Interactions of 17ß-Hydroxysteroid Dehydrogenase Type 10 and Cyclophilin D in Alzheimer's Disease.

The nucleus-encoded 17ß-hydroxysteroid dehydrogenase type 10 (17ß-HSD10) regulates cyclophilin D (cypD) in the mitochondrial matrix. CypD regulates opening of mitochondrial permeability transition pores. Both mechanisms may be affected by amyloid ß peptides accumulated in mitochondria in Alzheimer's disease (AD). In order to clarify changes occurring in brain mitochondria, we evaluated interactions of both mitochondrial proteins in vitro (by surface plasmon resonance biosensor) and detected levels of various complexes of 17ß-HSD10 formed in vivo (by sandwich ELISA) in brain mitochondria isolated from the transgenic animal model of AD (homozygous McGill-R-Thy1-APP rats) and in cerebrospinal fluid samples of AD patients. By surface plasmon resonance biosensor, we observed the interaction of 17ß-HSD10 and cypD in a direct real-time manner and determined, for the first time, the kinetic parameters of the interaction (ka 2.0 × 105 M1s-1, kd 5.8 × 104 s-1, and KD 3.5 × 10-10 M). In McGill-R-Thy1-APP rats compared to controls, levels of 17ß-HSD10-cypD complexes were decreased and those of total amyloid ß increased. Moreover, the levels of 17ß-HSD10-cypD complexes were decreased in cerebrospinal fluid of individuals with AD (in mild cognitive impairment as well as dementia stages) or with Frontotemporal lobar degeneration (FTLD) compared to cognitively normal controls (the sensitivity of the complexes to AD dementia was 92.9%, that to FTLD 73.8%, the specificity to AD dementia equaled 91.7% in a comparison with the controls but only 26.2% with FTLD). Our results demonstrate the weakened ability of 17ß-HSD10 to regulate cypD in the mitochondrial matrix probably via direct effects of amyloid ß. Levels of 17ß-HSD10-cypD complexes in cerebrospinal fluid seem to be the very sensitive indicator of mitochondrial dysfunction observed in neurodegeneration but unfortunately not specific to AD pathology. We do not recommend it as the new biomarker of AD.

Ionic Environment Affects Biomolecular Interactions of Amyloid-ß: SPR Biosensor Study.

In early stages of Alzheimer's disease (AD), amyloid beta (Aß) accumulates in the mitochondrial matrix and interacts with mitochondrial proteins, such as cyclophilin D (cypD) and 17ß-hydroxysteroid dehydrogenase 10 (17ß-HSD10). Multiple processes associated with AD such as increased production or oligomerization of Aß affect these interactions and disbalance the equilibrium between the biomolecules, which contributes to mitochondrial dysfunction. Here, we investigate the effect of the ionic environment on the interactions of Aß (Aß1-40, Aß1-42) with cypD and 17ß-HSD10 using a surface plasmon resonance (SPR) biosensor. We show that changes in concentrations of K+ and Mg2+ significantly affect the interactions and may increase the binding efficiency between the biomolecules by up to 35% and 65% for the interactions with Aß1-40 and Aß1-42, respectively, in comparison with the physiological state. We also demonstrate that while the binding of Aß1-40 to cypD and 17ß-HSD10 takes place preferentially around the physiological concentrations of ions, decreased concentrations of K+ and increased concentrations of Mg2+ promote the interaction of both mitochondrial proteins with Aß1-42. These results suggest that the ionic environment represents an important factor that should be considered in the investigation of biomolecular interactions taking place in the mitochondrial matrix under physiological as well as AD-associated conditions.

Functional gold nanoparticles for optical affinity biosensing.

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 carboxy-terminated oligo-ethylene thiolate linker layer. The following parameters of preparation of Ab-AuNP have been found to have a significant effect on Ab-AuNP performance in affinity biosensors: the time of reaction of activated AuNPs with antibody, concentrations of antibody and amino-coupling reagents, and composition of immobilization buffer (molarity and salt content). In contrast, pH of immobilization buffer has been demonstrated to have only a minor influence. Our experiments showed that the Ab-AuNPs prepared under optimum conditions offered a binding efficiency of Ab-AuNPs to CEA as high as 63%, which is more than 4 times better than the best efficiencies reported for similar functional AuNPs so far. We employed these Ab-AuNPs with a surface plasmon resonance (SPR) biosensor for the detection of CEA and showed that the Ab-AuNPs enhanced the sensor response to CEA by a factor of 1000. We also demonstrated that the Ab-AuNPs allow the biosensor to detect CEA at concentrations as low as 12 and 40 pg/mL in buffer and 50% blood plasma, respectively.

Pregnancy-Associated Plasma Protein A2 in Hemodialysis Patients: Significance for Prognosis.

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 of 102 long-term HD patients and 25 healthy controls. HD patients were prospectively followed up for five years (2009-2014). PAPP-A2 was measured by surface plasmon resonance biosensor, PAPP-A by time resolved amplified cryptate emission. RESULTS: PAPP-A2, similarly as PAPP-A, was significantly increased in HD patients (median (interquartile range)) PAPP-A2: 6.2 (2.6-10.8) ng/mL, vs. 3.0 (0.7-5.9) ng/mL, p=0.006; PAPP-A: 18.9 (14.3-23.4) mIU/L, vs. 9.5 (8.4-10.5) mIU/L, p<0.001). In HD patients, PAPP-A2 correlated weakly but significantly with PAPP-A (τ=0.193, p=0.004). Unlike PAPP-A, PAPP-A2 was not significant for prognosis of HD patients when tested alone. There was a significant interaction between PAPP-A and PAPP-A2 on the mortality due to infection of HD patients (p=0.008). If PAPP-A was below median, mortality due to infection was significantly higher for patients with PAPP-A2 values above median than for patients with low PAPP-A2 levels (p=0.011). CONCLUSION: PAPP-A2 is increased in HD patients and interacts with PAPP-A on patients´ prognosis.

Copolymer Brush-Based Ultralow-Fouling Biorecognition Surface Platform for Food Safety.

Functional polymer coatings that combine the ability to resist nonspecific fouling from complex media with high biorecognition element (BRE) immobilization capacity represent an emerging class of new functional materials for a number of bioanalytical and biosensor technologies for medical diagnostics, security, and food safety. Here, we report on a random copolymer brush surface - poly(CBMAA-ran-HPMAA) - providing high BRE immobilization capacity while simultaneously exhibiting ultralow-fouling behavior in complex food media. We demonstrate that both the functionalization and fouling resistance capabilities of such copolymer brushes can be tuned by changing the surface contents of the two monomer units: nonionic N-(2-hydroxypropyl) methacrylamide (HPMAA) and carboxy-functional zwitterionic carboxybetaine methacrylamide (CBMAA). It is demonstrated that the resistance to fouling decreases with the surface content of CBMAA; poly(CBMAA-ran-HPMAA) brushes with CBMAA molar content up to 15 mol % maintain excellent resistance to fouling from a variety of homogenized foods (hamburger, cucumber, milk, and lettuce) even after covalent attachment of BREs to carboxy groups of CBMAA. The poly(CBMAA 15 mol %-ran-HPMAA) brushes functionalized with antibodies are demonstrated to exhibit fouling resistance from food samples by up to 3 orders of magnitude better when compared with the widely used low-fouling carboxy-functional oligo(ethylene glycol) (OEG)-based alkanethiolate self-assembled monolayers (AT SAMs) and, furthermore, by up to 2 orders of magnitude better when compared with the most successful ultralow-fouling biorecognition coatings - poly(carboxybetaine acrylamide), poly(CBAA). When model SPR detections of food-borne bacterial pathogens in homogenized foods are used, it is also demonstrated that the antibody-functionalized poly(CBMAA 15 mol %-ran-HPMAA) brush exhibits superior biorecognition properties over the poly(CBAA).

5'-O-Methylphosphonate nucleic acids--new modified DNAs that increase the Escherichia coli RNase H cleavage rate of hybrid duplexes.

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 demonstrated that the increasing number of 5'-hydroxyphosphonate or 5'-O-methylphosphonate units in antisense oligonucleotides (AOs) significantly stabilizes the heteroduplexes, whereas 3'-O-methylphosphonate AOs cause strong destabilization of the heteroduplexes. Only the heteroduplexes with 5'-O-methylphosphonate units in the antisense strand exhibited a significant increase in Escherichia coli RNase H cleavage activity by up to 3-fold (depending on the ratio of phosphodiester and phosphonate linkages) in comparison with the natural heteroduplex. A similar increase in RNase H cleavage activity was also observed for heteroduplexes composed of miRNA191 and complementary AOs containing 5'-O-methylphosphonate units. We propose for this type of AOs, working via the RNase H mechanism, the abbreviation MEPNA (MEthylPhosphonate Nucleic Acid).

Monitoring RAYT activity by surface plasmon resonance biosensor.

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 known as repetitive extragenic palindrome elements (REPs). Although RAYT has been subject of numerous studies, where DNA binding and cleavage by RAYT have been confirmed for Escherichia coli, the molecular mechanism of DNA insertion has not been fully understood. In this work, it is demonstrated that surface plasmon resonance (SPR) biosensor technology combined with a system of DNA hairpin probes (mimicking the natural REP sequence) and short oligonucleotides (ONs) can provide a rapid and real-time platform for monitoring and quantification of RAYT activity. We utilized RAYT from E. coli (strain MG1655) as a model system, where we evaluated its activity towards both a natural REP sequence as well as REP sequences having modifications targeting specific features of the DNA crucial for the DNA binding and cleavage. The characteristics of the RAYT-DNA interaction obtained by means of the SPR approach were compared with the results of SDS-PAGE analysis.

Enhancing sensitivity of surface plasmon resonance biosensors by functionalized gold nanoparticles: size matters.

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 to their composition, size, and concentration, thus allowing for accurate predictions regarding the SPR sensor response to various AuNPs. The effect of the AuNP size is also investigated experimentally using an SPR biosensor for the detection of carcinoembryonic antigen (CEA) in which AuNPs covered with neutravidin (N-AuNPs) are used in the last step of a sandwich assay to enhance the sensor response to biotinylated secondary antibody against CEA. The experimental data are in excellent agreement with the results of the theoretical analysis. We demonstrate that the sensor response enhancement generated by the N-AuNPs is determined by (i) the sensor sensitivity to N-AuNP surface density (Sσ) and (ii) the ability of the N-AuNPs to bind to the functionalized surface of the sensor. Our results indicate that, while Sσ increases with the size of the N-AuNP, the ability of the functionalized surface of the sensor to bind the N-AuNPs is affected by steric effects and decreases with the size of N-AuNP.

Label-free biosensing in complex media: a referencing approach.

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 (SSR)) uses a single functionalized surface split into the detection and reference channel to which complex sample (detection channel) and complex sample mixed with biomolecules binding to the analyte and thus inhibiting the binding of the analyte to the functionalized surface (reference channel) is introduced. This approach ensures that (i) only the detection channel captures the analyte and (ii) nonspecific binding incurred in the detection and reference channels are the same. We evaluate this approach in a model biosensing experiment, detection of a cancer biomarker carcinoembryonic antigen (CEA) in blood plasma using antibody against CEA and a surface plasmon resonance (SPR) biosensor. We detect CEA in three different blood plasma samples and demonstrate that this novel referencing approach provides more accurate results and lower biological variability than the conventional referencing.

Using surface plasmon resonance, capillary electrophoresis and diffusion-ordered NMR spectroscopy to study drug release kinetics.

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., surface plasmon resonance biosensor technology (SPR), capillary electrophoresis, and 1H diffusion-ordered nuclear magnetic resonance spectroscopy, which were innovatively applied for drug release determination. The methods were optimised to quantify the pH-triggered release of three structurally different drugs from a polymer carrier. The suitability of these methods for drug release characterisation was evaluated and compared using several parameters including applicability for diverse samples, the biological relevance of the experimental setup, method complexity, and the analysis outcome. The SPR method was the most universal method for the evaluation of diverse drug molecule release allowing continuous observation in the flow-through setting and requiring a small amount of sample.

Biofunctionalized gold nanoparticles for SPR-biosensor-based detection of CEA in blood plasma.

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 antibody used in the second step of the CEA sandwich assay, and with (2) bovine serum albumin, to minimize the nonspecific interaction of the bio-AuNPs with complex samples (blood plasma). We demonstrate that this approach makes it possible for the SPR biosensor to detect CEA in blood plasma at concentrations as low as 0.1 ng/mL, well below normal physiological levels (approximately nanograms per milliliter). Moreover, the limit of detection achieved using this approach is better by a factor of more than 1,000 than limits of detection reported so far for CEA in blood plasma using SPR biosensors.

Shielding effect of monovalent and divalent cations on solid-phase DNA hybridization: surface plasmon resonance biosensor study.

Solid-phase hybridization, i.e. the process of recognition between DNA probes immobilized on a solid surface and complementary targets in a solution is a central process in DNA microarray and biosensor technologies. In this work, we investigate the simultaneous effect of monovalent and divalent cations on the hybridization of fully complementary or partly mismatched DNA targets to DNA probes immobilized on the surface of a surface plasmon resonance sensor. Our results demonstrate that the hybridization process is substantially influenced by the cation shielding effect and that this effect differs substantially for solid-phase hybridization, due to the high surface density of negatively charged probes, and hybridization in a solution. In our study divalent magnesium is found to be much more efficient in duplex stabilization than monovalent sodium (15 mM Mg2+ in buffer led to significantly higher hybridization than even 1 M Na+). This trend is opposite to that established for oligonucleotides in a solution. It is also shown that solid-phase duplex destabilization substantially increases with the length of the involved oligonucleotides. Moreover, it is demonstrated that the use of a buffer with the appropriate cation composition can improve the discrimination of complementary and point mismatched DNA targets.

Streptavidin-enhanced assay for sensitive and specific detection of single nucleotide polymorphism in TP53.

This paper reports an approach to detection of single nucleotide polymorphism based on special amplification assay and surface plasmon resonance biosensor technology. In this assay, a part of the target DNA is recognized by a probe (probe A) coupled with streptavidin-oligonucleotide (SON) complexes ex situ, and when the mixture is injected in the sensor, another part of the target DNA is recognized by a DNA probe (probe B) immobilized on the sensor surface. To achieve high sensitivity and specificity, the assay is optimized in terms of composition of SON complexes, probe design, and assay temperature. It is demonstrated that this approach provides high specificity (no response to targets containing single-mismatched bases) and sensitivity (improves sensor response to perfectly matched oligonucleotides by one order of magnitude compared to the direct detection method). The assay is applied to detection of a short synthetic analogue of TP53 containing a "hot spot"-single nucleotide mismatch frequently mutated in germ line cancer-at levels down to 40 pM.

Detecting attomolar concentrations of microRNA related to myelodysplastic syndromes in blood plasma using a novel sandwich assay with nanoparticle release.

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 release of nanoparticles from a sensor surface. We combine this assay (herein referred to as the nanoparticle-release (NPR) assay) with a surface plasmon resonance biosensor and show that the assay is able to enhance the specific sensor response associated with the binding of target miRNA while suppressing the interfering effects caused by the non-specific binding. We apply the assay to the detection of miRNAs related to myelodysplastic syndromes (miR-125b, miR-16) in blood plasma and demonstrate that the assay enables detection of miR-125b with a limit of detection (LOD) of 349 aM (corresponding to the lowest detectable amounts of 419 zmol). The achieved LOD is better by a factor of ∼100 when compared to the conventional nanoparticle-enhanced sandwich assay. Moreover, we demonstrate that the NPR assay may be combined with time-division multiplexing for the multiplexed miRNA detection.

Real-time monitoring of biomolecular interactions in blood plasma using a surface plasmon resonance biosensor.

We report a novel approach to biosensor-based observations of biomolecular interactions which enables real-time monitoring of biomolecular interactions in complex media. This approach is demonstrated by investigating the interaction between the human chorionic gonadotropin (hCG) and its antibody in blood plasma using a surface plasmon resonance biosensor and a dispersionless microfluidics system. The real-time binding data obtained in blood plasma are compared with those obtained in buffer and blood plasma using a conventional method. It is also demonstrated that the proposed approach can enhance the capability of the biosensor to detect biomolecules in complex samples in terms of detection time and sensitivity. In the model experiment, this approach is shown to enable direct detection of hCG in blood plasma at levels which are five times lower than those detected using the conventional detection approach.

Study of Biomolecular Interactions of Mitochondrial Proteins Related to Alzheimer's Disease: Toward Multi-Interaction Biomolecular Processes.

Progressive mitochondrial dysfunction due to the accumulation of amyloid beta (Aß) 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, Aß interacts with a number of biomolecules, including cyclophilin D (cypD) and 17ß-hydroxysteroid dehydrogenase type 10 (17ß-HSD10), and affects their physiological functions. However, despite intensive ongoing research, the exact mechanisms through which Aß impairs mitochondrial functions remain to be explained. In this work, we studied the interactions of Aß with cypD and 17ß-HSD10 in vitro using the surface plasmon resonance (SPR) method and determined the kinetic parameters (association and dissociation rates) of these interactions. This is the first work which determines all these parameters under the same conditions, thus, enabling direct comparison of relative affinities of Aß to its mitochondrial binding partners. Moreover, we used the determined characteristics of the individual interactions to simulate the concurrent interactions of Aß with cypD and 17ß-HSD10 in different model situations associated with the progression of AD. This study not only advances the understanding of Aß-induced processes in mitochondria during AD, but it also provides a new perspective on research into complex multi-interaction biomolecular processes in general.

Surface plasmon resonance study on HIV-1 integrase strand transfer activity.

Understanding the molecular mechanism of HIV-1 integrase (IN) activity is critical to find functional inhibitors for an effective AIDS therapy. A robust, fast, and sensitive method for studying IN activity is required. In this work, an assay for real-time label-free monitoring of the IN activity based on surface plasmon resonance was developed. This assay enabled direct monitoring of the integration of a viral doubled-stranded (ds) DNA into the host genome. The strand transfer reaction was detected by using two different DNA targets: supercoiled plasmid (pUC 19) and short palindrome oligonucleotide. The effect of the length of the DNA target on the possibility to monitor the actual process of the strand transfer reaction is discussed. The surface density of integrated ds-DNA was determined. IN binding to the oligonucleotide complexes and model DNA triplexes in the presence of various divalent ions as metal cofactors was investigated as well. The assay developed can serve as an important analytical tool to search for potential strand transfer reaction inhibitors as well as for the study of compounds interfering with the binding of ds long terminal repeats-IN complexes with the host DNA.

In vitro study of interaction of 17ß-hydroxysteroid dehydrogenase type 10 and cyclophilin D and its potential implications for Alzheimer's disease.

In early stages of Alzheimer's disease (AD), amyloid-ß (Aß) accumulates in neuronal mitochondria where it interacts with a number of biomolecules including 17beta-hydroxysteroide dehydrogenase 10 (17ß-HSD10) and cyclophilin D (cypD). It has been hypothesized that 17ß-HSD10 interacts with cypD preventing it from opening mitochondrial permeability transition pores and that its regulation during AD may be affected by the accumulation of Aß. In this work, we demonstrate for the first time that 17ß-HSD10 and cypD form a stable complex in vitro. Furthermore, we show that factors, such as pH, ionic environment and the presence of Aß, affect the ability of 17ß-HSD10 to bind cypD. We demonstrate that K+ and Mg2+ ions present at low levels may facilitate this binding. We also show that different fragments of Aß (Aß1-40 and Aß1-42) affect the interaction between 17ß-HSD10 and cypD differently and that Aß1-42 (in contrast to Aß1-40) is capable of simultaneously binding both 17ß-HSD10 and cypD in a tri-complex.

Peptide Functionalization of Gold Nanoparticles for the Detection of Carcinoembryonic Antigen in Blood Plasma via SPR-Based Biosensor.

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 biomolecular detection in complex matrices. In this work we show how the ζ-potential (Zpot) of bio-functionalized gold spherical NPs (Bio-NPs) is related to the SPR sensor response enhancement of an immune-sandwich-assay for the detection of the carcinoembryonic antigen (CEA), a cancer marker for colorectal carcinomas. In particular, we prepare bio-functional nanoparticles by varying the amount of peptide (either streptavidin or antibody against CEA) bound on their surface. Specific and non-specific sensor responses, reproducibility, and colloidal stability of those bio-functional nanoparticles are measured via SPR and compared to ζ-potential values. Those parameters are first measured in buffer solution, then measured again when the surface of the biosensor is exposed to blood plasma, and finally when the nanoparticles are immersed in blood plasma and flowed overnight on the biosensor. We found that ζ-potential values can guide the design of bio-functional NPs with improved binding efficiency and reduced non-specific sensor response, suitable reproducibility and colloidal stability, even in complex matrixes like blood plasma.

Advances in Surface Plasmon Resonance Imaging and Microscopy and Their Biological Applications.

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 these methods, in particular, in optical platforms and functional coatings. In addition, the biological applications of these methods are reviewed. These include the detection of a broad variety of analytes (nucleic acids, proteins, bacteria), the investigation of biological systems (bacteria and cells), and biomolecular interactions (drug-receptor, protein-protein, protein-DNA, protein-cell).