Kinetic discrimination of sequence-specific DNA-drug binding measured by surface plasmon resonance imaging and comparison to solution-phase measurements

Label-free observation of DNA-encoded liposome fusion by surface plasmon resonance

Assembly and fusion between different populations of lipid nanoparticles was mediated by membrane-anchored lipidated nucleic acid (LiNA) strands and observed using surface plasmon resonance (SPR) as a label-free real-time assay. Irreversible membrane fusion was distinguished from reversible assembly by enzymatical cleavage of dsDNA tethers in situ. The assay enables user-friendly monitoring and application of membrane fusion in the context of liposomal drug delivery or synthetic biology.

An Insight Into the Physicochemical Properties of Gold Nanoparticles in Relation to Their Clinical and Diagnostic Applications

The ease of formulation and surface modification of gold nanoparticles (AuNPs) by ligands, greater biocompatibility, non-cytotoxicity, and excellent optical properties are the characteristics that necessitate their application in clinical and genomic research. Not only that, but the extensive synthetic chemistry of AuNPs also offers precise control over physicochemical and optical properties owing to the inert, biocompatible, and non-toxic nature of the inner gold core. Another important property of AuNPs involves their incorporation into larger structures, including liposomes or polymeric materials, thereby increasing their capability of drug delivery in concurrent therapy and imaging labels for enhanced diagnostic applications. AuNPs are endowed with physical properties that suggest their use as adjuvants for radiotherapy and bio-imaging and in computed tomography (CT) scans, diagnostic systems, and therapy. Thus, these features strongly endorse the AuNPs in thrust areas of biomedical fields. The diverse properties of gold nanoparticles (AuNPs) have made them promising candidates in biomedical fields, including in the development of theranostics, which encompasses using these gold nanoparticles for both diagnosis and therapy simultaneously. To appreciate these and related applications, a need arises to review the basic principles and multifunctional attributes of AuNPs in relation to their advances in imaging, therapy, and diagnostics.

Dual-mode surface plasmon resonance sensor chip using a grating 3D-printed prism

The method for fabricating a grating prism surface plasmon resonance (SPR) sensor chip was developed. The grating prism was 3D-printed by a stereolithography 3D printer and subsequently created a grating pattern by soft lithography. A gold film was thermally evaporated on the grating prism. Moreover, a liquid cell was 3D-printed and assembled into a gold-coated grating prism. To make the sensor chip compact and practical, a compatible prism holder was 3D-printed by a fused deposition model 3D printer. The SPR sensor chip was mounted on the rotation stage and the SPR spectrum was recorded by spectrometer. The SPR excitation of the sensor chip can be extended to the near-infrared region by creating a grating pattern on the prism surface. A gold-coated grating prism exhibited dual modes of SPR excitations, namely, prism-coupling SPR (PC-SPR) and grating-coupling SPR (GC-SPR). The dual-mode SPR excitation was observed at the incident angles of 45°-80°. When the incident angle increased, the SPR excitation of the PC-SPR mode exhibited a blue shift in the wavelength region of 480-690 nm, whereas the GC-SPR mode exhibited a red shift in the wavelength region of 670-770 nm. The surface plasmon (SP) dispersion obtained from the dual-mode SPR configuration confirmed observable PC-SPR (which corresponded to + SP⁰ of the gold-resin interface) and GC-SPR (which corresponded to -SP⁺¹ of the gold-air interface), which could be excited from the developed substrate. The refractive index sensitivities of the PC-SPR and GC-SPR modes were 2924.4 and 414.9 nm RIU^-1, respectively. The SPR excitations of the sensor chip exhibited a simultaneous shift when the local refractive index of the materials adjacent to the gold-coated grating prism surface was changed, especially the material that had overlapping light absorption at the SPR excitation wavelength. Using this fabrication process, the prism is designed and then printed; moreover, the grating pattern on the prism surface can be employed to tune the SPR excitation wavelength of the sensor chip for the versatility and broad perspective of the optical sensing-based SPR.

Grating-coupled interferometry reveals binding kinetics and affinities of Ni ions to genetically engineered protein layers

Reliable measurement of the binding kinetics of low molecular weight analytes to their targets is still a challenging task. Often, the introduction of labels is simply impossible in such measurements, and the application of label-free methods is the only reliable choice. By measuring the binding kinetics of Ni(II) ions to genetically modified flagellin layers, we demonstrate that: (1) Grating-Coupled Interferometry (GCI) is well suited to resolve the binding of ions, even at very low protein immobilization levels; (2) it supplies high quality kinetic data from which the number and strength of available binding sites can be determined, and (3) the rate constants of the binding events can also be obtained with high accuracy. Experiments were performed using a flagellin variant incorporating the C-terminal domain of the nickel-responsive transcription factor NikR. GCI results were compared to affinity data from titration calorimetry. We found that besides the low-affinity binding sites characterized by a micromolar dissociation constant (Kd), tetrameric FliC-NikRC molecules possess high-affinity binding sites with Kd values in the nanomolar range. GCI enabled us to obtain real-time kinetic data for the specific binding of an analyte with molar mass as low as 59 Da, even at signals lower than 1 pg/mm2.

Fabrication of Miniature Surface Plasmon Resonance Sensor Chips by Using Confined Sessile Drop Technique

In this study, we demonstrate a simple and efficient method to fabricate miniature surface plasmon resonance (SPR) sensor chips by using confined sessile drop technique. A liquid optical adhesive (NOA 61) was dropped on the circular flat surface of cylindrical substrates made of poly(dimethylsiloxane) (PDMS). The formation of hemispherical optical prisms was accomplished by taking advantage of the sharp edges of cylindrical PDMS substrates that prevented the overflow of liquid NOA 61 at the edge of substrates. The size of the hemispherical optical prisms can be controlled by changing the diameter of the cylindrical PDMS substrates. After UV curing, the SPR sensor chips were obtained by the deposition of 3 nm thick chromium and 47 nm thick gold on the flat side of the prisms. The fabricated miniature SPR sensor chips were then mounted on a three-dimensional-printed flow cell to complete the microfluidic SPR sensor module. The miniature SPR sensor chips provided a comparable sensitivity to the conventional high-refractive-index glass SPR chips. To demonstrate the detection capability of nanometer-sized materials, we applied the miniature microfluidic SPR system for monitoring the deposition of layer-by-layer ultrathin films of poly(diallyldimethylammonium chloride)/poly(sodium 4-styrenesulfonate) and for detecting human immunoglobulin G.

Binding interaction of a heteroleptic silver(I) complex with DNA: A joint experimental and computational study

A new heteroleptic Ag(I) complex formulated as [Ag(daf)(phen)]NO₃, where daf and phen stand for 4,5-diazafluoren-9-one and 1,10-phenanthroline, respectively, has been prepared and structurally characterized by elemental analysis, spectroscopic methods (IR, ¹HNMR, and UV-Vis) and cyclic voltammetry. The geometry optimization around Ag(I) at the level of DFT has demonstrated that the Ag(I) center has been nested in a tetrahedral N4 coordination geometry which found to be in close agreement with the experimentally proposed structure. The bond lengths, angles, and the HOMO/LUMO energies have been calculated to substantiate the geometry of the complex. The DNA binding property of the Ag(I) complex has been explored in detail both theoretically (DFT and molecular docking) and experimentally (UV-Vis absorption spectroscopy, circular dichroism spectroscopy, luminescence quenching, competitive binding with ethidium bromide, cyclic voltammetry, and gel electrophoresis), indicating the good affinity of the Ag(I) complex for the intercalation (K_b (binding constant) = 3.45 × 10⁵ M^-1). Providing a fuller picture of Ag(I) complex-DNA interaction, the energy-minimized structure of the complex has been docked to the DNA with a d(AGACGTCT)₂ sequence and the results are in close agreement with experimental achievements and make a deeper insight into the relationship between the structure and biological activity of the complex.

Specific interaction of platinated DNA and proteins by surface plasmon resonance imaging

A surface plasmon resonance imaging method to differentiate the interaction between the protein human high mobility group box 1 or human nuclear protein positive cofactor 4 (PC4) and DNAs has been developed.

Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile

Understanding the molecular mechanism by which probes and chemotherapeutic agents bind to nucleic acids is a fundamental issue in modern drug design. From a computational perspective, valuable insights are gained by the estimation of free energy landscapes as a function of some collective variables (CVs), which are associated with the molecular recognition event. Unfortunately the choice of CVs is highly non-trivial because of DNA's high flexibility and the presence of multiple association-dissociation events at different locations and/or sliding within the grooves. Here we have applied a modified version of Locally-Scaled Diffusion Map (LSDMap), a nonlinear dimensionality reduction technique for decoupling multiple-timescale dynamics in macromolecular systems, to a metadynamics-based free energy landscape calculated using a set of intuitive CVs. We investigated the binding of the organic drug anthramycin to a DNA 14-mer duplex. By performing an extensive set of metadynamics simulations, we observed sliding of anthramycin along the full-length DNA minor groove, as well as several detachments from multiple sites, including the one identified by X-ray crystallography. As in the case of equilibrium processes, the LSDMap analysis is able to extract the most relevant collective motions, which are associated with the slow processes within the system, i.e., ligand diffusion along the minor groove and dissociation from it. Thus, LSDMap in combination with metadynamics (and possibly every equivalent method) emerges as a powerful method to describe the energetics of ligand binding to DNA without resorting to intuitive ad hoc reaction coordinates.

Silica nanowire arrays for diffraction-based bioaffinity sensing

Arrays of electrodeposited silica nanowires (SiO2 NWs) have been fabricated over large areas (cm(2)) on fluoropolymer thin films attached to glass substrates by a combination of photolithography and electrochemically triggered sol-gel nanoscale deposition. Optical and scanning electron microscopy (SEM) measurements revealed that the SiO2 NW arrays had an average spacing of ten micrometers and an average width of 700 nm with a significant grain structure that was a result of the sol-gel deposition process. The optical diffraction properties at 633 nm of the SiO2 NW arrays were characterized when placed in contact with solutions by using a prism-coupled total internal reflection geometry; quantification of changes in these diffraction properties was applied in various sensing applications. Bulk refractive index sensing by using the SiO2 NW grating was demonstrated with a sensitivity of 1.30×10(-5) RIU. Toposelectively chemically modified SiO2 NW arrays were used for diffraction biosensing measurements of surface binding events, such as the electrostatic adsorption of gold nanoparticles and the bioaffinity adsorption of streptavidin onto a biotin monolayer. Finally, the application of the SiO2 NW arrays for practical medical-diagnostic applications was demonstrated by monitoring the diffraction of SiO2 NW arrays functionalized with a single-stranded (ss)DNA aptamer to detect human α-thrombin from solutions at sub-pathologic nanomolar concentrations.

Microcantilevers bend to the pressure of clustered redox centers

The redox-activated deflection of microcantilevers has attracted interest for nanoactuation and chemical sensing. Microcantilever sensors are devices that transduce (bio)chemical reactions into a quantifiable nanomechanical motion via surface stress changes. Despite promising applications in analytical science, poor signal-to-noise ratios and a limited understanding of the molecular origins of the surface stress changes that cause the observed deflections remain obstacles to cantilever-based sensing becoming an established (bio)detection method, such as surface plasmon resonance and electrochemistry. We use phase-separated, binary self-assembled monolayers (SAMs) of ferrocenyldodecanethiolate and n-undecanethiolate as a model system to study the effect of the steric crowding of the redox centers on the surface stress change and cantilever deflection produced by the electrochemical oxidation of the surface-tethered ferrocene to ferrocenium. We correlate the measured surface stress change to the fraction of the clustered ferrocenyldodecanethiolate phase in the binary SAMs. The pairing of anions with the sterically crowded clustered ferroceniums induces a collective molecular reorientation which drives the cantilever deflection. The results provide fundamental insights into the response mechanism of microcantilever-based actuating and sensing technologies.

Solution-phase vs surface-phase aptamer-protein affinity from a label-free kinetic biosensor

Aptamers are selected DNA ligands that target biomolecules such as proteins. In recent years, they are showing an increasing interest as potential therapeutic agents or recognition elements in biosensor applications. In both cases, the need for characterizing the mating between the target and the aptamer either in solution or immobilized on a surface, is pressing. In this context, we have developed a kinetic biosensor made of micro-arrayed anti-thrombin aptamers to assess the kinetic parameters of this interaction. The binding of label-free thrombin on the biosensor was monitored in real-time by Surface Plasmon Resonance imaging. Remarkable performances were obtained for the quantification of thrombin without amplification (sub-nanomolar limit of detection and linear range of quantification to two orders of magnitude). The independent determinations of both the solution- and surface-phase affinities, respectively K_D^Sol and K_D^Surf, revealed distinct values illustrating the importance of probes, targets or surface interactions in biosensors. Interestingly, K_D^Surf values depend on the aptamer grafting density and linearly extrapolate towards K_D^Sol for highly diluted probes. This suggests a lesser impact of the surface compared to the probe or target cooperativity interactions since the latter decrease with a reduced grafting density.

Surface plasmon resonance sensing of nucleic acids: a review

Biosensors based on surface plasmon resonance (SPR) have become a central tool for the investigation and quantification of biomolecules and their interactions. Nucleic acids (NAs) play a vital role in numerous biological processes and therefore have been one of the major groups of biomolecules targeted by the SPR biosensors. This paper discusses the advances of NA SPR biosensor technology and reviews its applications both in the research of molecular interactions involving NAs (NA-NA, NA-protein, NA-small molecule), as well as for the field of bioanalytics in the areas of food safety, medical diagnosis and environmental monitoring.

Force spectroscopy reveals the DNA structural dynamics that govern the slow binding of Actinomycin D

Actinomycin D (ActD) is a small molecule with strong antibiotic and anticancer activity. However, its biologically relevant DNA-binding mechanism has never been resolved, with some studies suggesting that the primary binding mode is intercalation, and others suggesting that single-stranded DNA binding is most important. To resolve this controversy, we develop a method to quantify ActD’s equilibrium and kinetic DNA-binding properties as a function of stretching force applied to a single DNA molecule. We find that destabilization of double stranded DNA (dsDNA) by force exponentially facilitates the extremely slow ActD-dsDNA on and off rates, with a much stronger effect on association, resulting in overall enhancement of equilibrium ActD binding. While we find the preferred ActD–DNA-binding mode to be to two DNA strands, major duplex deformations appear to be a pre-requisite for ActD binding. These results provide quantitative support for a model in which the biologically active mode of ActD binding is to pre-melted dsDNA, as found in transcription bubbles. DNA in transcriptionally hyperactive cancer cells will therefore likely efficiently and rapidly bind low ActD concentrations (∼10 nM), essentially locking ActD within dsDNA due to its slow dissociation, blocking RNA synthesis and leading to cell death.

kinITC: a new method for obtaining joint thermodynamic and kinetic data by isothermal titration calorimetry

Isothermal titration calorimetry (ITC) is the method of choice for obtaining thermodynamic data on a great variety of systems. Here we show that modern ITC apparatus and new processing methods allow researchers to obtain a complete kinetic description of systems more diverse than previously thought, ranging from simple ligand binding to complex RNA folding. We illustrate these new features with a simple case (HIV-1 reverse transcriptase/inhibitor interaction) and with the more complex case of the folding of a riboswitch triggered by the binding of its ligand. The originality of the new kinITC method lies in its ability to dissect, both thermodynamically and kinetically, the two components: primary ligand binding and subsequent RNA folding. We are not aware of another single method that can yield, in a simple way, such deep insight into a composite process. Our study also rationalizes common observations from daily ITC use.

Studies of the binding mechanism between aptamers and thrombin by circular dichroism, surface plasmon resonance and isothermal titration calorimetry

Thrombin, a multifunctional serine protease, has both procoagulant and anticoagulant functions in human blood. Thrombin has two electropositive exosites. One is the fibrinogen-binding site and the other is the heparin-binding site. Over the past decade, two thrombin-binding aptamers (15-mer and 29-mer) were reported by SELEX technique. Recently, many studies examined the interactions between the 15-mer aptamer and thrombin extensively, but the data on the difference of these two aptamers binding to thrombin are still lacking and worth investigating for fundamental understanding. In the present study, we combined conformational data from circular dichroism (CD), kinetics and thermodynamics information from surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) to compare the binding mechanism between the two aptamers with thrombin. Special attentions were paid to the formation of G-quadruplex and the effects of ions on the aptamer conformation on the binding and the kinetics discrimination between specific and nonspecific interactions of the binding. The results indicated reasonably that the 15-mer aptamer bound to fibrinogen-binding site of thrombin using a G-quadruplex structure and was dominated by electrostatic interactions, while the 29-mer aptamer bound to heparin-binding site thrombin using a duplex structure and was driven mainly by hydrophobic effects.

Optical extinction combined with phase measurements for probing DNA-small-molecule interactions using an evanescent waveguide biosensor

We demonstrate the use of both optical extinction and phase measurements for probing the interactions between DNA and small molecules by dual polarization interferometry. On binding to DNA at the interface, mitoxantrone (MTX) and methylene blue (MB) induced reversible concentration-dependent optical extinction due to light absorption, which clearly revealed the association and dissociation of small molecules with DNA in real time. The binding constants of MTX-DNA and MB-DNA determined from the masses derived from optical extinction are 1.8 x 10(5) and 4.2 x 10(4) M(-1), respectively, and shown to be buffer salt concentration-dependent. Apart from optical extinction, phase measurements reflected the overall change of the interaction; namely, a combined result of the binding of small molecules and any changes in DNA structure. The masses derived from phase could be very different from those derived from optical extinction. The structural changes detected by phase measurements showed a contraction and densification of DNA upon intercalation by MTX or MB. The combination of optical extinction and phase measurements allows a detailed understanding of the interaction process.

Label-free technologies for quantitative multiparameter biological analysis

In the postgenomic era, information is king and information-rich technologies are critically important drivers in both fundamental biology and medicine. It is now known that single-parameter measurements provide only limited detail and that quantitation of multiple biomolecular signatures can more fully illuminate complex biological function. Label-free technologies have recently attracted significant interest for sensitive and quantitative multiparameter analysis of biological systems. There are several different classes of label-free sensors that are currently being developed both in academia and in industry. In this critical review, we highlight, compare, and contrast some of the more promising approaches. We describe the fundamental principles of these different methods and discuss advantages and disadvantages that might potentially help one in selecting the appropriate technology for a given bioanalytical application.

Redox actuation of a microcantilever driven by a self-assembled ferrocenylundecanethiolate monolayer: an investigation of the origin of the micromechanical motion and surface stress

The electrochemically induced motion of free-standing microcantilevers is attracting interest as micro/nanoactuators and robotic devices. The development and implementation of these cantilever-based actuating technologies requires a molecular-level understanding of the origin of the surface stress that causes the cantilever to bend. Here, we report a detailed study of the electroactuation dynamics of gold-coated microcantilevers modified with a model, redox-active ferrocenylundecanethiolate self-assembled monolayer (FcC(11)SAu SAM). The microcantilever transducer enabled the observation of the redox transformation of the surface-confined ferrocene. Oxidation of the FcC(11)SAu SAM in perchlorate electrolyte generated a compressive surface stress change of -0.20 +/- 0.04 N m(-1), and cantilever deflections ranging from approximately 0.8 microm to approximately 60 nm for spring constants between approximately 0.01 and approximately 0.8 N m(-1). A comparison of the charge-normalized surface stress of the FcC(11)SAu cantilever with values published for the electrochemical oxidation of polyaniline- and polypyrrole-coated cantilevers reveals a striking 10- to 100-fold greater stress for the monomolecular FcC(11)SAu system compared to the conducting polymer multilayers used for electroactuation. The larger stress change observed for the FcC(11)SAu microcantilever is attributable to steric constraints in the close-packed FcC(11)SAu SAM and an efficient coupling between the chemisorbed FcC(11)S- monolayer and the Au-coated microcantilever transducer (vs physisorbed conducting polymers). The microcantilever deflection vs quantity of electrogenerated ferrocenium obtained in cyclic voltammetry and potential step/hold experiments, as well as the surface stress changes obtained for mixed FcC(11)S-/C(11)SAu SAMs containing different populations of clustered vs isolated ferrocenes, have permitted us to establish the molecular basis of stress generation. Our results strongly suggest that the redox-induced deflection of a FcC(11)SAu microcantilever is caused by a monolayer volume expansion resulting from collective reorientational motions induced by the complexation of perchlorate ions to the surface-immobilized ferroceniums. The cantilever responds to the lateral pressure exerted by an ensemble of reorienting ferrocenium-bearing alkylthiolates upon each other rather than individual anion pairing events. This finding has general implications for using SAM-modified microcantilevers as (bio)sensors because it indicates that the cantilever responds to collective in-plane molecular interactions rather than reporting individual (bio)chemical events.

Surface plasmon resonance imaging of cells and surface-associated fibronectin

Background

A critical challenge in cell biology is quantifying the interactions of cells with their extracellular matrix (ECM) environment and the active remodeling by cells of their ECM. Fluorescence microscopy is a commonly employed technique for examining cell-matrix interactions. A label-free imaging method would provide an alternative that would eliminate the requirement of transfected cells and modified biological molecules, and if collected nondestructively, would allow long term observation and analysis of live cells.

Results

Using surface plasmon resonance imaging (SPRI), the deposition of protein by vascular smooth muscle cells (vSMC) cultured on fibronectin was quantified as a function of cell density and distance from the cell periphery. We observed that as much as 120 ng/cm² of protein was deposited by cells in 24 h.

Conclusion

SPRI is a real-time, low-light-level, label-free imaging technique that allows the simultaneous observation and quantification of protein layers and cellular features. This technique is compatible with live cells such that it is possible to monitor cellular modifications to the extracellular matrix in real-time.

Efficient biosensor interfaces based on space-controlled self-assembled monolayers

In this paper we demonstrate control over the spacing of surface-modifying probe molecules through the use of labile dendron spacers. During this process, anchor molecules are first adsorbed to a surface, with dendron modifiers attached. Steric interactions of the bulky dendrons control the density of anchor molecules bound to the surface. The dendron branches are subsequently detached from the anchor molecules, and the anchors are chemically modified with probe molecules, resulting in a surface with controlled spacing between probe molecules. Control over this spacing is important when the probe size is small in comparison with the target molecule. This importance is demonstrated for the binding of protein (streptavidin) targets to the probe (biotin) surface. The effect of probe space control on the efficiency of target capture is evaluated by examining the binding of streptavidin to thiolated biotin for a series of mixed monolayers. Surface modification is monitored by Fourier transform infrared reflection absorption spectroscopy (FTIR-RAS). The relative concentration of probe molecules at the surface is measured using X-ray photoelectron spectroscopy (XPS) measurements. Thiolated-biotin surfaces with optimized spacing show an increased capture efficiency for streptavidin relative to surfaces with nonoptimal or no control over probe spacing, as measured by surface plasmon resonance (SPR) spectroscopy. These results are of potential significance for the optimization and fabrication of micro- and nanoarrays used in chemical and biochemical measurements.

Quantitative surface plasmon resonance imaging: a simple approach to automated angle scanning

Here we present an automated angle-scanning surface plasmon resonance imaging (SPRi) instrument which provides multiplexed, quantitative reflectance data over a wide angular range. Angle-dependent artifacts, which arise from the simple optical setup, are corrected using software. This enables monitoring of significantly different surface coatings in many solvents, which would be outside the dynamic range of typical fixed-angle instruments. Operation in the visible to near-infrared range without the need for reconfiguration extends the instrument capabilities to increase sensitivity or to investigate the optical properties of surface films. This instrument provides maximum flexibility to study a wide range of systems with full exploitation of the quantitative capabilities of SPRi achieved by fitting data to the Fresnel model.

Combining self-assembled monolayers and mass spectrometry for applications in biochips

Biochip arrays have enabled the massively parallel analysis of genomic DNA and hold great promise for application to the analysis of proteins, carbohydrates, and small molecules. Surface chemistry plays an intrinsic role in the preparation and analysis of biochips by providing functional groups for immobilization of ligands, providing an environment that maintains activity of the immobilized molecules, controlling nonspecific interactions of analytes with the surface, and enabling detection methods. This review describes recent advances in surface chemistry that enable quantitative assays of a broad range of biochemical activities. The discussion emphasizes the use of self-assembled monolayers of alkanethiolates on gold as a structurally well-defined and synthetically flexible platform for controlling the immobilization and activity of molecules in an array. The review also surveys recent methods of performing label-free assays, and emphasizes the use of matrix-assisted laser desorption/ionization mass spectrometry to directly observe molecules attached to the self-assembled monolayers.