Refractive-index anisotropy and optical dispersion in films of deoxyribonucleic acid

Highly nonlinear optic nucleic acid thin-solid film to generate short pulse laser

Using aqueous precursors, we report successfully fabricating thin-solid films of two nucleic acids, ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). We investigated the potential of these films deposited on a fiber optic platform as all-fiber integrated saturable absorbers (SAs) for ultrafast nonlinear optics. RNA-SA performances were comparable to those of DNA-SA in terms of its nonlinear transmission, modulation depth, and saturation intensity. Upon insertion of these devices into an Erbium-doped fiber ring-laser cavity, both RNA and DNA SAs enabled efficient passive Q-switching operation. RNA-SA application further facilitated robust mode-locking and generated a transform-limited soliton pulse, exhibiting a pulse duration of 633 femtoseconds. A detailed analysis of these pulsed laser characteristics compared RNA and DNA fiber optic SAs with other nonlinear optic materials. The findings of this research establish the feasibility of utilizing RNA as a saturable absorber in ultrafast laser systems with an equal or higher potential as DNA, which presents novel possibilities for the nonlinear photonic applications of nucleic acid thin solid films.

Amplified Plasmonic Forces from DNA Origami-Scaffolded Single Dyes in Nanogaps

Developing highly enhanced plasmonic nanocavities allows direct observation of light-matter interactions at the nanoscale. With DNA origami, the ability to precisely nanoposition single-quantum emitters in ultranarrow plasmonic gaps enables detailed study of their modified light emission. By developing protocols for creating nanoparticle-on-mirror constructs in which DNA nanostructures act as reliable and customizable spacers for nanoparticle binding, we reveal that the simple picture of Purcell-enhanced molecular dye emission is misleading. Instead, we show that the enhanced dipolar dye polarizability greatly amplifies optical forces acting on the facet Au atoms, leading to their rapid destabilization. Using different dyes, we find that emission spectra are dominated by inelastic (Raman) scattering from molecules and metals, instead of fluorescence, with molecular bleaching also not evident despite the large structural rearrangements. This implies that the competition between recombination pathways demands a rethink of routes to quantum optics using plasmonics.

Water-resistant free-standing DNA-complexed films with antioxidant and H2O2-responsive activity

Water-insoluble DNA complexes are suitable for producing free-standing DNA films due to their low water sensitivity, which prevents their rapid degradation in aqueous environments. Here, we proposed two types of free-standing films that exhibit low dissolution rates in water: low molecular weight chitosan (LCS)-DNA films and phosphatidylcholine (PC)-cetyltrimethylammonium (CTMA)-DNA films. The structure and binding characteristics of the LCS-DNA and PC-CTMA-DNA complexes were investigated with UV-Vis spectroscopy and via the fluorescent characteristics of daunorubicin bound to them. A simple drop-casting method was then adopted for both complexes to fabricate free-standing films. An increase in antioxidant activity and water-resistance of the LCS-DNA DNA film was observed when the molar ratio of LCS to DNA was increased, but the dissolution rate of the LCS-DNA film was also dependent on the ionic strength of the dissolving solution. Fourteen days were required to dissolve the LCS-DNA film in deionized water, whereas immediate dissolution was observed in 1× phosphate-buffered saline (PBS). Deformation of the PC-CTMA-DNA film was accelerated by H₂O₂, such that the PC-CTMA-DNA film was degraded after 21 days of immersion in 1× PBS with H₂O₂. Due to the low dissolution rate in water and antioxidant activity, the free-standing LCS-DNA film should be able to store and protect embedded clinical materials, such as proteins and intercalating drugs, from moisture and enable localized delivery of treatments to designated sites. Also, the free-standing PC-CTMA-DNA film could be a biocompatible candidate for use as a membrane or sensor for detecting the levels of reactive oxygen species.

Anisotropy of DNA molecule detection and enhancement by GaN-based electronic sensor

An electrical characterization approach with a newly, to the best of our knowledge, defined electrical anisotropy (η) was proposed to characterize and enhance the anisotropy signals of DNA molecules. This approach utilizes L-shaped aluminum gratings on a gallium nitride PiN electronic sensor system to adjust and improve the η signals. Using this approach, the η signals of DNA molecules can be adjusted more easily and efficiently by changing the electrical parameters of the sensor. For instance, the η modes of DNA were enhanced more than 22 times with the change of the incident power and the reverse bias voltage of the PiN structure.

Linear and nonlinear optical properties of transfer ribonucleic acid (tRNA) thin solid films

We successfully obtained transfer ribonucleic acid (tRNA) thin solid films (TSFs) using an aqueous solution precursor in an optimized deposition process. By varying the concentration of RNA and deposition process parameters, uniform solid layers of solid RNA with a thickness of 30 to 46 nm were fabricated consistently. Linear absorptions of RNA TSFs on quartz substrates were experimentally investigated in a wide spectral range covering UV–VIS–NIR to find high transparency for λ > 350 nm. We analyzed the linear refractive indices, n(λ) of tRNA TSFs on silicon substrates by using an ellipsometer in the 400 to 900 nm spectral range to find a linear correlation with the tRNA concentration in the aqueous solution. The thermo-optic coefficient (dn/dT) of the films was also measured to be in a range −4.21 × 10⁻⁴ to −5.81 × 10⁻⁴ °C⁻¹ at 40 to 90 °C. We furthermore characterized nonlinear refractive index and nonlinear absorption of tRNA TSFs on quartz using a Z-scan method with a femtosecond laser at λ = 795 nm, which showed high potential as an efficient nonlinear optical material in the IR spectral range.

Optical measurements of one of the vital biological molecules (RNA) in the human body.

Solvent Effect to the Uniformity of Surfactant-Free Salmon-DNA Thin Films

Fabrication of surfactant-modified DNA thin films with high uniformity, specifically DNA-CTMA, has been well considered via drop-casting and spin-coating techniques. However, the fabrication of thin films with pure DNA has not been sufficiently studied. We characterize the uniformity of thin films from aqueous salmon DNA solutions mixed with ethanol, methanol, isopropanol, and acetone. Measurements of thickness and macroscopic uniformity are made via a focused-beam ellipsometer. We discuss important parameters for optimum uniformity and note what the effects of solvent modifications are. We find that methanol- and ethanol-added solutions provide optimal fabrication methods, which more consistently produce high degrees of uniformity with film thickness ranging from 20 to 200 nm adjusted by DNA concentration and the physical parameters of spin-coating methods.

Generation of 2D DNA Microstructures via Topographic Control and Shearing

2D DNA microstructures are fabricated by applying the shear force to the DNA solution on the microchannels. The "U"-like textures of DNA are clearly observed when the mechanical shearing is applied on the aqueous DNA sample under the topographic confinement, in which the shearing direction is perpendicular to the grooves. The optical textures of U-like microstructures are directly observed by polarized optical microscopy (POM) and laser scanning fluorescent confocal polarizing microscopy (FCPM). The DNA microstructures can be modified by varying the width, showing the multiple U-patterns along with channel direction due to the synergistic interaction between the elastic behavior of DNA chains and topographic boundary condition. The resultant microstructures can be used to align rod-like liquid crystals (LCs) to generate alternatively oriented nematic phase and tilted focal conic domains (FCDs) in the smectic A phase. It is believed that this approach can suggest a hint to use to DNA materials for organizing multiscale hierarchical structures of soft- and biomaterials.

Morphological and Mechanical Characterization of DNA SAMs Combining Nanolithography with AFM and Optical Methods

The morphological and mechanical properties of thiolated ssDNA films self-assembled at different ionic strength on flat gold surfaces have been investigated using Atomic Force Microscopy (AFM). AFM nanoshaving experiments, performed in hard tapping mode, allowed selectively removing molecules from micro-sized regions. To image the shaved areas, in addition to the soft contact mode, we explored the use of the Quantitative Imaging (QI) mode. QI is a less perturbative imaging mode that allows obtaining quantitative information on both sample topography and mechanical properties. AFM analysis showed that DNA SAMs assembled at high ionic strength are thicker and less deformable than films prepared at low ionic strength. In the case of thicker films, the difference between film and substrate Young’s moduli could be assessed from the analysis of QI data. The AFM finding of thicker and denser films was confirmed by X-Ray Photoelectron Spectroscopy (XPS) and Spectroscopic Ellipsometry (SE) analysis. SE data allowed detecting the DNA UV absorption on dense monomolecular films. Moreover, feeding the SE analysis with the thickness data obtained by AFM, we could estimate the refractive index of dense DNA films.

Uracil-doped DNA thin solid films: a new way to control optical dispersion of DNA film using a RNA constituent

Among five nucleobases, adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U), uracil is a key distinctive constituent existing only in ribonucleic acid (RNA). RNA shares the common A, G, and C with deoxyribonucleic acid (DNA) made of A-T, G-C hydrogen bonding. We explored a new attempt to combine uracil (U) with DNA, successfully realizing U-doped DNA thin solid films for the first time. Impacts of uracil on optical properties of the films were thoroughly investigated. The method was based on optimal spin-coating of an aqueous solution of DNA and uracil over silicon or silica substrates. Optical absorption of both aqueous solution and U-doped DNA thin solid films was characterized in a wide spectral range covering UV-visible-IR. Immobilization of uracil within DNA thin solid films was experimentally confirmed by FTIR spectroscopy studies. By using an ellipsometer, we measured the refractive indices of the films and discovered that U-doping was a very effective means to control optical dispersion DNA thin solid film. We further investigated thermo-optic behavior to find impacts of U-doping in DNA films. Detailed thin film processes and optical characterizations are discussed.

Electron Beam Patterning of Polymerizable Ionic Liquid Films for Application in Photonics

Planar photonic components can be fabricated with high resolution by electron beam patterning of polymer thin films on solid substrates such as silicon and glass. However, polymer films are normally formed by spin-coating lithographic resists containing not only polymers but also volatile solvents, which is a serious environmental and health issue. Therefore, we investigate a new type of material for planar structure fabrication (i.e., room-temperature ionic liquids (RTILs) with a polymerizable allyl group) that is electron-beam-curable, solvent-free, and thus potentially interesting for processing materials with weak resistance to solvents. We fabricate planar polymer microstructures by electron beam patterning of RTIL thin films in vacuum, which is possible because of the negligible volatility of ionic liquids. Three different polymerizable ionic liquids {i.e., [Allmim][Cl] (1-allyl-3-methylimidazolium chloride), [Allmim][NTf₂] (1-allyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide), and [Allmmim][NTf₂] (1-allyl-2,3-dimethylimidazolium bis(trifluoromethylsulfonyl)imide)} are compared in terms of the quality of the fabricated microstructures. We demonstrate that the shape of the more viscous RTIL with the Cl^- anion is less distorted during electron-beam-activated polymerization than the shape of the less viscous RTILs with a large NTf₂^- anion. Furthermore, the surface tension of the NTf₂-based ionic liquid decreases significantly with temperature as compared to that of the Cl-based ionic liquid. Thus, we suggest that the thermocapillary effect, that is, the Marangoni flow caused by a temperature gradient, might be responsible for the differences in the shape of the RTIL-derived microstructures. Also, we analyze the chemistry of the electron-beam-activated polymerization of RTIL by the use of Fourier-transform infrared spectroscopy (FTIR) and conclude that because of the disappearance of C═C bonds the free radical polymerization is a probable reaction mechanism. Finally, we show that polymerized microstructures are potentially attractive as planar photonic components because of good optical properties such as a high refractive index.

Hierarchical Assembly of Plasmonic Nanoparticle Heterodimer Arrays with Tunable Sub-5 nm Nanogaps

Nanoparticle assemblies have generated intense interest because of their novel optical, electronic, and magnetic properties that open up numerous opportunities in fundamental and applied nanophotonics, -electronics, and -magnetics. However, despite the great scientific and technological potential of these structures, it remains an outstanding challenge to reliably fabricate such assemblies with both nanometer-level structural control and precise spatial arrangements on a macroscopic scale. It is the combination of these two features that is key to realizing nanoparticle assemblies' potential, particular for device applications. To address this challenge, we propose a hierarchical assembly approach consisting of both template-particle and particle-particle interactions, whereby the former ensures precise addressability of assemblies on a surface and the latter provides nanometer-level structural control. Template-particle interactions are harnessed via chemical-pattern-directed assembly, and the particle-particle interactions are controlled using DNA-directed self-assembly. To demonstrate the potential of this hierarchical assembly approach, we demonstrate the fabrication of a particularly fascinating assembly: the nanoparticle heterodimer, which possesses a surprisingly rich set of plasmonic properties and is a promising candidate to enable a variety of imaging and sensing applications. Each heterodimer is placed on the surface at predetermined locations, and the precise control of the nanogaps is confirmed by far-field scattering measurements of individual dimers. We further demonstrate that the gap size can be effectively tuned by varying the DNA length. By correlating measured spectra with finite-difference time-domain (FDTD) simulations, we determine the gap sizes to be 4.2 and 5.0 nm-with subnm deviation-for the two DNA lengths investigated. This is one of the best gap uniformities ever demonstrated for surface-bound nanoparticle assemblies. The estimated surface-enhanced Raman scattering (SERS) enhancement factor of these heterodimers is on the order of 10⁵-10⁶ with high reproducibility and predictable polarization-dependence. This hierarchical fabrication technique-employing both template-particle and particle-particle interactions-constitutes a novel platform for the realization of functional nanoparticle assemblies on surfaces and thereby creates new opportunities to implement these structures in a variety of applications.

Magneto-optical and thermal characteristics of magnetite nanoparticle-embedded DNA and CTMA-DNA thin films

Recently, DNA molecules embedded with magnetite (Fe₃O₄) nanoparticles (MNPs) drew much attention for their wide range of potential usage. With specific intrinsic properties such as low optical loss, high transparency, large band gap, high dielectric constant, potential for molecular recognition, and their biodegradable nature, the DNA molecule can serve as an effective template or scaffold for various functionalized nanomaterials. With the aid of cetyltrimethylammonium (CTMA) surfactant, DNA can be used in organic-based applications as well as water-based ones. Here, DNA and CTMA-DNA thin films with various concentrations of MNPs fabricated by the drop-casting method have been characterized by optical absorption, refractive index, Raman, and cathodoluminescence measurements to understand the binding, dispersion, chemical identification/functional modes, and energy transfer mechanisms, respectively. In addition, magnetization was measured as a function of either applied magnetic field or temperature in field cooling and zero field cooling. Saturation magnetization and blocking temperature demonstrate the importance of MNPs in DNA and CTMA-DNA thin films. Finally, we examine the thermal stabilities of MNP-embedded DNA and CTMA-DNA thin films through thermogravimetric analysis, derivative thermogravimetry, and differential thermal analysis. The unique optical, magnetic, and thermal characteristics of MNP-embedded DNA and CTMA-DNA thin films will prove important to fields such as spintronics, biomedicine, and function-embedded sensors and devices.

Optical dispersion control in surfactant-free DNA thin films by vitamin B2 doping

A new route to systematically control the optical dispersion properties of surfactant-free deoxyribonucleic acid (DNA) thin solid films was developed by doping them with vitamin B2, also known as riboflavin. Surfactant-free DNA solid films of high optical quality were successfully deposited on various types of substrates by spin coating of aqueous solutions without additional chemical processes, with thicknesses ranging from 18 to 100 nm. Optical properties of the DNA films were investigated by measuring UV-visible-NIR transmission, and their refractive indices were measured using variable-angle spectroscopic ellipsometry. By doping DNA solid films with riboflavin, the refractive index was consistently increased with an index difference Δn ≥ 0.015 in the spectral range from 500 to 900 nm, which is sufficiently large to make an all-DNA optical waveguide. Detailed correlation between the optical dispersion and riboflavin concentration was experimentally investigated and thermo-optic coefficients of the DNA-riboflavin thin solid films were also experimentally measured in the temperature range from 20 to 85 °C, opening the potential to new bio-thermal sensing applications.

Non-ionising UV light increases the optical density of hygroscopic self assembled DNA crystal films

We report on ultraviolet (UV) light induced increases in the UV optical density of thin and optically transparent crystalline DNA films formed through self assembly. The films are comprised of closely packed, multi-faceted and sub micron sized crystals. UV-Vis spectrophotometry reveals that DNA films with surface densities up to 0.031 mg/mm2 can reduce the transmittance of incident UVC and UVB light by up to 90%, and UVA transmittance by up to 20%. Subsequent and independent film irradiation with either UVA or UVB dosages upwards of 80 J/cm2 both reduce UV transmittance, with reductions scaling monotonically with UV dosage. To date the induction of a hyperchromic effect has been demonstrated using heat, pH, high salt mediums, and high energy ionising radiation. Both hyperchromicity and increased light scattering could account for the increased film optical density after UV irradiation. Additional characterisation of the films reveal they are highly absorbent and hygroscopic. When coated on human skin, they are capable of slowing water evaporation and keeping the tissue hydrated for extended periods of time.

Quantitative refractive index distribution of single cell by combining phase-shifting interferometry and AFM imaging

Cell refractive index, an intrinsic optical parameter, is closely correlated with the intracellular mass and concentration. By combining optical phase-shifting interferometry (PSI) and atomic force microscope (AFM) imaging, we constructed a label free, non-invasive and quantitative refractive index of single cell measurement system, in which the accurate phase map of single cell was retrieved with PSI technique and the cell morphology with nanoscale resolution was achieved with AFM imaging. Based on the proposed AFM/PSI system, we achieved quantitative refractive index distributions of single red blood cell and Jurkat cell, respectively. Further, the quantitative change of refractive index distribution during Daunorubicin (DNR)-induced Jurkat cell apoptosis was presented, and then the content changes of intracellular biochemical components were achieved. Importantly, these results were consistent with Raman spectral analysis, indicating that the proposed PSI/AFM based refractive index system is likely to become a useful tool for intracellular biochemical components analysis measurement, and this will facilitate its application for revealing cell structure and pathological state from a new perspective.

Ultrafast nonlinear optical properties of thin-solid DNA film and their application as a saturable absorber in femtosecond mode-locked fiber laser

A new extraordinary application of deoxyribonucleic acid (DNA) thin-solid-film was experimentally explored in the field of ultrafast nonlinear photonics. Optical transmission was investigated in both linear and nonlinear regimes for two types of DNA thin-solid-films made from DNA in aqueous solution and DNA-cetyltrimethylammonium chloride (CTMA) in an organic solvent. Z-scan measurements revealed a high third-order nonlinearity with n₂ exceeding 10⁻⁹ at a wavelength of 1570 nm, for a nonlinarity about five orders of magnitude larger than that of silica. We also demonstrated ultrafast saturable absorption (SA) with a modulation depth of 0.43%. DNA thin solid films were successfully deposited on a side-polished optical fiber, providing an efficient evanescent wave interaction. We built an organic-inorganic hybrid all-fiber ring laser using DNA film as an ultrafast SA and using Erbium-doped fiber as an efficient optical gain medium. Stable transform-limited femtosecond soliton pulses were generated with full width half maxima of 417 fs for DNA and 323 fs for DNA-CTMA thin-solid-film SAs. The average output power was 4.20 mW for DNA and 5.46 mW for DNA-CTMA. Detailed conditions for DNA solid film preparation, dispersion control in the laser cavity and subsequent characteristics of soliton pulses are discussed, to confirm unique nonlinear optical applications of DNA thin-solid-film.

A sandwich-like strategy for the label-free detection of oligonucleotides by surface plasmon fluorescence spectroscopy (SPFS)

Cutting surface-bound optical molecular beacons results in a sandwich-like detection strategy with lower background fluorescence.

For the detection of oligonucleotides a sandwich-like detection strategy has been developed by which the background fluorescence is significantly lowered in comparison with surface-bound molecular beacons. Surface bound optical molecular beacons are DNA hairpin structures comprising a stem and a loop. The end of the stem is modified with a fluorophore and a thiol anchor for chemisorption on gold surfaces. In the closed state the fluorophore is in close proximity to the gold surface, and most of the fluorescence is quenched. After hybridization with a target the hairpin opens, the fluorophore and surface become separated, and the fluorescence drastically increases. Using this detection method the sensitivity is limited by the difference in the fluorescence intensity in the closed and open state. As the background fluorescence is mainly caused by non-quenched fluorophores, a strategy to reduce the background fluorescence is to cut the beacon in two halves. First a thiolated ssDNA capture probe strand (first half) is chemisorbed to a gold surface together with relatively short thiol spacers. Next the target is hybridized by one end to the surface-anchored capture probe and by the other to a fluorophore-labeled reporter probe DNA (second half). The signal readout is done by surface plasmon fluorescence spectroscopy (SPFS). Using this detection strategy the background fluorescence can be significantly lowered, and the detection limit is lowered by more than one order of magnitude. The detection of a target takes only a few minutes and the sensor chips can be used for multiple detection steps without a significant decrease in performance.

Critical View on Electrochemical Impedance Spectroscopy Using the Ferri/Ferrocyanide Redox Couple at Gold Electrodes

Electrochemical or faradaic impedance spectroscopy (EIS) using the ferri/ferrocyanide couple as a redox probe at gold working electrodes was evaluated with respect to its ability to monitor consecutive surface modification steps. As a model reaction, the reversible hybridization and dehybridization of DNA was studied. Thiol-modified single stranded DNA (ssDNA, 20 bases, capture probe) was chemisorbed to a gold electrode and treated with a solution of short thiols to release nonspecifically adsorbed DNA before hybridization with complementary ssDNA (20 bases, target) was carried out. Reversible dehybridization was achieved by intense rinsing with pure water. The experimental procedures were optimized by kinetic surface plasmon resonance (SPR) and quartz crystal microbalance with dissipation (QCM-D) measurements to maximize the increase in reflectivity or decrease in frequency upon hybridization before hybridization/dehybridization was also monitored by EIS. In contrast to SPR and QCM-D, repeatable EIS measurements were not possible at first. Combined SPR/EIS and QCM-D/EIS measurements revealed that during EIS the gold surface is seriously damaged due to the presence of CN(-) ions, which are released from the ferri/ferrocyanide redox probe. Even at optimized experimental conditions, etching the gold electrodes could not be completely suppressed and the repeatability of the EIS measurements was limited. In three out of four experimental runs, only two hybridization/dehybridization steps could be monitored reversibly by EIS. Thereafter etching the gold electrode significantly contributed to the EIS spectra whereas the QCM-D response was still repeatable. Hence great care has to be taken when this technique is used to monitor surface modification at gold electrodes.

A method based on light scattering to estimate the concentration of virus particles without the need for virus particle standards

Most often the determination of the concentration of virus particles is rendered difficult by the availability of proper standards. We have adapted a static light scattering based method for the quantification of virus particles (shown for poliovirus) without the need of virus particle standards. Instead, as standards, well-characterized polymeric nanoparticle solutions are used. The method is applicable for virus particles acting as Rayleigh scatterers, i.e., virus particles with equivalent diameters up to ca. 1/10th of the wavelength of the scattered monochromatic light (∼70 nm diameter). Further limitations may arise if the refractive index of the virus is unavailable or cannot be calculated based on its composition, such as in case of enveloped viruses. The method is especially relevant for preparation of virus particle concentration standards and to vaccine formulations based on attenuated or inactivated virus particles where the classical plaque forming assays cannot be applied. The method consists of:

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Measuring the intensity of the light scattered by viruses suspended in an aqueous solution.

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Measuring the intensity of the light scattered by polymeric nanoparticles of known concentration and comparable size with the investigated virus particle.

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The concentration of virus nanoparticles can be calculated based on the two measured scattered light intensities by knowing the refractive index of the dispersing solution, of the polymer and virus nanoparticles as well as their relative sphere equivalent diameters.

Physically transient photonics: random versus distributed feedback lasing based on nanoimprinted DNA

Room-temperature nanoimprinted, DNA-based distributed feedback (DFB) laser operation at 605 nm is reported. The laser is made of a pure DNA host matrix doped with gain dyes. At high excitation densities, the emission of the untextured dye-doped DNA films is characterized by a broad emission peak with an overall line width of 12 nm and superimposed narrow peaks, characteristic of random lasing. Moreover, direct patterning of the DNA films is demonstrated with a resolution down to 100 nm, enabling the realization of both surface-emitting and edge-emitting DFB lasers with a typical line width of <0.3 nm. The resulting emission is polarized, with a ratio between the TE- and TM-polarized intensities exceeding 30. In addition, the nanopatterned devices dissolve in water within less than 2 min. These results demonstrate the possibility of realizing various physically transient nanophotonics and laser architectures, including random lasing and nanoimprinted devices, based on natural biopolymers.

A reusable sensor for the label-free detection of specific oligonucleotides by surface plasmon fluorescence spectroscopy

The development of a reusable molecular beacon (MB)-based sensor for the label-free detection of specific oligonucleotides using surface plasmon fluorescence spectroscopy (SPFS) as the readout method is described. The MBs are chemisorbed at planar gold surfaces serving as fluorescence quenching units. Target oligonucleotides of 24 bases can be detected within a few minutes at high single-mismatch discrimination rates.

Measuring the density of DNA films using ultraviolet-visible interferometry

In order to determine a proper value for the density of dry DNA films we have used a method based upon the measurement of interference effects in transmission spectra of thin DNA layers. Our results show that the methodology is effective and the density of DNA in this state, 1.407 g/cm(3), is much lower than the commonly used 1.7 g/cm(3). Obtaining accurate values for the DNA film density will allow the optical constants for DNA to be recalculated, which were previously obtained assuming a higher DNA density. Furthermore, since our recent investigations have shown a strong dependence of the sample composition on DNA film formation and thus on its density, such a method will be important in characterizing particle interactions with DNA film and their dose dependence.

Spectral backscattering properties of marine phytoplankton cultures

The backscattering properties of marine phytoplankton, which are assumed to vary widely with differences in size, shape, morphology and internal structure, have been directly measured in the laboratory on a very limited basis. This work presents results from laboratory analysis of the backscattering properties of thirteen phytoplankton species from five major taxa. Optical measurements include portions of the volume scattering function (VSF) and the absorption and attenuation coefficients at nine wavelengths. The VSF was used to obtain the backscattering coefficient for each species, and we focus on intra- and interspecific variability in spectral backscattering in this work. Ancillary measurements included chlorophyll-a concentration, cell concentration, and cell size, shape and morphology via microscopy for each culture. We found that the spectral backscattering properties of phytoplankton deviate from theory at wavelengths where pigment absorption is significant. We were unable to detect an effect of cell size on the spectral shape of backscattering, but we did find a relationship between cell size and both the backscattering ratio and backscattering cross-section. While particulate backscattering at 555 nm was well correlated to chlorophyll-a concentration for any given species, the relationship was highly variable between species. Results from this work indicate that phytoplankton cells may backscatter light at significantly higher efficiencies than what is predicted by Mie theory, which has important implications for closing the underwater and remotely sensed light budget.

Applied chemistry of natural DNA

Recently, natural DNA has emerged as an appealing biomacromolecule for functional materials. It is abundant and renewable, and possesses the well known double helix structure that promises many unique properties difficult to find in other polymers. Natural DNA has been applied in electronic, optical and biomaterials, as a catalyst for enantioselective reactions, and as a material for cleaning the environment. Most of the applications are based on combining DNA with other chemicals or nanoparticles by electrostatic binding, intercalation or groove binding. In this critical review article, recent developments in utilizing natural DNA are reviewed by focusing on three basic properties of DNA: the electrostatic property as a polyelectrolyte, selective affinity for small molecules, and biocompatibility (128 references).

Liquid crystal alignment on a chiral surface: interfacial interaction with sheared DNA films

We explore the alignment of various achiral liquid crystals on films of aligned double-stranded helical DNA. In all cases and both for the nematic and smectic A phases, we find a distinctly chiral interfacial structure, with the mean orientation of the liquid crystal in contact with the DNA-treated surfaces chirally rotated through a substantial angle with respect to the mean DNA orientation. This rotation originates in the chirality of double-stranded DNA and depends on the liquid crystal molecular structure. We discuss the role of dipolar and hydrophobic coupling in determining the observed orientation.

Brewster angle microscopy and PMIRRAS study of DNA interactions with BGTC, a cationic lipid used for gene transfer

The lipid bis(guanidinium)-tris(2-aminoethyl)amine-cholesterol (BGTC) is a cationic cholesterol derivative bearing guanidinium polar headgroups which displays high transfection efficiency in vitro and in vivo when used alone or formulated as liposomes with the neutral colipid 1,2-di-[ cis-9-octadecenoyl]- sn-glycero-3-phosphoethanolamine (DOPE). Since transfection may be related to the structural and physicochemical properties of the self-assembled supramolecular lipid-DNA complexes, we used the Langmuir monolayer technique coupled with Brewster angle microscopy (BAM) and polarization modulation infrared reflection absorption spectroscopy (PMIRRAS) to investigate DNA-BGTC and DNA-BGTC/DOPE interactions at the air/water interface. We herein show that BGTC forms stable monolayers at the air/water interface. When DNA is injected into the subphase, it adsorbs to BGTC at 20 mN/m. Whatever the (+/-) charge ratio of the complexes used, defined as the ratio of positive charges of BGTC in the monolayer versus negative charges of DNA injected in the subphase, the DNA interacts with the cationic lipid and forms either an incomplete (no constituent in excess) or a complete (DNA in excess) monolayer of oriented double strands parallel to the lipid monolayer plan. We also show that, under a homogeneous BGTC/DOPE (3/2) monolayer at 20 mN/m, DNA adsorbs homogeneously to form an organized but incomplete layer whatever the charge ratio used (DNA in default or in excess). Compression beyond the collapse of these mixed DNA-BGTC/DOPE systems leads to the formation of dense DNA monolayers under an asymmetric lipid bilayer with a bottom layer of BGTC in contact with DNA and a top layer mainly constituted of DOPE. These results allow a better understanding of the mechanisms underlying the formation of the supramolecular BGTC-DNA complexes efficient for gene transfection.

Biopolymer-based material used in optical image correlation

We investigate the possible application of a modified deoxyribonucleic acid (DNA)-dye system for dynamic processing of optical information, e.g., optical correlation. The system consists of a biopolymeric matrix made of DNA substituted with the cationic surfactant molecule cetyltrimethyl-ammonium chloride (CTMA) and doped with a photochromic Disperse Red 1 dye. Fast dynamics (millisecond range of rise and fall times) of output correlation signal formation was measured in a joint Fourier transform optical correlator experimental setup. Full reversibility of the correlation signal and reproducibility were observed even after long-time exposures.