Design of two-dimensional photonic crystal biosensor using DNA detection

Abstract

In this paper, the photonic crystal biosensor is investigated theoretically with, concomitantly, high quality factor, transmission and sensitivity. This biosensor is made out of two waveguide couplers and one L2 resonant cavity formed by removing two air holes. For biosensor analysis, the 2D finite difference time domain (FDTD) method and the plane-wave expansion (PWE) approach are applied. Four slots placed into the cavity and the three rows of functionalized holes nearby the resonant cavities are filled with DNA. For the optimized structure, the biosensor quality factor is found to be over 3.7468?×?10⁶ and the sensitivity is of order 460?nm/RIU. The designed structure has high sensitivity, which is an important parameter in biosensing applications.     

Enhancing the fluorescence intensity of DNA microarrays by using cationic surfactants

DNA microarrays have been used as powerful tools in genomics studies and single nucleotide polymorphisms analysis. However, the fluorescence detection used in most conventional DNA microarrays is still limited by its sensitivity. The aim of this study is to use a cationic surfactant, cetyl trimethylammonium bromide (CTAB), to enhance the fluorescence intensity of 6-carboxy-fluorescene (FAM)-labeled DNA probes immobilized on a DNA microarray. We show that in the presence of CTAB the immobilized FAM-labeled DNA probes is 11-fold brighter than that without exposure to CTAB. Similarly, when we hybridize FAM-labeled DNA targets to a DNA microarray and treat the surface with CTAB solution, the fluorescence intensity shows a 26-fold increase for perfect-match DNA targets. More importantly, the contrast between perfect-match and 1-mismatch DNA is also increased from 1.3-fold to 15-fold. This method offers a simple and efficient technique to enhance the detection limit of DNA microarrays.     

Ultrafast excited-state dynamics of DNA fluorescent intercalators: new insight into the fluorescence enhancement mechanism

The excited-state dynamics of the DNA bisintercalator YOYO-1 and of two derivatives has been investigated using ultrafast fluorescence up-conversion and time-correlated single photon counting. The free dyes in water exist in two forms: nonaggregated dyes and intramolecular H-type aggregates, the latter form being only very weakly fluorescent because of excitonic interaction. The excited-state dynamics of the nonaggregated dyes is dominated by a nonradiative decay with a time constant of the order of 5 ps associated with large amplitude motion around the monomethine bridge of the cyanine chromophores. The strong fluorescence enhancement observed upon binding of the dyes to DNA is due to both the inhibition of this nonradiative deactivation of the nonaggregated dyes and the dissociation of the aggregates and thus to the disruption of the excitonic interaction. However, the interaction between the two chromophoric moieties in DNA is sufficient to enable ultrafast hopping of the excitation energy as revealed by the decay of the fluorescence anisotropy. Finally, these dyes act as solvation probes since a dynamic fluorescence Stokes shift was observed both in bulk water and in DNA. Very similar time scales were found in bulk water and in DNA.     

Enhanced electrophoretic DNA separation in photonic crystal fiber

Joule heating generated by the electrical current in capillary electrophoresis leads to a temperature gradient along the separation channel and consequently affects the separation quality. We describe a method of reducing the Joule heating effect by incorporating photonic crystal fiber into a micro capillary electrophoresis chip. The photonic crystal fiber consists of a bundle of extremely narrow hollow channels, which ideally work as separation columns. Electrophoretic separation of DNA fragments was simultaneously but independently carried out in 54 narrow capillaries with a diameter of 3.7 μm each. The capillary bundle offers more efficient heat dissipation owing to the high surface-to-volume ratio. Under the same electrical field strength, notable improvement in resolution was obtained in the capillary bundle chip.     

Label-free cell-based assays using photonic crystal optical biosensors

Biosensor technologies that have been primarily used in the past for characterizing biomolecular interactions are now being used to develop new approaches for performing cell-based assays. Biosensors monitor cell attachment to a transducer surface, and thus provide information that is fundamentally different from that provided by microscopy, as the sensor is capable of monitoring temporal evolution of integrin-surface interactions that are difficult to measure by other means. Label-free biosensor technologies are especially advantageous for monitoring the behavior of cells because they do not require stains that typically result in cell death, and are not subject to effects such as photobleaching. As a result, cells can be quantitatively monitored in their culture environment over an extended period of time while processes such as proliferation, apoptosis, cytotoxicity, chemotaxis, ion channel activation, and membrane-bound protein activation are modulated by the introduction of a variety of chemical or biological stimuli. This review describes the application of photonic crystal optical biosensor microplates to a variety of cell-based assays. Detection instruments for photonic crystals measure the aggregate behavior of large cell populations, or, using recently developed biosensor imaging detection, independent monitoring of individual cells. These technological developments offer the ability to perform assays with a limited number of available cells for applications such as high throughput screening with primary cells or stem cells.     

2-D array photonic crystal sensing motif

We have developed the first high-diffraction-efficiency two-dimensional (2-D) photonic crystals for molecular recognition and chemical sensing applications. We prepared close-packed 2-D polystyrene particle arrays by self-assembly of spreading particle monolayers on mercury surfaces. The 2-D particle arrays amazingly diffract 80% of the incident light. When a 2-D array was transferred onto a hydrogel thin film showing a hydrogel volume change in response to a specific analyte, the array spacing was altered, shifting the 2-D array diffraction wavelength. These 2-D array photonic crystals exhibit ultrahigh diffraction efficiencies that enable them to be used for visual determination of analyte concentrations.     

Enhancement of X-ray fluorescence intensity from an ultra-thin sandwiched layer at grazing-emission angles

Ni ultra-thin films sandwiched with carbon thin films of different thickness are measured by a laboratory grazing-emission X-ray fluorescence instrument. The Ni Kα intensity of the Ni ultra-thin film sandwiched with carbon layers is three times enhanced in comparison with the Ni ultra-thin film without carbon layers. In addition, oscillations caused by interference effects of directly observed X-ray beams and the reflected X-ray beams on the surface of the Pt substrate, are clearly observed. The periods of the oscillations depends on the thickness of the carbon layer, that is, the position of the Ni layer. Therefore, the thickness of the carbon layer can be estimated.     

Ultrafast excited-state dynamics of oxazole yellow DNA intercalators

The excited-state dynamics of the DNA intercalator YO-PRO-1 and of three derivatives has been investigated in water and in DNA using ultrafast fluorescence spectroscopy. In the free form, the singly charged dyes exist both as monomers and as H-dimers, while the doubly charged dyes exist predominantly as monomers. Both forms are very weakly fluorescent: the monomers because of ultrafast nonradiative deactivation, with a time constant on the order of 3-4 ps, associated with large amplitude motion around the methine bridge, and the H-dimers because of excitonic interaction. Upon intercalation into DNA, large amplitude motion is inhibited, H-dimers are disrupted, and the molecules become highly fluorescent. The early fluorescence dynamics of these dyes in DNA exhibits substantial differences compared with that measured with their homodimeric YOYO analogues, which are ascribed to dissimilarities in their local environment. Finally, the decay of the fluorescence polarization anisotropy reveals ultrafast hopping of the excitation energy between the intercalated dyes. In one case, a marked change of the depolarization dynamics upon increasing the dye concentration is observed and explained in terms of a different binding mode.     

The fabrication of polymer dispersed liquid crystal based on SiO2 photonic crystal template

The conductance of polymer matrix is an important factor for the property of the polymer dispersed liquid crystal (PDLC). The nanographites are dispersed into the polymer matrix for optimising the dielectric conductive property. The synthesised nanoparticles SiO₂ was used as photonic crystal (PC) to work as a template for fabricating PDLC films. A mixture of pre-polymer and liquid crystals (LCs) was infiltrated into the void of the PC and polymerised under ultraviolet light. The void of the PC made uniform the dispersion of the liquid crystals in the films. The optical property of the PDLC films was optimised by doped nanographites and negative charge SiO₂ template. The effect of negative charge SiO₂ and nanographites on the threshold voltage and driving voltage was researched. The morphology of the PDLC films was studied by the FTIR image. The dispersed LCs droplets were uniformly affected by the addition of the nanographites. The LCs droplets dispersed in the polymer were located in the void of the SiO₂ photonic crystal.     

Determination of aliphatic amines using fluorescence intensity of 4-methyl umbelliferone

Effect of aliphatic amines and their concentration on fluorescence intensity of 4-methyl umbelliferone (4-MU) one of coumarin derivative were investigated. This compound has blue light emission under UV lamp in methanolic solution. Spectral investigation of 4-MU solution containing amine compounds showed lower intensity at 350-410 nm (quenching region) and higher intensity at 430-500 nm (enhancing region) as compared to pure methanolic solution of 4-MU. Fluorescence intensity at isoemitting point was independent from concentration of amines. The variation of fluorescence intensity could be used for determination of aliphatic amines in both quenching and enhancing region. Linear ranges for determination of amines in the quenching region were obtained from Stern-Volmer diagram of 4-MU. Determination of amines at fluorescence enhancing region using inverse fluorescence intensity against inverse amine concentration (bireciprocal plot) were investigated and related equations was also proposed.     

Enhancement of anion-exchange chromatography of DNA using compaction agents

The use of adsorptive chromatography for preparative nucleic acid separations is often limited by low capacity. The possibility that the adsorbent surface area sterically accessible to nucleic acid molecules could be increased by reducing their radius of gyration with compaction agents has been investigated. The equilibrium adsorption capacity of Q Sepharose anion-exchange matrix for plasmid DNA at 600 mM NaCl was enhanced by up to ca. 40% in the presence of 2.5 mM spermine. In addition, compaction agent selectivity has been demonstrated. Spermine, for example, enhances the adsorption of both plasmid and genomic DNA, spermidine enhances binding only of plasmid, and hexamine cobalt enhances only the binding of genomic DNA. Compaction may be generally useful for enhancing adsorptive separations of nucleic acids.     

Express and sensitive detection of multiple miRNAs via DNA cascade reactors functionalized photonic crystal array

Array based detection techniques with fluorescence signal reading is a powerful tool for multiple targets analysis. However,when applied fluorescence array for micro RNA detection, time-consuming multi-steps surface signal amplification is usually required due to the low abundance of micro RNA in total RNA expressions, which impairs detection efficiency and limits its application in point of care test(POCT) manner. Herein, DNA cascade reactors(DCRs) functionalized photonic crystal(PC)array was fabricated for express and sensitive detections of mi RNA-21 and mi RNA-155. DCRs were assembled by interval conjugation of self-quenched hairpin DNA probes to single strand DNA nanowire synthesized by rolling circle amplification,which generated cascade DNA hybridization reactions in response to target mi RNAwith instant fluorescence recovery signal. PC array patterns with multi-structure colors further amplified fluorescence with their respective photonic bandgaps(PBGs)matching with the emission peaks of fluorescence molecules labelled on DCRs. The as-prepared DCRs functionalized PC array demonstrated express and sensitive simultaneous detections of mi RNA-21 and mi RNA-155 with hundreds f M detection limits only in 15 min, and was successfully applied in fast quantifications of low abundance mi RNAs from cell lysates and spiked mi RNAs from human serum, which would hold great potential for disease diagnosis and therapeutic effect monitoring with a POCT manner.     

pH and ionic strength responsive photonic polymers fabricated by using colloidal crystal templating

In this paper, monodispersed silica particles were synthesized using tetraethoxysiliane hydrolyzing in ethanol by a Stöber–Fink–Bobn method and then self-assembled on cleaning glass slides to form silica colloidal crystals. After photopolymerization of methacrylic acid mixing with ethylene glycol dimethylacrylate and hydrofluoric acid etching, the pH-responsive polymers were obtained with highly 3D-ordered macroporous structures templated by silica colloidal crystals. These polymers films can swell or deswell in response to external stimuli, causing a change of Bragg diffraction to read pH or ionic strength of various solutions by optical signals or electrochemical signals. As an application, they can be used as chemical sensors to detect pH or ionic strength variation of environment.     

DNA biosensor based on the electrochemiluminescence of Ru(bpy)3(2+) with DNA-binding intercalators

This paper reports a novel detection method for DNA hybridization based on the electrochemiluminescence (ECL) of Ru(bpy)(3)(2+) with a DNA-binding intercalator as a reductant of Ru(bpy)(3)(3+). Some ECL-inducible intercalators have been screened in this study using electrochemical methods combined with a chemiluminescent technique. The double-stranded DNA intercalated by doxorubicin, daunorubicin, or 4',6-diamidino-2-phenylindole (DAPI) shows a good ECL with Ru(bpy)(3)(2+) at +1.19 V (versus Ag/AgCl), while the non-intercalated single-stranded DNA does not. In order to stabilize the self-assembled DNA molecules during ECL reaction, we constructed the ECL DNA biosensor separating the ECL working electrode with an immobilized DNA probe. A gold electrode array on a plastic plate was assembled with a thru-hole array where oligonucleotide probes were immobilized in the side wall of thru-hole array. The fabricated ECL DNA biosensor was used to detect several pathogens using ECL technique. A good specificity of single point mutations for hepatitis disease was obtained by using the DAPI-intercalated Ru(bpy)(3)(2+) ECL.     

Responsive photonic crystal for the sensing of environmental pollutants

This review covers the concepts of photonic crystal (PhC) and its usage for the sensing of environmental pollutants. PhCs are composed of periodic and ordered nanostructures which can manipulate the diffraction or reflection of light propagation through the structures. If the light spectra locate in the visible range, the color of materials can be observed by naked eye. The optical properties of PhCs are determined by the lattice constant of the crystal or by the refractive index contrast between the colloids and the surrounding medium. Based on these features, responsive PhCs can be designed to detect the environmental pollutants. In this review, we primarily described the photonic crystals for the sensing of volatile organic compounds (VOCs), organophosphates (OPs), heavy metal ions and endocrine disrupting chemicals (EDCs), and these sensors exhibited excellent sensitivity and are promising for the on-site monitoring of pollutants.     

Influence of substrate on self-assembled photonic crystal

Freestanding monolayers of two-dimensional particle arrays, in which fine particles are two-dimensionally self-assembled in a highly oriented manner, was prepared to examine the influence of substrate on the transmission spectra of 2D particle array; as a result, the spectrum of the freestanding 2D particle array has less noise than that of the 2D particle array on the substrate, and besides, agree with the theoretical result particularly in the near-field discussion.     

2-Aminopurine flipped into the active site of the adenine-specific DNA methyltransferase M.TaqI: crystal structures and time-resolved fluorescence

We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed with DNA, showing the fluorescent adenine analog, 2-aminopurine, flipped out of the DNA helix and occupying virtually the same position in the active site as the natural target adenine. Time-resolved fluorescence spectroscopy of the crystalline complex faithfully reports this state: base flipping is accompanied by the loss of the very short ( approximately 50 ps) lifetime component associated with fully base-stacked 2-aminopurine in DNA, and 2-aminopurine is subject to considerable quenching by pi-stacking interactions with Tyr108 in the catalytic motif IV (NPPY). This proves 2-aminopurine to be an excellent probe for studying base flipping by M.TaqI and suggests similar quenching in the active sites of DNA and RNA adenine-N6 as well as DNA cytosine-N4 methyltransferases sharing the conserved motif IV. In solution, the same distinctive fluorescence response confirms complete destacking from DNA and is also observed when the proposed key residue for base flipping by M.TaqI, the target base partner thymine, is substituted by an abasic site analog. The corresponding cocrystal structure shows 2-aminopurine in the active site of M.TaqI, demonstrating that the partner thymine is not essential for base flipping. However, in this structure, a shift of the 3' neighbor of the target base into the vacancy left after base flipping is observed, apparently replicating a stabilizing role of the missing partner thymine. Time-resolved fluorescence and acrylamide quenching measurements of M.TaqI complexes in solution provide evidence for an alternative binding site for the extra-helical target base within M.TaqI and suggest that the partner thymine assists in delivering the target base into the active site.