory cytokine, which is extensively expressed by immune system in response to various pathogens. In this work we present a biosensor for the direct detection of hIFNγ based on surface plasmon resonance (SPR) and engineered proteins derived from albumin binding domain (ABD) of protein G. We comp...

Here we present a theoretical study of the sensing capability of a biosensor based on localized surface plasmons (LSP). The sensing structure consists of an array of gold cylinders which support coupling of LSP with Rayleigh anomalies, resulting in a narrow line spectrum. We utilize numerical simulations pertaining to both the photonic and masstran...

Surface plasmon resonance (SPR) sensor has become a crucial tool for characterizing and quantifying biomolecular interactions. This chapter describes the principles of SPR biosensors. It presents a brief overview of the advances in SPR optical platforms, in particular within the last decade. It is organized into four subsections, based on the metho...

We report on the use of new biofunctionalized gold nanoparticles (bio-AuNPs) that enable a surface plasmon resonance (SPR) biosensor to detect low levels of carcinoembryonic antigen (CEA) in human blood plasma. Bio-AuNPs consist of gold nanoparticles functionalized both with (1) streptavidin, to provide high affinity for the biotinylated secondary...

Despite great advances in our understanding of the molecular basis of many diseases, there are still substantial gaps in our understanding of oncohematological diseases as well as in the development of effective strategies for early diagnosis and for treatment. The current interest in proteomics is growing partly due to the prospects that proteomic...

Cell volume and its regulation are key factors for cellular integrity and also serve as indicators of various cell pathologies. SPR sensors represent an efficient tool for real-time and label-free observations of changes in cell volume and shape. Here, we extend this concept by employing the use of long-range surface plasmons (LRSP). Due to the enh...

Surface plasmon-coupled emission (SPCE) from emitters in a close proximity to a plasmonic Bragg grating is investigated. In this study, the directional fluorescence emission mediated by Bragg-scattered surface plasmons and surface plasmons diffraction cross-coupled through a thin metallic film is observed by using the reverse Kretschmann configurat...

Recombinant ligands derived from small protein scaffolds show promise as robust research and diagnostic reagents and next generation protein therapeutics. Here, we derived high-affinity binders of human interferon gamma (hIFNγ) from the three helix bundle scaffold of the albumin-binding domain (ABD) of protein G from Streptococcus G148. Computation...

Surface plasmon resonance (SPR) sensors are known to be able to detect very low surface concentrations of (bio)molecules on macroscopic areas. To explore the potential of SPR biosensors to achieve single-molecule detection, we have minimized the read-out area (to ∼ 64 μm 2 ) by employing a sensor system based on spectroscopy of surface plasmons gen...

We present a portable surface plasmon resonance (SPR) sensor based on spectroscopy of surface plasmons on a special diffractive structure. The sensor combines a microfluidic cartridge incorporating the special diffractive structure functionalized with DNA probes and a compact SPR reader. We apply the sensor to detection of nucleic acids employing t...