DNA conformation on surfaces measured by fluorescence self-interference

Reproducibly Measuring Plasmon-Enhanced Fluorescence in Bulk Solution Across a 20-Fold Range of Optical Densities

It is well-known that plasmonic nanoparticles can modify the spectroscopic properties of nearby optical probes, for example, enhanced emission of a fluorescent dye. Yet, the detection and quantification of this effect in bulk solution remain challenging even while size- and shape-controlled nanoparticles have become readily available. We investigated this problem and identified two main difficulties which we were able to overcome through systematic studies. For the detection of fluorescence emanating from optically dense nanoparticle solutions, we describe an analytical model that provides guidelines for experimentalists to maximize the fluorescence intensity by optimizing the concentration, light paths, and excitation-detection volume of the sample. For the quantification of enhancement, which critically hinges upon the comparison to an accurate reference sample, we exploit the tools of DNA nanotechnology to remove the fluorophore from plasmonic coupling on-demand, forming an in situ reference. Using a model system of fluorophore Cy3 and 80 nm gold nanoparticles, we show that these strategies enable the quantitative measurement of plasmonic enhancement across a 20-fold range of optical densities. We anticipate that the presented experimental framework will allow for routine, quantitative measurements for the research and development of plasmon-enhanced phenomena.

Axial localization and tracking of self-interference nanoparticles by lateral point spread functions

Sub-diffraction limited localization of fluorescent emitters is a key goal of microscopy imaging. Here, we report that single upconversion nanoparticles, containing multiple emission centres with random orientations, can generate a series of unique, bright and position-sensitive patterns in the spatial domain when placed on top of a mirror. Supported by our numerical simulation, we attribute this effect to the sum of each single emitter’s interference with its own mirror image. As a result, this configuration generates a series of sophisticated far-field point spread functions (PSFs), e.g. in Gaussian, doughnut and archery target shapes, strongly dependent on the phase difference between the emitter and its image. In this way, the axial locations of nanoparticles are transferred into far-field patterns. We demonstrate a real-time distance sensing technology with a localization accuracy of 2.8 nm, according to the atomic force microscope (AFM) characterization values, smaller than 1/350 of the excitation wavelength.

Here, the authors show that single upconversion nanoparticles can generate position-sensitive patterns in the spatial domain when placed on a mirror. They attribute this to the single emitter’s interference with its own mirror image and show how this can be used to obtain axial localisation of the particle.

A versatile fluorometric in situ hybridization method for the quantitation of hairpin conformations in DNA self-assembled monolayers

As the performance of hairpin DNA (hpDNA)-based biosensors is highly dependent on the yield of stem-loop (hairpin) conformations, we report herein a versatile fluorometric in situ hybridization protocol for examining hpDNA self-assembled monolayers (SAMs) on popularly used biochip substrates. Specifically, the ratio of fluorescence (FL) intensities of hpDNA SAMs (in an array format) before and after hybridization was adopted as the key parameter for performing such a determination. Upon confirming the existence of mixed and tunable DNA conformations in binary deposition solutions and efficient hybridization of the hairpin strands with the target DNA via gel electrophoresis assays, we tested the fluorometric protocol for determining the coverages of hpDNA in hpDNA/ssDNA SAMs prepared on gold; its accuracy was validated by Exonuclease I (Exo I)-assisted electrochemical quantitation. To further confirm its versatility, this FL protocol was adopted for quantifying hairpin conformations formed on glass and polycarbonate (PC) substrates. The molar ratios of surface-tethered hairpin conformations on the three different substrates were all found to be proportional to but less than those in the binary deposition solutions, and were dependent on the substrate morphology. The findings reported herein are beneficial for the construction of highly efficient DNA hairpin-based sensing surfaces, which essentially facilitates the creation of hpDNA-based biosensors with optimal detection performance.

A force sensor that converts fluorescence signal into force measurement utilizing short looped DNA

A force sensor concept is presented where fluorescence signal is converted into force information via single-molecule Förster resonance energy transfer (smFRET). The basic design of the sensor is a ~100 base pair (bp) long double stranded DNA (dsDNA) that is restricted to a looped conformation by a nucleic acid secondary structure (NAS) that bridges its ends. The looped dsDNA generates a tension across the NAS and unfolds it when the tension is high enough. The FRET efficiency between donor and acceptor (D&A) fluorophores placed across the NAS reports on its folding state. Three dsDNA constructs with different lengths were bridged by a DNA hairpin and KCl was titrated to change the applied force. After these proof-of-principle measurements, one of the dsDNA constructs was used to maintain the G-quadruplex (GQ) construct formed by thrombin binding aptamer (TBA) under tension while it interacted with a destabilizing protein and stabilizing small molecule. The force required to unfold TBA-GQ was independently investigated with high-resolution optical tweezers (OT) measurements that established the relevant force to be a few pN, which is consistent with the force generated by the looped dsDNA. The proposed method is particularly promising as it enables studying NAS, protein, and small molecule interactions using a highly-parallel FRET-based assay while the NAS is kept under an approximately constant force.

An interferometric imaging biosensor using weighted spectrum analysis to confirm DNA monolayer films with attogram sensitivity

Interferometric imaging biosensors are powerful and convenient tools for confirming the existence of DNA monolayer films on silicon microarray platforms. However, their accuracy and sensitivity need further improvement because DNA molecules contribute to an inconspicuous interferometric signal both in thickness and size. Such weaknesses result in poor performance of these biosensors for low DNA content analyses and point mutation tests. In this paper, an interferometric imaging biosensor with weighted spectrum analysis is presented to confirm DNA monolayer films. The interferometric signal of DNA molecules can be extracted and then quantitative detection results for DNA microarrays can be reconstructed. With the proposed strategy, the relative error of thickness detection was reduced from 88.94% to merely 4.15%. The mass sensitivity per unit area of the proposed biosensor reached 20 attograms (ag). Therefore, the sample consumption per unit area of the target DNA content was only 62.5 zeptomoles (zm), with the volume of 0.25 picolitres (pL). Compared with the fluorescence resonance energy transfer (FRET), the measurement veracity of the interferometric imaging biosensor with weighted spectrum analysis is free to the changes in spotting concentration and DNA length. The detection range was more than 1µm. Moreover, single nucleotide mismatch could be pointed out combined with specific DNA ligation. A mutation experiment for lung cancer detection proved the high selectivity and accurate analysis capability of the presented biosensor.

Label-Free Method Using a Weighted-Phase Algorithm To Quantitate Nanoscale Interactions between Molecules on DNA Microarrays

White light interference is used as a label-free method to detect nanoscale changes on surfaces. However, the signal-to-noise ratio of the white light interference method is very low, thus resulting in inaccurate results. In this paper, we report a corrected label-free method based on hyperspectral interferometry to overcome the shortcoming of the white light interference method. A platform based on hyperspectral interferometry was established, and a DNA hybridization microarray was constructed to quantitate thickness variation of molecules on a solid surface. We used fluorescence resonance energy transfer (FRET) to validate the results of our method. Compared to conventional fluorescence-labeled method like FRET, our method has advantages because it does not require a fluorescent label and has a detection limit of 1.78 nm, a high accuracy, and wide detection range (5-64 bp).

Quantitative characterization of conformational-specific protein-DNA binding using a dual-spectral interferometric imaging biosensor

DNA-binding proteins play crucial roles in the maintenance and functions of the genome and yet, their specific binding mechanisms are not fully understood. Recently, it was discovered that DNA-binding proteins recognize specific binding sites to carry out their functions through an indirect readout mechanism by recognizing and capturing DNA conformational flexibility and deformation. High-throughput DNA microarray-based methods that provide large-scale protein-DNA binding information have shown effective and comprehensive analysis of protein-DNA binding affinities, but do not provide information of DNA conformational changes in specific protein-DNA complexes. Building on the high-throughput capability of DNA microarrays, we demonstrate a quantitative approach that simultaneously measures the amount of protein binding to DNA and nanometer-scale DNA conformational change induced by protein binding in a microarray format. Both measurements rely on spectral interferometry on a layered substrate using a single optical instrument in two distinct modalities. In the first modality, we quantitate the amount of binding of protein to surface-immobilized DNA in each DNA spot using a label-free spectral reflectivity technique that accurately measures the surface densities of protein and DNA accumulated on the substrate. In the second modality, for each DNA spot, we simultaneously measure DNA conformational change using a fluorescence vertical sectioning technique that determines average axial height of fluorophores tagged to specific nucleotides of the surface-immobilized DNA. The approach presented in this paper, when combined with current high-throughput DNA microarray-based technologies, has the potential to serve as a rapid and simple method for quantitative and large-scale characterization of conformational specific protein-DNA interactions.

Nanoscale characterization of DNA conformation using dual-color fluorescence axial localization and label-free biosensing

Quantitative determination of the density and conformation of DNA molecules tethered to the surface can help optimize and understand DNA nanosensors and nanodevices, which use conformational or motional changes of surface-immobilized DNA for detection or actuation. We present an interferometric sensing platform that combines (i) dual-color fluorescence spectroscopy for precise axial co-localization of two fluorophores attached at different nucleotides of surface-immobilized DNA molecules and (ii) independent label-free quantification of biomolecule surface density at the same site. Using this platform, we examined the conformation of DNA molecules immobilized on a three-dimensional polymeric surface and demonstrated simultaneous detection of DNA conformational change and binding in real-time. These results demonstrate that independent quantification of both surface density and molecular nanoscale conformation constitutes a versatile approach for nanoscale solid-biochemical interface investigations and molecular binding assays.

Characteristic investigation of scanning surface plasmon microscopy for nucleotide functionalized nanoarray

A calculation based on surface plasmon coupling condition and Maxwell-Garnett equation was performed for predicting the coupling angle shift and thin film thickness in scanning surface plasmon microscopy (SSPM). The refractive index sensitivity and lateral resolution of an SSPM system was also investigated. The limit of detection of angle shift was 0.01°, the limit of quantification of angle shift was 0.03°, and the sensitivity was around 0.12° shift per nm ZnO film when the film thickness was less than 22.6 nm. Two partially connected Au nano-discs with a center-to-center distance of 1.1 μm could be identified as two peaks. The system was applied to image nanostructure defects and a virus-probe functionalized nanoarray. We expect the potential application in nanobiosensors with further optimization in the future.

QCM-based measurement of bond rupture forces in DNA double helices for complementarity sensing

After fixing the DNA molecule in the form of a double helix on the surface of a thickness shear mode resonator (QCM), mechanical oscillations at increasing amplitude cause detorsion of the helix. The force necessary for detorsion can be determined from the voltage applied to the QCM at the rupture moment. The high sensitivity of this method is due to the fact that measurements are carried out in the frequency region around the QCM resonance, where any (even very weak) distortions of the consistent oscillating system cause noticeable distortions of the amplitude-frequency dependence, and these distortions are used to fix the rupture moment. The measured rupture forces were within 30-40 pN, and the sensitivity was 10(8) molecules. It was demonstrated that the proposed procedure allows one to determine the factors that affect the stability of the DNA double helix. This procedure can be the basis for the development of a new method of rapid DNA analysis. Experiments performed with model DNA showed that it is possible to reveal complementarity between two DNA samples.

BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE

Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.

4Pi fluorescence detection and 3D particle localization with a single objective

Coherent detection through two opposing objectives (4Pi configuration) improves the precision of three-dimensional (3D) single-molecule localization substantially along the axial direction, but suffers from instrument complexity and maintenance difficulty. To address these issues, we have realized 4Pi fluorescence detection by sandwiching the sample between the objective and a mirror, and create interference of direct incidence and mirror-reflected signal at the camera with a spatial light modulator. Multifocal imaging using this single-objective mirror interference scheme offers improvement in the axial localization similar to the traditional 4Pi method. We have also devised several PSF engineering schemes to enable 3D localization with a single emitter image, offering better axial precision than normal single-objective localization methods such as astigmatic imaging.

A new microarray substrate for ultra-sensitive genotyping of KRAS and BRAF gene variants in colorectal cancer

Molecular diagnostics of human cancers may increase accuracy in prognosis, facilitate the selection of the optimal therapeutic regimen, improve patient outcome, reduce costs of treatment and favour development of personalized approaches to patient care. Moreover sensitivity and specificity are fundamental characteristics of any diagnostic method. We developed a highly sensitive microarray for the detection of common KRAS and BRAF oncogenic mutations. In colorectal cancer, KRAS and BRAF mutations have been shown to identify a cluster of patients that does not respond to anti-EGFR therapies; the identification of these mutations is therefore clinically extremely important. To verify the technical characteristics of the microarray system for the correct identification of the KRAS mutational status at the two hotspot codons 12 and 13 and of the BRAF^V600E mutation in colorectal tumor, we selected 75 samples previously characterized by conventional and CO-amplification at Lower Denaturation temperature-PCR (COLD-PCR) followed by High Resolution Melting analysis and direct sequencing. Among these samples, 60 were collected during surgery and immediately steeped in RNAlater while the 15 remainders were formalin-fixed and paraffin-embedded (FFPE) tissues. The detection limit of the proposed method was different for the 7 KRAS mutations tested and for the V600E BRAF mutation. In particular, the microarray system has been able to detect a minimum of about 0.01% of mutated alleles in a background of wild-type DNA. A blind validation displayed complete concordance of results. The excellent agreement of the results showed that the new microarray substrate is highly specific in assigning the correct genotype without any enrichment strategy.

Entropy-driven collective interactions in DNA brushes on a biochip

Cell-free gene expression in localized DNA brushes on a biochip has been shown to depend on gene density and orientation, suggesting that brushes form compartments with partitioned conditions. At high density, the interplay of DNA entropic elasticity, electrostatics, and excluded volume interactions leads to collective conformations that affect the function of DNA-associated proteins. Hence, measuring the collective interactions in dense DNA, free of proteins, is essential for understanding crowded cellular environments and for the design of cell-free synthetic biochips. Here, we assembled dense DNA polymer brushes on a biochip along a density gradient and directly measured the collective extension of DNA using evanescent fluorescence. DNA of 1 kbp in a brush undergoes major conformational changes, from a relaxed random coil to a stretched configuration, following a universal function of density to ionic strength ratio with scaling exponent of 1/3. DNA extends because of the swelling force induced by the osmotic pressure of ions, which are trapped in the brush to maintain local charge neutrality, in competition with the restoring force of DNA entropic elasticity. The measurements reveal in DNA crossover between regimes of osmotic, salted, mushroom, and quasineutral brush. It is surprising to note that, at physiological ionic strength, DNA density does not induce collective stretch despite significant chain overlap, which implies that excluded volume interactions in DNA are weak.

Efficient self-assembly of DNA-functionalized fluorophores and gold nanoparticles with DNA functionalized silicon surfaces: the effect of oligomer spacers

Although strategies for the immobilization of DNA oligonucleotides onto surfaces for bioanalytical and top-down bio-inspired nanobiofabrication approaches are well developed, the effect of introducing spacer molecules between the surface and the DNA oligonucleotide for the hybridization of nanoparticle–DNA conjugates has not been previously assessed in a quantitative manner. The hybridization efficiency of DNA oligonucleotides end-labelled with gold nanoparticles (1.4 or 10 nm diameter) with DNA sequences conjugated to silicon surfaces via hexaethylene glycol phosphate diester oligomer spacers (0, 1, 2, 6 oligomers) was found to be independent of spacer length. To quantify both the density of DNA strands attached to the surfaces and hybridization with the surface-attached DNA, new methodologies have been developed. Firstly, a simple approach based on fluorescence has been developed for determination of the immobilization density of DNA oligonucleotides. Secondly, an approach using mass spectrometry has been created to establish (i) the mean number of DNA oligonucleotides attached to the gold nanoparticles and (ii) the hybridization density of nanoparticle–oligonucleotide conjugates with the silicon surface–attached complementary sequence. These methods and results will be useful for application with nanosensors, the self-assembly of nanoelectronic devices and the attachment of nanoparticles to biomolecules for single-molecule biophysical studies.

Interferometric silicon biochips for label and label-free DNA and protein microarrays

Protein and DNA microarrays hold the promise to revolutionize the field of molecular diagnostics. Traditional microarray applications employ labeled detection strategies based on the use of fluorescent and chemiluminescent secondary antibodies. However, the development of high throughput, sensitive, label-free detection techniques is attracting attention as they do not require labeled reactants and provide quantitative information on binding kinetics. In this article, we will provide an overview of the recent author's work in label and label-free sensing platforms employing silicon/silicon oxide (Si/SiO(2)) substrates for interferometric and/or fluorescence detection of microarrays. The review will focus on applications of Si/SiO(2) with controlled oxide layers to (i) enhance the fluorescence intensity by optical interferences, (ii) quantify with sub-nanometer accuracy the axial locations of fluorophore-labeled probes tethered to the surface, and (iii) detect protein-protein interactions label free. Different methods of biofunctionalization of the sensing surface will be discussed. In particular, organosilanization reactions for monodimensional coatings and polymeric coatings will be extensively reviewed. Finally, the importance of calibration of protein microarrays through the dual use of labeled and label-free detection schemes on the same chip will be illustrated.

Fluorescence axial localization with nanometer accuracy and precision

We describe a new technique, standing wave axial nanometry (SWAN), to image the axial location of a single nanoscale fluorescent object with sub-nanometer accuracy and 3.7 nm precision. A standing wave, generated by positioning an atomic force microscope tip over a focused laser beam, is used to excite fluorescence; axial position is determined from the phase of the emission intensity. We use SWAN to measure the orientation of single DNA molecules of different lengths, grafted on surfaces with different functionalities.

Exploiting the light–metal interaction for biomolecular sensing and imaging

The ability of metal surfaces and nanostructures to localize and enhance optical fields is the primary reason for their application in biosensing and imaging. Local field enhancement boosts the signal-to-noise ratio in measurements and provides the possibility of imaging with resolutions significantly better than the diffraction limit. In fluorescence imaging, local field enhancement leads to improved brightness of molecular emission and to higher detection sensitivity and better discrimination. We review the principles of plasmonic fluorescence enhancement and discuss applications ranging from biosensing to bioimaging.

Immobilized smart RNA on graphene oxide nanosheets to specifically recognize and adsorb trace peptide toxins in drinking water

The contaminations of peptide toxins in drinking water lead directly to sickness and even death in both humans and animals. A smart RNA as aptamer is covalently immobilized on graphene oxide to form a polydispersed and stable RNA-graphene oxide nanosheet. RNA-graphene oxide nanosheets can resist nuclease and natural organic matter, and specifically adsorb trace peptide toxin (microcystin-LR) in drinking water. The adsorption data fit the pseudo-second-order kinetics and the Langmuir isotherm model. The adsorption capacity of RNA-graphene oxide nanosheets decreases at extreme pH, temperature, ionic strength and natural organic matter, but it is suitable to adsorb trance pollutants in contaminated drinking water. Compared with other chemical and biological sorbents, RNA-graphene oxide nanosheets present specific and competitive adsorption, and are easily synthesized and regenerated. Aptamer (RNA) covalently immobilized on graphene oxide nanosheets is a potentially useful tool in recognizing, enriching and separating small molecules and biomacromolecules in the purification of contaminated water and the preparation of samples.

Impact of spacer and strand length on oligonucleotide conjugation to the surface of ligand-free laser-generated gold nanoparticles

Gold nanoparticles conjugated to nucleic acids are widely used for biomedical targeting and sensing applications; however, little is known about the conjugation chemistry covering the impact of steric dimension and strand orientation of single-stranded oligonucleotides (ssO) on the conjugation process and binding efficiencies. In this context, we present an extensive investigation concerning the attachment of thiolated ssO to the surface of laser-generated gold nanoparticles, altering both strand length and binding orientation by the insertion of different spacer types at either the 3' or 5' ssO terminus. A significant reduction of conjugation efficiency of about 30-50% is determined for spacer-prolonged bionanoconjugates due to coiling effects of the flexible ssO strand on the particle surface which increases deflection angle of oligonucleotides and limits the number of biomolecules attached to the nanoparticles.

Plasmonic Mach-Zehnder interferometer for ultrasensitive on-chip biosensing

We experimentally demonstrate a plasmonic Mach-Zehnder interferometer (MZI) integrated with a microfluidic chip for ultrasensitive optical biosensing. The MZI is formed by patterning two parallel nanoslits in a thin metal film, and the sensor monitors the phase difference, induced by surface biomolecular adsorptions, between surface plasmon waves propagating on top and bottom surfaces of the metal film. The combination of a nanoplasmonic architecture and sensitive interferometric techniques in this compact sensing platform yields enhanced refractive index sensitivities greater than 3500 nm/RIU and record high sensing figures of merit exceeding 200 in the visible region, greatly surpassing those of previous plasmonic sensors and still hold potential for further improvement through optimization of the device structure. We demonstrate real-time, label-free, quantitative monitoring of streptavidin-biotin specific binding with high signal-to-noise ratio in this simple, ultrasensitive, and miniaturized plasmonic biosensor.

Free energy considerations for nucleic acids with dangling ends near a surface: a coarse grained approach

A coarse grained model for the thermodynamics of nucleic acid hybridization near surfaces has been extended and parameterized to consider the contribution of unpaired dangling ends. The parameters of the model differ when representing a double stranded DNA section or a single stranded DNA section. The thermodynamic effects of the possibility of different dangling end combinations were considered in the presence of different types of surfaces. Configurational sampling was achieved by the Metropolis Monte Carlo method. To gain a more complete picture of the free energy changes, an estimation of the conformational entropy was included. We find a strong thermodynamic effect for dangling mismatches due to sequence requirements when they are nearer the surface as opposed to being held away from the surface.

Three-dimensional arrangement of short DNA oligonucleotides at surfaces via the synthesis of DNA-branched polyacrylamide brushes by SI-ATRP

Short DNA oligonucleotide branches are incorporated into acrylamide brushes via surface initiated atom transfer radical polymerization in an attempt to increase DNA surface density by building three-dimensional molecular architectures. ATR-FTIR as well as hybridization studies followed by SPR confirm the incorporation of the DNA sequences into the polymer backbone. MALDI-TOF analysis further suggests that six acrylamide monomer units are typically separating DNA branches present on a single brushes approximately 26 units long. This new approach offers a promising alternative to SAM-based nucleic acid and aptamer sensors and could enable the realization of more complex soft materials of controlled architecture capable of both recognition and signaling by including additional optically or electrochemically active moieties.

A nanoelectromechanical biosensor based on precise quantification and control of DNA orientation

We utilize spectral self-interference fluorescent microscopy (SSFM) to measure fluorophore height with sub-nm precision to precisely quantify DNA orientation. A novel polymeric 3D scaffold is used to functionalize the sensor surface and to control orientation of the surface anchored DNA.

A model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface: a Coarse Grained Approach

New methods based on surfaces or beads have allowed measurement of properties of single DNA molecules in very accurate ways. Theoretical coarse grained models have been developed to understand the behavior of single stranded and double stranded DNA. These models have been shown to be accurate and relatively simple for very short systems of 6-8 base pairs near surfaces. Comparatively less is known about the influence of a surface on the secondary structures of longer molecules important to many technologies. Surface fields due to either applied potentials and/or dielectric boundaries are not in current surface mounted coarse grained models. To gain insight into longer and surface mounted sequences we parameterized a discretized worm-like chain model. Each link is considered a sphere of 6 base pairs in length for dsDNA, and 1.5 bases for ssDNA (requiring an always even number of spheres). For this demonstration of the model, the chain is tethered to a surface by a fixed length, non-interacting 0.536 nm linker. Configurational sampling was achieved via Monte-Carlo simulation. Our model successfully reproduces end to end distance averages from experimental results, in agreement with polymer theory and all atom simulations. Our average tilt results are also in agreement with all atom simulations for the case of dense systems.

Three-dimensional nano-localization of single fluorescent emitters

We present a combination of self-interference microscopy with lateral super-resolution microscopy and introduce a novel approach for localizing a single nano-emitter to within a few nanometers in all three dimensions over a large axial range. We demonstrate nanometer displacements of quantum dots placed on top of polymer bilayers that undergo swelling when changing from an air to a water environment, achieving standard deviations below 10 nm for axial and lateral localization.

Platform for in situ real-time measurement of protein-induced conformational changes of DNA

A platform for in situ and real-time measurement of protein-induced conformational changes in dsDNA is presented. We combine electrical orientation of surface-bound dsDNA probes with an optical technique to measure the kinetics of DNA conformational changes. The sequence-specific Escherichia coli integration host factor is utilized to demonstrate protein-induced bending upon binding of integration host factor to dsDNA probes. The effects of probe surface density on binding/bending kinetics are investigated. The platform can accommodate individual spots of microarrayed dsDNA on individually controlled, lithographically designed electrodes, making it amenable for use as a high throughput assay.

Vertical plasmonic Mach-Zehnder interferometer for sensitive optical sensing

Vertical plasmonic Mach-Zehnder Interferometers are investigated theoretically and experimentally, and their potential for ultra-sensitive optical sensing is discussed. Plasmonic interferences arise from coherently coupled pairs of subwavelength slits, illuminated by a broadband optical source, and this interference modulates the intensity of the far-field scattering spectrum. Experimental results, obtained using a simple experimental setup, are presented to validate theoretically predicted interferences introduced by the surface plasmon modes on top and bottom surfaces of a metal film. By observing the wavelength shift of the peaks or valleys of the interference pattern, this highly compact device has the potential to achieve a very high sensitivity relative to other nanoplasmonic architectures reported.

Stress and DNA assembly differences on cantilevers gold coated by resistive and e-beam evaporation techniques

Changes in the sign of differential surface stress of gold-coated cantilevers produced by thiol-derivatized single-stranded DNA immobilization are observed, depending on the method used to deposit the gold. While the DNA immobilization on e-beam gold-coated cantilevers produces a compressive differential surface stress in the metallic layer, the opposite is observed for resistively coated cantilevers under the same immobilization conditions. The gold films exhibit quite a similar morphology, and the immobilization differences seem to be related to the charge state of the metallic layer surface. This in turn produces a different distribution of the orientation of the DNA strands on the gold layer. A tentative explanation for the observed effect is proposed.

Quantification of DNA and protein adsorption by optical phase shift

A primary advantage of label-free detection methods over fluorescent measurements is its quantitative detection capability, since an absolute measure of adsorbed material facilitates kinetic characterization of biomolecular interactions. Interferometric techniques relate the optical phase to biomolecular layer density on the surface, but the conversion factor has not previously been accurately determined. We present a calibration method for phase shift measurements and apply it to surface-bound bovine serum albumin, immunoglobulin G, and single-stranded DNA. Biomolecules with known concentrations dissolved in salt-free water were spotted with precise volumes on the array surface and upon evaporation of the water, left a readily calculated mass. Using our label-free technique, the calculated mass of the biolayer was compared with the measured thickness, and we observed a linear dependence over 4 orders of magnitude. We determined that the widely accepted conversion of 1 nm of thickness corresponds to approximately 1 ng/mm(2) surface density held reasonably well for these substances and through our experiments can now be further specified for different types of biomolecules. Through accurate calibration of the dependence of thickness on surface density, we have established a relation allowing precise determination of the absolute number of molecules for single-stranded DNA and two different proteins.

Closed-form representations of field components of fluorescent emitters in layered media

Dipole radiation in and near planar stratified dielectric media is studied theoretically within the context of fluorescence microscopy, as fluorescent emitters are generally modeled by electric dipoles. Although the main emphasis of this study is placed on the closed-form representations of the field components of fluorescent emitters in layered environments in near- and far-field regions, the underlying motive is to understand the limits of spectral self-interference fluorescence microscopy in studying the dipole orientation of fluorophores. Since accurate calculations of the field components of arbitrarily polarized electric dipoles in layered environments are computationally very time-consuming, a method for finding their closed-form representations is proposed using the closed-form potential Green's functions previously developed for microwave applications. The method is verified on typical geometries used in spectral self-interference microscopy experiments, where a dipole emitter is positioned over a slab of SiO(2) on top of a Si substrate. In addition to facilitating efficient calculation of near and intermediate fields of fluorescent emitters, closed-form Green's functions for fields would also play a crucial role in developing efficient and rigorous computational analysis and design tools for optical passive devices such as optical antennas by significantly improving the computational cost of the numerical solution of the integral equation.

Development of new substrates for high-sensitive genotyping of minority mutated alleles

An unsurpassed level of sensitivity was reached in the detection of minority mutated alleles. A low-density microarray was printed on a substrate specifically designed to provide an interference effect which amplifies the collection of the light emitted on the support and reinforces the intensity of excitation light. Optimal performance of the array was obtained by maximizing the probe density and the binding efficiency to the target through a polymeric coating made by the adsorption of a copolymer of N,N-dimethylacrylamide (97% of moles), N,N-acryloyloxysuccinimide (2%) and 3-(trimethoxysilyl)propyl methacrylate (1%) synthesized by free radical copolymerization. The new substrate was used in the identification of fetal mutations in the maternal plasma DNA. Amino-modified amplicons from genomic DNA corresponding to the locus of eight beta-thalassemia mutations were immobilized and interrogated with dual-color oligonucleotide targets. Compared with the conventional glass substrates, the new substrate showed a great enhancement of fluorescence signals thanks to the combination of the optics with the highly efficient polymeric coating, allowing specific detection of all mutations. The high sensitivity and selectivity obtained made it possible to develop assays for the identification of paternally inherited mutations on fetal DNA in the maternal plasma in couples at risk for beta-thalassemia.

Direct observation of conformation of a polymeric coating with implications in microarray applications

The conformation of a three-dimensional polymeric coating (copoly(DMA-NAS-MAPS)) and immobilization and hybridization of DNA strands on the polymer coated surface are investigated. A conformational change, specifically the swelling of the surface adsorbed polymer upon hydration, is quantified in conjunction with the application of this polymer coating for DNA microarray applications. Fluorescently labeled short DNA strands (23mers) covalently linked to the functional groups on the adsorbed polymer are used as probes to measure the swelling of the polymer. A fluorescence microscopy technique, Spectral Self-Interference Fluorescence Microscopy (SSFM), is utilized to directly measure the change in axial position of fluorophores due to swelling with subnanometer accuracy. Additionally, immobilization characteristics of single stranded DNA (ssDNA) and double stranded DNA (dsDNA) probes, as well as hybridization of ssDNA with target strands have been studied. The results show that ssDNA further away from the surface is hybridized more efficiently, which strengthens the earlier analysis of this polymeric coating as a simple but highly efficient and robust DNA microarray surface chemistry.