Enhanced surface nanoanalytics of transient biomolecular processes

Fundamental knowledge of the physical and chemical properties of biomolecules is key to understanding molecular processes in health and disease. Bulk and single-molecule analytical methods provide rich information about biomolecules but often require high concentrations and sample preparation away from physiologically relevant conditions. Here, we present the development and application of a lab-on-a-chip spray approach that combines rapid sample preparation, mixing, and deposition to integrate with a range of nanoanalytical methods in chemistry and biology, providing enhanced spectroscopic sensitivity and single-molecule spatial resolution. We demonstrate that this method enables multidimensional study of heterogeneous biomolecular systems over multiple length scales by nanoscopy and vibrational spectroscopy. We then illustrate the capabilities of this platform by capturing and analyzing the structural conformations of transient oligomeric species formed at the early stages of the self-assembly of α-synuclein, which are associated with the onset of Parkinson's disease.

Evaluation of adsorption of DNA/PEI polyplexes to tubing materials

Nucleic acid drugs hold great promise for potential treatment of a variety of diseases. But efficient delivery is still the major challenge impeding translation. Nanoformulations based on polymers and lipids require preparation processes such as microfluidic mixing, spray drying or final filling, where pumping is a crucial step. Here, we studied the effect of pumping on the component and overall loss of a binary polyplex formulation made of DNA and polyethyleneimine (PEI). We varied tubing length and material with a focus on subsequent spray drying. Interestingly, product loss increased with the length of silicon tubing. Losses of DNA were prevented by using Pumpsil. The following spray drying process did not affect DNA content but caused PEI loss. Characterization of the different tubing materials revealed similar hydrophobicity of all tubing materials and showed neutral Pumpsil® surface charge, negative Santoprene™ surface charge, and a positive Silicon surface charge. Hence, adsorption of DNA onto tubing material was concluded to be the root cause for DNA loss after pumping and is based upon an interplay of ionic and hydrophobic interactions between polyplexes and tubing material. Overall, selecting the appropriate tubing material for processing nucleic acid nanoparticles is key to achieving satisfactory product quality.

Recent Advances in Fluorescence Recovery after Photobleaching for Decoupling Transport and Kinetics of Biomacromolecules in Cellular Physiology

Among the new molecular tools available to scientists and engineers, some of the most useful include fluorescently tagged biomolecules. Tools, such as green fluorescence protein (GFP), have been applied to perform semi-quantitative studies on biological signal transduction and cellular structural dynamics involved in the physiology of healthy and disease states. Such studies focus on drug pharmacokinetics, receptor-mediated endocytosis, nuclear mechanobiology, viral infections, and cancer metastasis. In 1976, fluorescence recovery after photobleaching (FRAP), which involves the monitoring of fluorescence emission recovery within a photobleached spot, was developed. FRAP allowed investigators to probe two-dimensional (2D) diffusion of fluorescently-labelled biomolecules. Since then, FRAP has been refined through the advancements of optics, charged-coupled-device (CCD) cameras, confocal microscopes, and molecular probes. FRAP is now a highly quantitative tool used for transport and kinetic studies in the cytosol, organelles, and membrane of a cell. In this work, the authors intend to provide a review of recent advances in FRAP. The authors include epifluorescence spot FRAP, total internal reflection (TIR)/FRAP, and confocal microscope-based FRAP. The underlying mathematical models are also described. Finally, our understanding of coupled transport and kinetics as determined by FRAP will be discussed and the potential for future advances suggested.

Solid-phase silica-based extraction leads to underestimation of residual DNA in decellularized tissues

Decellularization of animal tissues is a novel route to obtain biomaterials for use in tissue engineering and organ transplantation. Successful decellularization is required as animal DNA causes inflammatory reactions and contains endogenous retroviruses, which could be transmitted to the patient. One of the criteria for successful decellularization is digestion (fragmentation) and elimination (residual quantity) of DNA from the tissue. Quantification of DNA can be done in many ways, but it has recently been shown that silica‐based solid‐phase extraction methods often do not completely purify in particular small DNA fragments. In the context of decellularization, this means that the measured DNA amount is underestimated, which could compromise safety of the processed tissue for in‐patient use. In this article, we review DNA quantification methods used by researchers and assess their influence on the reported DNA contents after decellularization. We find that underestimation of residual DNA amount after silica‐based solid‐phase extraction may be as large as a factor of ten. We therefore recommend a direct assessment of DNA amount in tissue lysate using dsDNA‐specific binding dyes, such as Picogreen, due to their higher accuracy for small fragment detection as well as ease of use and widespread availability.

Influence of Oligonucleotide Grafting Density on Surface-Mediated DNA Transport and Hybridization

Adsorption of soluble DNA to surfaces decorated with complementary DNA plays an important role in many bionanotechnology applications, and previous studies have reported complex dependencies of the surface density of immobilized DNA on hybridization. While these effects have been speculatively ascribed to steric or electrostatic effects, the influence of surface-mediated molecular transport (i.e., intermittent "hopping diffusion") has not been fully appreciated. Here, single-molecule tracking and Förster resonance energy transfer (FRET) were employed to characterize the mobility and the hybridization efficiency of adsorbed ssDNA oligonucleotides ("target") at solid-liquid interfaces exhibiting surface-immobilized ssDNA ("probe") over a wide range of surface grafting densities. Two distinct regimes were observed, with qualitatively different transport and hybridization behaviors. At dilute grafting density, only 1-3% of target molecules were observed to associate with probes (i.e., to hybridize). Adsorbing target molecules often searched unsuccessfully and "flew", via desorption-mediated diffusion, to secondary locations before hybridizing. In contrast, at high probe grafting density, approximately 20% of target DNA hybridized to immobilized probes, and almost always in the vicinity of initial adsorption. Moreover, following a dehybridization event, target molecules rehybridized at high probe density, but rehybridization was infrequent in the dilute density regime. Interestingly, the intermittent interfacial transport of mobile target molecules was suppressed by the presence of immobilized probe DNA, presumably due to an increased probability of readsorption following each "hop". Together, these findings suggested that many salient effects of grafting density on surface-mediated DNA hybridization can be directly related to the mechanisms of surface-mediated intermittent diffusion.

Advances, challenges and opportunities for point-of-need screening of mycotoxins in foods and feeds

Recent advances in analytical methods for mycotoxin screening in foods and feeds are reviewed, focusing on point-of-need detection using integrated devices.

Electrostatic melting in a single-molecule field-effect transistor with applications in genomic identification

The study of biomolecular interactions at the single-molecule level holds great potential for both basic science and biotechnology applications. Single-molecule studies often rely on fluorescence-based reporting, with signal levels limited by photon emission from single optical reporters. The point-functionalized carbon nanotube transistor, known as the single-molecule field-effect transistor, is a bioelectronics alternative based on intrinsic molecular charge that offers significantly higher signal levels for detection. Such devices are effective for characterizing DNA hybridization kinetics and thermodynamics and enabling emerging applications in genomic identification. In this work, we show that hybridization kinetics can be directly controlled by electrostatic bias applied between the device and the surrounding electrolyte. We perform the first single-molecule experiments demonstrating the use of electrostatics to control molecular binding. Using bias as a proxy for temperature, we demonstrate the feasibility of detecting various concentrations of 20-nt target sequences from the Ebolavirus nucleoprotein gene in a constant-temperature environment.

DNA hybridization of two single-strands to form a double-stranded helix is widely used for genomic identification applications. Here, Vernick et al. record duplex formation of 20-mer oligonucleotide using a single-molecule field-effect transistor, where DNA kinetics is affected by electrostatic bias.

Influence of nanopore surface charge and magnesium ion on polyadenosine translocation

We investigate the influence of a nanopore surface state and the addition of Mg(2+) on poly-adenosine translocation. To do so, two kinds of nanopores with a low aspect ratio (diameter ∼3-5 nm, length 30 nm) were tailored: the first one with a negative charge surface and the second one uncharged. It was shown that the velocity and the energy barrier strongly depend on the nanopore surface. Typically if the nanopore and polyA exhibit a similar charge, the macromolecule velocity increases and its global energy barrier of entrance in the nanopore decreases, as opposed to the non-charged nanopore. Moreover, the addition of a divalent chelating cation induces an increase of energy barrier of entrance, as expected. However, for a negative nanopore, this effect is counterbalanced by the inversion of the surface charge induced by the adsorption of divalent cations.

DNA hairpin stabilization on a hydrophobic surface

DNA hybridization in the vicinity of surfaces is a fundamental process for self-assembled nanoarrays, nanocrystal superlattices, and biosensors. It is widely recognized that solid surfaces alter molecular forces governing hybridization relative to a bulk solution, and these effects can either favor or disfavor the hybridized state depending on the specific sequence and surface. Results presented here provide new insights into the dynamics of DNA hairpin-coil conformational transitions in the vicinity of hydrophilic oligo(ethylene glycol) (OEG) and hydrophobic trimethylsilane (TMS) surfaces. Single-molecule methods are used to observe the forward and reverse hybridization hairpin-coil transition of adsorbed species while simultaneously measuring molecular surface diffusion in order to gain insight into surface interactions with individual DNA bases. At least 35 000 individual molecular trajectories are observed on each type of surface. It is found that unfolding slows and the folding rate increases on TMS relative to OEG, despite stronger attractions between TMS and unpaired nucleobases. These rate differences lead to near-complete hairpin formation on hydrophobic TMS and significant unfolding on hydrophilic OEG, resulting in the surprising conclusion that hydrophobic surface coatings are preferable for nanotechnology applications that rely on DNA hybridization near surfaces.

Development of a single-step subtraction method for eukaryotic 18S and 28S ribonucleic acids

The abundance of mammalian 18S and 28S ribosomal RNA can decrease the detection sensitivity of bacterial or viral targets in complex host-pathogen mixtures. A method to capture human RNA in a single step was developed and characterized to address this issue. For this purpose, capture probes were covalently attached to magnetic microbeads using a dendrimer linker and the solid phase was tested using rat thymus RNA (mammalian components) with Escherichia coli RNA (bacterial target) as a model system. Our results indicated that random capture probes demonstrated better performance than specific ones presumably by increasing the number of possible binding sites, and the use of a tetrame-thylammonium-chloride (TMA-Cl-) based buffer for the hybridization showed a beneficial effect in the selectivity. The subtraction efficiency determined through real-time RT-PCR revealed capture-efficiencies comparable with commercially available enrichment kits. The performance of the solid phase can be further fine tuned by modifying the annealing time and temperature.

Effects of humic acid on recoverability and fractal structure of alum-kaolin flocs

Particle surface characteristics, floc recoverability and fractal structure of alum-kaolin flocs were investigated using in situ particle image velocimetry (PIV) and microbalance with or without humic acid. Experimental results indicated that the zeta potential of kaolin particle surface after adsorption of humic acid was related with humic acid concentration and its acid-base buffering capacity. Adsorption of humic acid resulted in more negative electrophoresis on the particle surface. Coagulant dosages for particles to form flocs would increase with increasing humic concentration. PIV was used to evaluate floc structural fragmentation, floc surface erosion as well as recoverability after high shear. It was found that the floc size during the steady phase of growth was small, while the regrowing capability decreased in the presence of humic acid. The recoverability was closely related with floc breakage modes including floc structural fragmentation and floc surface erosion. The fractal dimensions of alum-kaolin flocs by mass-size method based on microbalance would decrease with increasing humic concentration. This study proved that humic acid had adverse influences on the performance of coagulation process.

An investigation on interaction between 14mer DNA oligonucleotide and CTAB by fluorescence and fluorescence resonance energy transfer studies

Possible interaction mechanisms between oligonucleotide (DNA) of 14 base pairs with cetyl trimethyl ammonium bromide (CTAB) were postulated based on fluorescence and fluorescence resonance energy transfer (FRET) studies. Detailed FRET investigations were carried out by fluorometric titrations of the surfactant with various oligonucleotide duplexes with 5'-tagged fluorescein (donor) (D(D)), 5'-tagged TAMRA (acceptor) (D(A)) and both (D(DA)). In general, fluorescence spectra of the duplexes (D(D), D(A) and D(DA)) revealed a reduction in the fluorescence intensities of 5'-fluorescein as well as 5'-TAMRA and thereafter an attainment of saturation with increase in the surfactant concentration. The observed changes in the oligonucleotide fluorescence intensities for the duplexes under investigation could be attributed to the microenvironmental changes during the oligonucleotide-CTAB interaction. Considering together, it appeared that the interaction is a three-stage process, wherein the initial addition of surfactant caused neutralization of the 14mer at Z(+/-)(1) = 0.8, which is manifested by a slight reduction in fluorescence intensity. Further, addition of the surfactant molecules sharply reduced the fluorescence intensity of the oligonucleotide depicting oligonucleotide induced self-assembly until the second break point (Z(+/-)(2) = 1.7). From the second break point, a striking resonance energy transfer was observed from donor to acceptor, which revealed shortening of distance between 5' ends of the oligonucleotides that attained a saturation at Z(+/-)(3) = 2.5. Similar three-stage interaction of oligonucleotide with the surfactant has also been observed through fluorometric titrations in the presence of NaCl. However, in the presence of the salt, neutralization of oligonucleotide, surfactant aggregation and FRET occurred at higher charge ratios due to the screening effect of Na+ ions followed by an increase in critical association concentration (CAC) of the surfactant. Overall, investigations probe possible structural changes in the 14mer oligonucleotide-CTAB complex upon increase in the surfactant concentration.

Controlling DNA adsorption and diffusion on lipid bilayers by the formation of lipid domains

We describe the influence of membrane heterogeneity on the adsorption and diffusion of DNA. Cellular membranes are believed to contain domains (lipid rafts) that influence processes ranging from signal transduction to the diffusion of membrane components. By analogy, we demonstrate that the formation of raft-like domains in supported lipid bilayers provides control over the adsorption and diffusion of DNA. The formation of bilayers from a mixture of the gel phase zwitterionic lipid 1,2-distearoyl-sn-glycero-3-phosphatidylcholine (DSPC) and the fluid phase cationic lipid 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) yielded coexisting DSPC-enriched and DOTAP-enriched phases. We demonstrated the ability to pattern the adsorption of DNA on the heterogeneous bilayers, with the adsorption being restricted to the DOTAP-enriched phase. We further demonstrated that the DSPC-enriched domains acted as obstacles to the lateral diffusion of adsorbed DNA. Fluorescence recovery after photobleaching (FRAP) analysis revealed that the diffusivity of the adsorbed DNA tracked that of the underlying lipid, although the lipid diffusivity changed by an order of magnitude with changes in bilayer composition. Fundamental insight into the adsorption and diffusion of DNA on heterogeneous surfaces may be useful for the design of novel techniques for the size-based separation of DNA.

Particle tracking single protein-functionalized quantum dot diffusion and binding at silica surfaces

We evaluate commercial QD585 and QD605 streptavidin-functionalized quantum dots (QDs) for single-particle tracking microscopy at surfaces using total internal reflectance fluorescence and measure single QD diffusion and nonspecific binding at silica surfaces in static and flow conditions. The QD diffusion coefficient on smooth, near-ideal, highly hydroxylated silica surfaces is near bulk-solution diffusivity, as expected for repulsive surfaces, but many QD trajectories on rougher, less-than-ideal surfaces or regions display transient adsorptions. We attribute the binding to defect sites or adsorbates, possibly in conjunction with protein conformation changes, and estimate binding energies from the transient adsorption lifetimes. We also assess QD parameters relevant to tracking, including hydrodynamic radius, charge state, signal levels, blinking reduction with reducing solutions, and photoinduced blueing and bleaching.

Chemiluminescent bead-based hybridization assay for the detection of genomic DNA from E. coli in purified plasmid samples

A bead-based hybridization assay was developed for detection of traces of E. coli genomic DNA (gDNA) present in purified plasmid DNA (pDNA) samples. Standards of gDNA and pDNA samples were sheared by sonication and adsorbed onto aminopropyl controlled pore glass (CPG) particles (130 microm). A preliminary study was conducted to optimize the amount of DNA adsorbed on the particles. Results indicated that maximum attachment efficiency was obtained by adsorbing DNA for 2 h in 0.2 x SSC, pH 5.7. The DNA-bound particles were hybridized overnight with a 181-bp digoxigenin-labeled probe, specific for gDNA. Following a chemiluminescent detection protocol, signal intensities of the standards were plotted as a function of initial gDNA concentration. The calculated detection limit (LOD) was 1.4 pM of gDNA. The assay was able to detect gDNA in pure plasmid preparations at the 1% level even in the presence of 1,000-fold excess of noncomplementary target. Hybridization results were compared with a quantitative real-time PCR assay. Both methods afforded similar accurate results at the 95% confidence level.

Controlling the reactivity of adsorbed DNA on template surfaces

The ability to place DNA on surfaces with increased and controllable reactivity is of fundamental importance in the development of next-generation DNA and protein biochips. The present work demonstrates the ability to control both the localization of the DNA on a surface and its reactivity by a self-assembly approach that is dependent on two variables: DNA structure and surface environment. Here we utilize a two-step adsorption scheme to control the adsorption and reactivity of DNA embedded within two types of alkyl thiol monolayers (either methyl-terminated or hydroxyl-terminated). In addition, by changing the structure of the chemisorbed DNA from fully single stranded to a 50% double stranded at its side adjacent to the surface, we were able to observe a clear dependence of DNA reactivity on both the DNA structure and the type of alkyl thiol monolayer covering the surface. The adsorption and the reactivity yield of the DNA were monitored either by its ability to hybridize to a complementary target molecule or by an enzymatic reaction involving DNA phosphorylation catalyzed by the enzyme T4 polynucleotide kinase.

DNA electrochemical sensor based on conducting polymer: dependence of the "signal-on" detection on the probe sequence localization

We show in this work that it is possible to make selective direct electrochemical hybridization detection of a target strand onto a probe strand immobilized on a conducting polymer modified with a quinone group, which presents cation-exchange properties. This leads to a "signal-on"detection, a unique behavior in comparison to similar systems described in the literature. It is shown that this system is efficient for various probe and target lengths (10-30 bp) and can discriminate a single mismatch. To go further in comprehension of the detection mechanism, a systematic study of the electrochemical response versus the probe sequence localization onto the immobilized strand is performed. For example, a 30-bp target strand is divided into three shorter 10-bp sequences (A-C, respectively), and we investigate the successive hybridization of these 1/3 strands onto the 30-bp probe strand. It is shown that one probe strand can be used to address several shorter targets.

Modeling of nucleic acid adsorption on 3D prisms in microchannels

Understanding nucleic acid adsorption in microchannels is critical to improve the efficiency of purifying and extracting nucleic acid (NA) from sample solutions by microfluidic technologies. Using a microchannel with 3D prismatic silica elements on the wall can dramatically increase the surface area-to-volume ratio, and hence facilitate the nucleic acid adsorption on the wall. In this study a theoretical model for modeling adsorption in a microchannel with a designed 3D surface structure was developed, and five dimensionless numbers were found to be the key parameters in the adsorption process. Extensive numerical simulations were conducted. Two flow modes, the electroosmotic flow (EOF) and pressure-driven flow (PDF), were investigated for their effect on the adsorption. It was found that the EOF is more desirable than PDF. The 3D prismatic elements can increases the NA molecule adsorption not only by providing more surface areas, but also by the induced pressure resisting the central bulk electroosmotic flow. Finally, the effects of adsorption kinetic parameters (i.e., the kinetic association/dissociation constants, the diffusion coefficient, the total site density, the loading concentration, and the channel height), on the adsorption process were discussed in detail.

Lipid mobility controls the diffusion of small biopolymer adsorbates

Recent studies on the diffusion of adsorbed polymers such as DNA on supported lipid bilayers have suggested that such strongly adsorbed polymers can be treated similarly to a polymer "in" a 2D fluid, but this conjecture has not been experimentally verified. To test this hypothesis and also to gain a better understanding of polymer dynamics in two dimensions, we designed an experimental protocol-the lateral transport of a short, single-stranded DNA oligonucleotide adsorbed on a supported cationic lipid bilayer. Fluorescence recovery after photobleaching (FRAP) analysis reveals that the diffusivity of the adsorbed DNA quantitatively tracks that of the underlying lipid, even though the bilayer mobility changes by 2 orders of magnitude with changes in temperature. Interestingly, our results for short, extended, adsorbed biopolymers quantitatively track those for globular proteins in lipid bilayers. We thus conclude that short macromolecules that are strongly adsorbed on lipid bilayers can be treated similarly to macromolecules in the bilayer.

Dual polarisation interferometry characterisation of DNA immobilisation and hybridisation detection on a silanised support

Dual polarisation interferometry is an analytical technique that allows the simultaneous determination of thickness, density and mass of a biological layer on a sensing waveguide surface in real time. We evaluated, for the first time, the ability of this technique to characterise the covalent immobilisation of single stranded probe DNA and the selective detection of target DNA hybridisation on a silanised support. Two immobilisation strategies have been evaluated: direct attachment of the probe molecule and a more complex chemistry employing a 1,2 homobifunctional crosslinker molecule. With this technique we demonstrate it was possible to determine probe orientation and measure probe coverage at different stages of the immobilisation process in real time and in a single experiment. In addition, by measuring simultaneously changes in thickness and density of the probe layer upon hybridisation of target DNA, it was possible to directly elucidate the impact that probe mobility had on hybridisation efficiency. Direct covalent attachment of an amine modified 19 mer resulted in a thickness change of 0.68 nm that was consistent with multipoint attachment of the probe molecule to the surface. Blocking with BSA formed a dense layer of protein molecules that absorbed between the probe molecules on the surface. The observed hybridisation efficiency to target DNA was approximately 35%. No further significant reorientation of the probe molecule occurred upon hybridisation. The initial thickness of the probe layer upon attachment to the crosslinker molecule was 0.5 nm. Significant reorientation of the probe molecule surface normal occurred upon hybridisation to target DNA. This indicated that the probe molecule had greater mobility to hybridise to target DNA. The observed hybridisation efficiency for target DNA was approximately 85%. The results show that a probe molecule attached to the surface via a crosslinker group is better able to hybridise to target DNA due to its greater mobility.

Dual polarization interferometry size and density characterisation of DNA immobilisation and hybridisation

Investigation of nucleic acid interactions was performed using dual polarization interferometry, a novel approach to elucidating molecular interactions. This paper presents a preliminary study of adsorption of single stranded DNA onto functionalised silicon oxynitride, compared with covalent linkage, and avidin-biotin immobilisation. The effect of probe concentration on hybridisation efficiency was also examined. We found that increasing the electrolyte concentration resulted in a decrease of adsorbed DNA and that capture of a biotinylated duplex DNA on an adsorbed avidin layer resulted in four times fewer molecules per cm(2) than for duplex DNA covalently bound via an amine end terminal. The rate of thickness increase of a biotin probe layer on an adsorbed avidin capture layer increased 10-fold when the probe concentration was increased from 0.1 microM to 1 microM. The close grafting density of the higher concentration probe meant that the immobilised probes were unavailable for hybridisation.

Electric-field assisted immobilization and hybridization of DNA oligomers on thin-film microchips

Single, square voltage pulses in the microsecond timescale result in selective 5'-end covalent bonding (immobilization) of thiolated single-stranded (ss) DNA probes to a modified silicon dioxide flat surface and in specific hybridization of ssDNA targets to the immobilized probe. Immobilization and hybridization rates using microsecond voltage pulses at or below 1 V are at least 10(8) times faster than in the passive control reactions performed without electric field (E), and can be achieved with at least three differently functionalized thin-film surfaces on plastic or glass substrates. The systematic study of the effect of DNA probe and target concentrations, of DNA probe and target length, and the application of asymmetric pulses on E-assisted DNA immobilization and hybridization showed that: (1) the rapidly rising edge of the pulse is most critical to the E-assisted processes, but the duration of the pulse is also important; (2) E-assisted immobilization and hybridization can be performed with micrometre-sized pixels, proving the potential for use on microelectronic length scales, and the applied voltage can be scaled down together with the electrode spacing to as low as 25 mV; and (3) longer DNA chains reduce the yield in the E-assisted immobilization and hybridization because the density of physisorbed single-stranded DNA is reduced. The results show that the E-induced reactions can be used as a general method in DNA microarrays to produce high-density DNA chips (E-immobilization) and speed the microarray-based analysis (E-hybridization).

Single DNA Molecules as Probes of Chromatographic Surfaces

YOYO-I-labeled lambda-DNA was employed as a nanoprobe for different functionalized surfaces to elucidate adsorption in chromatography. While the negatively charged backbone is not adsorbed, the 12-base unpaired ends of this DNA provide exposed purine and pyrimidine groups for adsorption. Self-assembled monolayers (SAMs) formed on gold substrate provide a wide range of choices of surface with well-defined and well-organized functional groups. Patterns of amino-terminated, carboxylic acid-terminated, and hydroxyl-terminated SAMs are generated by lithography. Patterns of metal oxides are generated spontaneously after deposition of metals. By recording the real-time dynamic motion of DNA molecules at the SAMs/aqueous interface, one can study the various parameters governing the retentivity of an analyte during chromatographic separation. Even subtle differences among adsorptive forces can be revealed.

Dynamics of single biomolecules in free solution

Instrumental advances have allowed the continuous observation of single-molecule trajectories in free solution. Diffraction-limited spectral resolution at video frame rates is routinely achieved by using commercial, intensified, charge-coupled device cameras, low-power continuous-wave lasers, and standard optical microscopes. Either the native fluorescence from large biomolecules or emission from conjugated fluorescence labels can be employed to follow multiple molecules over many seconds. Both molecular motion at the liquid/solid interface and in bulk solution can be recorded. The former reveals adsorption and desorption probabilities that are related to chromatographic retention processes and to the applicability of biocompatible materials. The latter allows the manipulation of particles and large biomolecules to facilitate separation and identification.

Direct Observation of Single Native DNA Molecules in a Microchannel by Differential Interference Contrast Microscopy

Direct observation of single native DNA molecules in a microchannel was monitored without fluorescence-dye labeling. At a PDMS/glass microchip, the image of individual lambda-DNA molecules appear sharp and distinct in Nomarski differential interference contrast microscopy. Intercalator dyes affected the physical properties and dynamic behavior of individual DNA molecules. From the migration velocities in the microchannel it is evident that native DNA molecules migrated faster than DNA molecules labeled with the intercalator YOYO-1. This is because YOYO-1 increases the molecular weight and size of lambda-DNA and decreases the charge. The electric field strength and pH also affected the dynamics of single DNA molecules. We also observed that YOYO-labeled DNA was more stretched out compared to native DNA.

Aptamer-based biosensor arrays for detection and quantification of biological macromolecules

We have developed a chip-based biosensor for multiplex analysis of protein analytes. The biosensor utilizes immobilized DNA and RNA aptamers, selected against several different protein targets, to simultaneously detect and quantify levels of individual proteins in complex biological mixtures. Aptamers were each fluorescently labeled and immobilized on a glass substrate. Fluorescence polarization anisotropy was used for solid- and solution-phase measurements of target protein binding. We show that solid-phase aptamer-protein interactions recapitulate binding interactions seen in solution. Furthermore, we demonstrate specific detection and quantitation of cancer-associated proteins (inosine monophosphate dehydrogenase II, vascular endothelial factor, basic fibroblast growth factor) in the context of human serum and in cellular extracts. It is expected that this technology could speed diagnosis of cancer by enabling direct detection of the expression and modification of proteins closely correlated with disease.

Modeling of DNA hybridization kinetics for spatially resolved biochips

The marriage of microfluidics with detection technologies that rely on highly selective nucleic acid hybridization will provide improvements in bioanalytical methods for purposes such as detection of pathogens or mutations and drug screening. The capability to deliver samples in a controlled manner across a two-dimensional hybridization detection platform represents a substantial technical challenge in the development of quantitative and reusable biochips. General theoretical and numerical models of heterogeneous hybridization kinetics are required in order to design and optimize such biochips and to develop a quantitative method for online interpretation of experimental results. In this work we propose a general kinetic model of heterogeneous hybridization and develop a technique for estimating the kinetic coefficients for the case of well-spaced, noninteracting surface-bound probes. The experimentally verified model is then incorporated into the BLOCS (biolab-on-a-chip simulation) 3D microfluidics finite element code and used to model the dynamic hybridization on a biochip surface in the presence of a temperature gradient. These simulations demonstrate how such a device can be used to discriminate between fully complementary and single-base-pair mismatched hybridization using fluorescence detection by interpretation of the unique spatially resolved intensity pattern. It is also shown how the dynamic transport of the targets is likely to affect the rate and location of hybridization as well as that, although nonspecific hybridization is present, the change in the concentration of hybridized targets over the sensor platform is sufficiently high to determine if a fully complementary match is present. Practical design information such as the optimum transport speed, target concentration, and channel height is presented. The results presented here will aid in the interpretation of results obtained with such a temperature-gradient biochip.

Interactions of phospholipid bilayer with chitosan: effect of molecular weight and pH

Chitosan has demonstrated its potentials as a gene carrier and a membrane perturbant for subsequent drug delivery to cells. However, there is currently a lack of experimental correlation between the physiochemical properties of chitosan and the resulting degree of lipid bilayer destabilization. In this study, the effect of pH and chitosan molecular weight on the interaction between chitosan and dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayer was examined with cross-polarization microscopy, differential scanning calorimetry (DSC), and Fourier transform- (FT-) Raman spectroscopy. Cross-polarized images showed that the direct hydration of the DPPC/chitosan mixture led to the formation of larger DPPC multilamellar vesicles (MLV), and pure chitosan also induced fusions of individual MLV. Under the influence of chitosan, the calorimetric enthalpy of DPPC was reduced in a concentration-dependent manner, and a new phase appeared at 28 degrees C during sample cooling. Even the lowest chitosan mole fraction of 0.04% reduced the cooperative unit of the DPPC bilayer by more than 70%. In addition, the electrostatic effect between chitosan and DPPC tuned the degree of membrane bilayer perturbation. Reduction of pH increased the number of protonated amines on the chitosan backbone and caused further disruption on the membrane organization. Mixing DPPC with chitosan in an organic medium before hydration enhanced the hydrophobic interactions between the two molecules and greatly reduced the cooperative unit among individual lipids during the main phase transition. The increase of chitosan molecular weight also affected the cooperativity in the thermotropic transition of DPPC bilayer. FT-Raman spectroscopy provided additional evidence that chitosan directly perturbed the organizations of the hydrophobic inner core of the DPPC bilayer.

Interaction of liposome with immobilized chitosan during main phase transition

It has been recently demonstrated that chitosan in aqueous solution alters the phase behavior and structure of a phospholipid bilayer (Fang, N.; et al. Biomacromolecules 2001, 2, 1161-1168). Until now, the physical driving forces between chitosan and the phospholipid bilayer upon their initial encounter remains unknown. In this study, confocal reflectance interference contrast microscopy (C-RICM), phase contrast microscopy and bioadhesion modeling are concurrently applied to probe the interaction of phospholipid vesicle with immobilized chitosan at various temperatures, pH, and osmotic stress. First, the successful immobilization of chitosan on amino-silanized glass is indicated by the increases in both the degree of vesicle deformation and adhesion energy of vesicles adhering on chitosan modified substrate in comparison with those on amino-silanized glass. Second, the phase transition of a phospholipid bilayer does not modulate the adhesion strength at the chitosan-biomembrane interface at pH 7.4. With increase of the degree of protonation on the chitsoan backbone at pH 4, the adhesion energy is increased by 5-fold for vesicles of all sizes compared to that in pH 7.4. Furthermore, pH reduction amplifies the thermal-induced response of larger vesicles on the immobilized chitosan layer. Interestingly, a moderate increase of osmotic stress maximizes the degree of vesicle deformation and adhesion energy at 23 degrees C and dampens the effect of phase transition on vesicle adhesion. Overall, this study demonstrates the quantitation of chitosan-biomembrane interactions that will be critical for future applications of chitosan in biological systems.

Molecular interactions between DNA and an aminated glass substrate

With the development of DNA arrays, the immobilization of DNA strands onto solid substrates remains an essential research topic. DNA arrays have potential applications in DNA sequencing, mutation detection, and pathogen identification. DNA bound to solid substrates must still be accessible and retain the ability to hybridize with its complementary strands. One technology to produce these arrays involves linking DNA molecule probes to a silanized substrate in microspot patterns and exposing them to a solution of fluorescently labeled samples of DNA targets. The behavior of both the target and probe DNA and their interactions with each other at the substrate surface, particularly with respect to molecular interactions, are poorly understood at the present time. The objective of this work is to model simply the interface interactions between DNA and glass slides modified with an aminosilane (gamma-aminopropyltriethoxysilane, APTS). In aqueous solutions, DNA behaves as a polyacid over a wide range of pH. A glass substrate treated with APTS is positively or negatively charged, depending on the pH. A model of the surface charge of APTS-treated glass has been developed from results of wetting experiments performed at various pH. It has been demonstrated that the surface charge of APTS-treated glass is well described by a model of constant capacitance of the electrical double layer. A good correlation between experimental data on DNA retention at various pH's and the variation of the surface charge of the APTS-treated glass is obtained. This provides an indication of the role of ionic interactions in the adsorption of DNA molecules onto aminated glass slides.

Dynamics of single-protein molecules at a liquid/solid interface: implications in capillary electrophoresis and chromatography

The behavior of individual molecules of R-phycoerythrin (RPE) was monitored by fluorescence imaging at various pHs and ionic strengths within the evanescent-field layer (EFL) at a water/fused-silica interface. Above the isoelectric point (pI), the individual protein molecules moved between exposures with random motion. As the pH approached the pI of the protein, the RPE molecules were partially adsorbed onto the fused-silica surface. The residence time and the number of molecules within the EFL also increased near the pI. Below the pI, the protein molecules were completely and permanently adsorbed onto the surface. However, the observed number of distinct molecule spots was decreased somewhat because of aggregation. At a given buffer condition, plots of residence times and molecule numbers exhibit asymmetry nearly identical to the corresponding elution peaks of the proteins in capillary electrophoresis and capillary liquid chromatography. These results provide insights into the fundamental interactions for the adsorption/desorption of proteins at the liquid/solid interface.

Thermal induced modification of the contact mechanics of adhering liposomes on cationic substrate

The correlation between the mechanical property and the thermotropic transition of the phospholipid bilayer has been recently demonstrated (Chem. Phys. Lipids 110 (2001) 27). However, the role of thermal induced mechanical responses of phospholipid bilayer on the contact mechanics of liposome adhering on a cationic substrate has not been determined. In this study, confocal-reflectance interference contrast microscopy, phase contrast microscopy and contact mechanics modeling are applied to probe the adhesion mechanisms of liposomes in the presence of electrostatic interactions during the thermotropic transition of the lipid bilayer. When temperature increases from 23 to 49 degrees C at pH 7.4, the degree of liposome deformation (a/R) and adhesion energy of dipalmitoyl-sn-glycero-3-phosphocholine liposome increases by 10% and remains constant, respectively, on 3-amino-propyl-triethoxy-silane (APTES) modified substrate. The extents of increase in these two parameters are highly dependent on the physicochemical properties of the rigid substrate. At pH 4, the adhesion energies above and below the phase transition temperature (T(m)) are increased by one order of magnitude due to the formation of the free silanol groups on APTES substrate. In hypotonic condition, the degree of vesicle deformation remains constant and the adhesion energy reduces by 20% during sample heating. Under all conditions, the adhesion energy of the adhering liposome spans a few orders of magnitude against the increase of liposome size as the surface area to volume ratio is maximized in smallest vesicle.

Immobilization of oligonucleotides on poly(ethylene glycol) brush-coated Si surfaces

High-density poly(ethylene glycol) (PEG) molecules are grafted onto Si surfaces in a brush-like configuration. We demonstrate that this surface is an excellent substrate for oligonucleotide immobilization. p-Maleimidophenyl isocyanate is used as a heterobifunctional cross-linker to tether thiol-modified oligonucleotides to terminal OH groups on the PEG brush. This approach gives excellent immobilization specificity and low background. The immobilized oligonucleotides show high sensitivity for the detection of complementary targets.

Nucleic acid biotechnology

Driven by advances in the acquisition of genetic sequence information and the ability to manipulate small quantities of nucleic acid, a number of technologies are emerging that exploit nucleic acids for research, diagnostic, and therapeutic utility. In this review, we cover three technologies based on nucleic acids--DNA microarrays, antisense technology, and gene therapy--that are especially promising and may make a substantial impact in the laboratory and in the clinic during the coming years. For each of these areas, an overview of the current status and applications is provided, followed by a discussion of critical issues and challenges to be faced for further advancement of the technology; an emphasis is placed on quantitative and engineering aspects.

Real-time dynamics of single-DNA molecules undergoing adsorption and desorption at liquid-solid interfaces

The conformational dynamics and adsorption/desorption behavior of individual lambda-DNA molecules at liquid-solid interfaces were monitored by imaging within the evanescent field layer using total internal reflection fluorescence microscopy. At a fused-silica surface, molecular conformation and adsorption behavior were found to depend on both pH and buffer composition. A histogram of individual lambda-DNA adsorption durations measured by hydrodynamically flowing molecules along the interface exhibited asymmetry nearly identical to that of the corresponding elution peaks found in capillary liquid chromatography and capillary electrophoresis. The accessibility of the surface to the molecules, which is proportional to the capillary surface area-to-volume ratio, can be correlated with the capacity factor and the relative adsorption factor. At a C18 surface, the dynamics of individual DNA molecules changed with the addition of organic solvent as well as with pH. Hydrophobic interaction rather than electrostatic interaction was the major driving force for adsorption of individual DNA molecules.