Label-free detection of nucleic acid and protein microarrays by scanning Kelvin nanoprobe

Fabrication of PEDOT:PSS-based solution gated organic electrochemical transistor array for cancer cells detection

Organic electrochemical transistor (OECT) was applied in chemical and biological sensing. In this work, we developed a simple and repeatable method to fabricate OECT array, which had been successfully used to detect cancer cells. PEDPT:PSS conductive film between source and drain electrodes were patterned through photolithography, which can achieve uniform devices with same electrical characterization. When MCF-7 cancer cells are captured on the PEDOT:PSS surface via specifical antibody, the transfer characteristic of OECT shifts to higher gate electrode voltage due to the electrostatic interaction between cancer cells and device. The effective gate voltage shift can reach about 63 mV when the concentration of cancer cells increased to 5000. The shift of effective gate voltage is related to the cancer cell morphology, which is increased in the first 1 h and decreased when the capture time was larger than 1 h. The device of OECT array can increase the sample flux and make the detection result more accurate. It is expected that OECT array will have promising practical applications in single cancer cell detection in the future.

Tuning the Surface Molecular Charge of Organic Photoelectrochemical Transistors with Significantly Improved Signal Resolution: A General Strategy toward Sensitive Bioanalysis

Nature makes use of molecular charges to operate specific biological synthesis and reactions. Targeting advanced opto-bioelectronic sensors, organic photoelectrochemical transistors (OPECTs), taking advantage of the light fuel substituting an external gate potential, is now debuting and expected to serve as a universal platform for studying the rich light-biomatter interplay for new bioanalytics. Given the ubiquity of charged biomolecules in nature, molecular charge manipulation should underpin a generic route for innovative OPECT regulation and operation, which nevertheless has remained unachieved. Herein, this work manifests the biological tuning of surface charge toward the OPECT biosensor, which was exemplified by a light-sensitive CdS quantum dot (QD) gate electrode interfaced by a smart DNA superstructure with adenosine triphosphate (ATP) responsiveness. Highly negative-charged supramolecular DNA concatemers were self-assembled via sequential hybridization, and the ATP-triggered disassembly of the DNA concatemers would cause a tandem change of the effective gate voltage and transfer characteristics with significantly improved resolution. The present opto-bioelectronic device translates the events of charged molecules into amplified electrical signals and outlines a generic format for the future exploitation of rich biological tunability and light-biomatter interplay for innovative bioanalytics and beyond.

Ultrasensitive Label-Free DNA Detection Based on Solution-Gated Graphene Transistors Functionalized with Carbon Quantum Dots

Developing highly sensitive, reliable, cost-effective label-free DNA biosensors is challenging with traditional fluorescence, electrochemical, and other techniques. Most conventional methods require labeling fluorescence, enzymes, or other complex modification. Herein, we fabricate carbon quantum dot (CQD)-functionalized solution-gated graphene transistors for highly sensitive label-free DNA detection. The CQDs are immobilized on the surface of the gate electrode through mercaptoacetic acid with the thiol group. A single-stranded DNA (ssDNA) probe is immobilized on CQDs by strong π-π interactions. The ssDNA probe can hybridize with the ssDNA target and form double-stranded DNA, which led to a shift of Dirac voltage and the channel current response. The limit of detection can reach 1 aM which is 2-5 orders of magnitude lower than those of other methods reported previously. The sensor also exhibits a good linear range from 1 aM to 0.1 nM and has good specificity. It can effectively distinguish one-base mismatched target DNA. The response time is about 326 s for the 1 aM target DNA molecules. This work provides good perspectives on the applications in biosensors.

A sensitive platform for DNA detection based on organic electrochemical transistor and nucleic acid self-assembly signal amplification

Highly sensitive detection of DNA is of great importance for the detection of genetic damage and errors for the diagnosis of many diseases. Traditional highly sensitive organic electrochemical transistor (OECT)-based methods mainly rely on good conductivity materials, which may be limited by complex synthesis and modification steps. In this work, DNA biosensor based on OECT and hybridization chain reaction (HCR) signal amplification was demonstrated for the first time. Au nanoparticles were electrochemically deposited on the Au gate electrode to increase the surface area. Then, the HCR products, long negatively charged double-stranded DNA, were connected to the target by hybridization, which can increase the effective gate voltage offset of OECT. This sensor exhibited high sensitivity and even 0.1 pM target DNA could be directly detected with a significant voltage shift. In addition, it could discriminate target DNA from the mismatched DNA with good selectivity. This proposed method based on HCR in DNA detection exhibited an efficient amplification performance on OECT, which provided new opportunities for highly sensitive and selective detection of DNA.

A new method has been developed for DNA detection by integrating hybridization chain reaction signal amplification with organic electrochemical transistor device for the first time.

Ultrafast, sensitive, and portable detection of COVID-19 IgG using flexible organic electrochemical transistors

The outbreak of COVID-19 and its continued spread have seriously threatened public health. Antibody testing is essential for infection diagnosis, seroepidemiological analysis, and vaccine evaluation. However, convenient, fast, and accurate antibody detection remains a challenge in this protracted battle. Here, we report an ultrafast, low-cost, label-free, and portable SARS-CoV-2 immunoglobulin G (IgG) detection platform based on organic electrochemical transistors (OECTs), which can be remotely controlled by a mobile phone. To enable faster detection, voltage pulses are applied on the gate electrode of the OECT to accelerate binding between the antibody and antigen. By optimizing ion concentrations and pH values of test solutions, we realize specific detection of SARS-CoV-2 IgG in several minutes with a detectable region from 10 fM to 100 nM, which encompasses the range of serum SARS-CoV-2 IgG levels in humans. These portable sensors show promise for use in diagnosis and prognosis of COVID-19.

Label-Free Split Aptamer Sensor for Femtomolar Detection of Dopamine by Means of Flexible Organic Electrochemical Transistors

The detection of chemical messenger molecules, such as neurotransmitters in nervous systems, demands high sensitivity to measure small variations, selectivity to eliminate interferences from analogues, and compliant devices to be minimally invasive to soft tissue. Here, an organic electrochemical transistor (OECT) embedded in a flexible polyimide substrate is utilized as transducer to realize a highly sensitive dopamine aptasensor. A split aptamer is tethered to a gold gate electrode and the analyte binding can be detected optionally either via an amperometric or a potentiometric transducer principle. The amperometric sensor can detect dopamine with a limit of detection of 1 μM, while the novel flexible OECT-based biosensor exhibits an ultralow detection limit down to the concentration of 0.5 fM, which is lower than all previously reported electrochemical sensors for dopamine detection. The low detection limit can be attributed to the intrinsic amplification properties of OECTs. Furthermore, a significant response to dopamine inputs among interfering analogues hallmarks the selective detection capabilities of this sensor. The high sensitivity and selectivity, as well as the flexible properties of the OECT-based aptasensor, are promising features for their integration in neuronal probes for the in vitro or in vivo detection of neurochemical signals.

Amplification of aptamer sensor signals by four orders of magnitude via interdigitated organic electrochemical transistors

Electrochemical aptamer receptor/transducer systems are key elements of emerging E-AB sensors (aptasensor) used for the detection of various kinds of targets. However, the performance of these amperometric sensors is often limited by the low density of receptors attached to the sensor surface and high background signals. In the present work, interdigitated organic electrochemical transistors (iOECT) were used as a transducer to enhance the sensitivity and dynamic detection range of aptasensors. Therefore, the electrode of an amperometric sensor was utilized as gate electrode to operate the iOECT. This device was used to detect the low weight target molecule adenosine triphosphate (ATP), a common biomarker, which plays an important role for cardiovascular, neurodegenerative, and immune deficiency diseases. The novel aptasensor can selectively detect ATP with ultrahigh sensitivity down to the concentration of 10 pM, which is four orders of magnitude lower than the detection limit of the same aptasensor using an amperometric transducer principle (limit-of-detection of 106 nM) and most other previously reported electrochemical sensors. Furthermore, sensor regeneration was demonstrated, which facilitates reusability of OECT aptasensors. The small device size in combination with high transconductances paves the way for the development of highly sensitive integrated micro-biosensors for point-of-care applications.

Enhanced electrostatic force microscopy reveals higher-order DNA looping mediated by the telomeric protein TRF2

Shelterin protein TRF2 modulates telomere structures by promoting dsDNA compaction and T-loop formation. Advancement of our understanding of the mechanism underlying TRF2-mediated DNA compaction requires additional information regarding DNA paths in TRF2-DNA complexes. To uncover the location of DNA inside protein-DNA complexes, we recently developed the Dual-Resonance-frequency-Enhanced Electrostatic force Microscopy (DREEM) imaging technique. DREEM imaging shows that in contrast to chromatin with DNA wrapping around histones, large TRF2-DNA complexes (with volumes larger than TRF2 tetramers) compact DNA inside TRF2 with portions of folded DNA appearing at the edge of these complexes. Supporting coarse-grained molecular dynamics simulations uncover the structural requirement and sequential steps during TRF2-mediated DNA compaction and result in folded DNA structures with protruding DNA loops as seen in DREEM imaging. Revealing DNA paths in TRF2 complexes provides new mechanistic insights into structure-function relationships underlying telomere maintenance pathways.

Label and Label-Free Detection Techniques for Protein Microarrays

Protein microarray technology has gone through numerous innovative developments in recent decades. In this review, we focus on the development of protein detection methods embedded in the technology. Early microarrays utilized useful chromophores and versatile biochemical techniques dominated by high-throughput illumination. Recently, the realization of label-free techniques has been greatly advanced by the combination of knowledge in material sciences, computational design and nanofabrication. These rapidly advancing techniques aim to provide data without the intervention of label molecules. Here, we present a brief overview of this remarkable innovation from the perspectives of label and label-free techniques in transducing nano-biological events.

Label-free DNA sensing platform with low-voltage electrolyte-gated transistors

We report a method to measure DNA hybridization potentiometrically in a manner conducive to portable or hand-held biosensors. An electrolyte-gated transistor (EGT) based on poly(3-hexylthiophene) (P3HT) and an ion-gel serves as a transducer for surface hybridization of DNA. The key aspect of the design is the use of a floating-gate electrode functionalized with ssDNA whose potential is determined by both capacitive coupling with a primary, addressable gate electrode and the presence of adsorbed molecules. When DNA is hybridized at the floating gate, it offsets the primary gate voltage felt by the P3HT semiconductor; the offset is directly measurable and quantitatively related to the number density of dsDNA molecules. The presented sensing strategy can be readily adapted to other biomolecules of interest and integrated into a microfluidic system for field applications of biosensors.

Label-free detection techniques for protein microarrays: prospects, merits and challenges

Protein microarrays, on which thousands of discrete proteins are printed, provide a valuable platform for functional analysis of the proteome. They have been widely used for biomarker discovery and to study protein–protein interactions. The accomplishments of DNA microarray technology, which had enabled massive parallel studies of gene expression, sparked great interest for the development of protein microarrays to achieve similar success at the protein level. Protein microarray detection techniques are often classified as being label‐based and label‐free. Most of the microarray applications have employed labelled detection such as fluorescent, chemiluminescent and radioactive labelling. These labelling strategies have synthetic challenges, multiple label issues and may exhibit interference with the binding site. Therefore, development of sensitive, reliable, high‐throughput, label‐free detection techniques are now attracting significant attention. Label‐free detection techniques monitor biomolecular interactions and simplify the bioassays by eliminating the need for secondary reactants. Moreover, they provide quantitative information for the binding kinetics. In this article, we will review several label‐free techniques, which offer promising applications for the protein microarrays, and discuss their prospects, merits and challenges.

Characterization of the porous nature of a phthalocyanine derivative with axial ligation designed to prevent aggregation

Judiciously designed phthalocyanines (Pcs), such as silicon-Pc bis(3,5-diphenyl)benzoate (1c), with axial substituents which prevent aggregation, can self-assemble to form ordered nanoporous films on electrode surfaces. In this paper, complementary techniques such as Scanning Kelvin Nanoprobe (SKN) microscopy, Atom Force Microscopy (AFM) and electrochemical measurements are used to demonstrate that films formed by silicon-Pc bis(3,5-diphenyl)benzoate allow size- and charge- selective transport of probe molecules through well-defined intermolecular cavities. In contrast, the analogs silicon-Pc bis(4-tert-butylbenzoate) (1a) and silicon-Pc bis(3-thienyl)acetate (1b) have different film morphologies when solvent-cast in the same manner and block the electrode surface. The role of the different axial substituents in orienting the molecules on the substrate is discussed.

The new future of scanning probe microscopy: Combining atomic force microscopy with other surface-sensitive techniques, optical microscopy and fluorescence techniques

Atomic force microscopy (AFM) is in its thirties and has become an invaluable tool for studying the micro- and nanoworlds. As a stand-alone, high-resolution imaging technique and force transducer, it defies most other surface instrumentation in ease of use, sensitivity and versatility. Still, the technique has limitations to overcome. A promising way is to integrate the atomic force microscope into hybrid devices, a combination of two or three complementary techniques in one instrument. In this way, a comprehensive description of molecular processes is at hand; morphological, (electro)chemical, mechanical and kinetic information are simultaneously obtained in one experiment. Hereby we review the recent efforts towards such development, describing the aim and the applications resulting from the combination of AFM with spectroscopic, optical, mechanical or electrochemical techniques. Interesting possibilities include using AFM to bring optical microscopies beyond the diffraction limit and also bestowing spectroscopic capabilities on the atomic force microscope.

Dispersions, novel nanomaterial sensors and nanoconjugates based on carbon nanotubes

Nanomaterials are structures with dimensions characteristically much below 100 nm. The unique physical properties (e.g., conductivity, reactivity) have placed these nanomaterials in the forefront of emerging technologies. Significant enhancement of optical, mechanical, electrical, structural, and magnetic properties are commonly found through the use of novel nanomaterials. One of the most exciting classes of nanomaterials is represented by the carbon nanotubes. Carbon nanotubes, including single-wall carbon nanotubes, multi-wall carbon nanotubes, and concentric tubes have been shown to possess superior electronic, thermal, and mechanical properties to be attractive for a wide range of potential applications They sometimes bunch to form "ropes" and show great potential for use as highly sensitive electronic (bio)sensors due to the very small diameter, directly comparable to the size of single analyte molecules and that every single carbon atom is in direct contact with the environment, allowing optimal interaction with nearby molecules. Composite materials based on integration of carbon nanotubes and some other materials to possess properties of the individual components with a synergistic effect have gained growing interest. Materials for such purposes include conducting polymers, redox mediators and metal nanoparticles. These tubes provide the necessary building blocks for electronic circuits and afford new opportunities for chip miniaturization, which can dramatically improve the scaling prospects for the semiconductor technologies and the fabrication of devices, including field-effect transistors and sensors. Carbon nanotubes are one of the ideal materials for the preparation of nanoelectronic devices and nanosensors due to the unique electrical properties, outstanding electrocatalytic properties, high chemical stability and larger specific surface area of nanotubes. Carbon nanotubes are attractive material for supercapacitors due to their unique one-dimensional mesoporous structure, high specific surface area, low resistivity and good chemical stability. Nanoscaled composite materials based on carbon nanotubes have been broadly used due to their high chemical inertness, non-swelling effect, high purity and rigidity. The integration of carbon nanotubes with organics, biomaterials and metal nanoparticles has led to the development of new hybrid materials and sensors. Hybrid nanoscale materials are well established in various processes such as organic and inorganic compounds, nucleic acid detachment, protein separation, and immobilization of enzymes. Those nanostructures can be used as the building blocks for electronics and nanodevices because uniform organic and metal coatings with the small and monodisperse domain sizes are crucial to optimize nanoparticle conductivity and to detect changes in conductivity and absorption induced by analyte adsorption on these surfaces. The highly ordered assembly of zero-dimensional and one-dimensional nanoparticles is not only necessary for making functional devices, but also presents an opportunity to develop novel collective properties.

Detection of charge distributions in insulator surfaces

Charge distribution in insulators has received considerable attention but still poses great scientific challenges, largely due to a current lack of firm knowledge about the nature and speciation of charges. Recent studies using analytical microscopies have shown that insulators contain domains with excess fixed ions forming various kinds of potential distribution patterns, which are also imaged by potential mapping using scanning electric probe microscopy. Results from the authors' laboratory show that solid insulators are seldom electroneutral, as opposed to a widespread current assumption. Excess charges can derive from a host of charging mechanisms: excess local ion concentration, radiochemical and tribochemical reactions added to the partition of hydroxonium and hydronium ions derived from atmospheric water. The last factor has been largely overlooked in the literature, but recent experimental evidence suggests that it plays a decisive role in insulator charging. Progress along this line is expected to help solve problems related to unwanted electrostatic discharges, while creating new possibilities for energy storage and handling as well as new electrostatic devices.

Label-free detection of the aptamer binding on protein patterns using Kelvin probe force microscopy (KPFM)

Anti-lysozyme aptamers are found to preferentially bind to the edge of a tightly packed lysozyme pattern. Such edge-binding is due to the better accessibility and flexibility of the edge lysozyme molecules. Kelvin probe force microscopy (KPFM) was used to study the aptamer-lysozyme binding. Our results show that KPFM is capable of detecting the aptamer-protein binding down to the 30 nm scale. The surface potential of the aptamer-lysozyme complex is approximately 12 mV lower than that of the lysozyme. The surface potential images of the aptamer-bound lysozyme patterns have the characteristic shoulder steps around the pattern edge, which is much wider than that of a clean lysozyme pattern. These results demonstrate the potentials of KPFM as a label-free method for the detection of protein-DNA interactions.

Imparting chemical specificity to nanometer-spaced electrodes

In this paper we are demonstrating an electrochemically driven self-assembling approach to achieve the space-resolved chemical functionalization of nanoelectrodes. After forming a self-assembled monolayer of electroactive quinones on a pair of nano-spaced (<100 nm) electrodes, we enabled the binding of ssDNA exclusively on a single nanoelectrode by controlling the oxidation state at each modified electrode. This procedure attained the chemical differentiation of otherwise identical nanoelectrodes as the immobilized ssDNA retained its hybridization ability. Furthermore, we established that Kelvin probe force microscopy is a suitable space-resolved analytical technique for detecting this chemical functionalization at the nanoscale. The reported approach, enabling the space-selective patterning of (bio)molecules on nanoelectrode surfaces, can find application in complex nanosensor structure and molecular electronics implementations.

Large-scale assembly of carbon nanotube-based flexible circuits for DNA sensors

We present a simple but efficient method to prepare carbon nanotube (CNT)-based flexible devices embedded in polymer substrates. In this strategy, a methyl-terminated self-assembled monolayer is first coated on a solid substrate as a release layer, and CNT-network devices fabricated on it are directly transferred into a poly(dimethylsiloxane) (PDMS) mold, resulting in flexible CNT-network devices embedded in PDMS. The embedded circuits exhibit stable operation even after significant bending. We also propose Raman spectroscopy as a powerful tool to remotely characterize the CNT-network device structures covered by a polymer layer. As a proof of concept, we demonstrate DNA sensors utilizing the fabricated CNT-network devices.

High-throughput nanohole array based system to monitor multiple binding events in real time

We have developed an integrated label-free, real-time sensing system that is able to monitor multiple biomolecular binding events based on the changes in the intensity of extraordinary optical transmission (EOT) through nanohole arrays. The core of the system is a sensing chip containing multiple nanohole arrays embedded within an optically thick gold film, where each array functions as an independent sensor. Each array is a square array containing 10 x 10 nanoholes (150 nm in diameter), occupying a total area of 3.3 mum x 3.3 mum. The integrated system includes a laser light source, a temperature-regulated flow cell encasing the sensing chip, motorized optics, and a charge-coupled detector (CCD) camera. For demonstration purposes, sensing chips containing 25 nanohole arrays were studied for their use in multiplexed detection, although the sensing chip could be easily populated to contain up to 20 164 nanohole arrays within its 0.64 cm2 sensing area. Using this system, we successfully recorded 25 separate binding curves between glutathione S-transferase (GST) and anti-GST simultaneously in real time with good sensitivity. The system responds to binding events in a concentration-dependent manner, showing a sharp linear response to anti-GST at concentrations ranging from 13 to 290 nM. The EOT intensity-based approach also enables the system to monitor multiple bindings simultaneously and continuously, offering a temporal resolution on milliseconds scale that is decided only by the camera speed and exposure time. The small footprint of the sensing arrays combined with the EOT intensity-based approach enables the system to resolve binding events that occurred on nanohole sensing arrays spaced 96 mum apart, with a reasonable prediction of resolving binding events spaced 56 mum apart. This work represents a new direction that implements nanohole arrays and EOT intensity to meet high-throughput, spatial and temporal resolution, and sensitivity requirements in drug discovery and proteomics studies.

Label-free and high-resolution protein/DNA nanoarray analysis using Kelvin probe force microscopy

Using the scanning probe technique known as Kelvin probe force microscopy it is possible to successfully devise a sensor for charged biomolecules. The Kelvin probe force microscope is a tool for measuring local variations in surface potential across a substrate of interest. Because many biological molecules have a native state that includes the presence of charge centres (such as the negatively charged backbone of DNA), the formation of highly specific complexes between biomolecules will often be accompanied by local changes in charge density. By spatially resolving this variation in surface potential it is possible to measure the presence of a specific bound target biomolecule on a surface without the aid of special chemistries or any form of labelling. The Kelvin probe force microscope presented here is based on an atomic force microscopy nanoprobe offering high resolution (<10 nm), sensitivity (<50 nM) and speed (>1,100 microm s(-1)), and the ability to resolve as few as three nucleotide mismatches.

Unravelling microbial communities with DNA-microarrays: challenges and future directions

High-throughput technologies are urgently needed for monitoring the formidable biodiversity and functional capabilities of microorganisms in the environment. Ten years ago, DNA microarrays, miniaturized platforms for highly parallel hybridization reactions, found their way into environmental microbiology and raised great expectations among researchers in the field. In this article, we briefly summarize the state-of-the-art of microarray approaches in microbial ecology research and discuss in more detail crucial problems and promising solutions. Finally, we outline scenarios for an innovative combination of microarrays with other molecular tools for structure-function analysis of complex microbial communities.

Antibody microarrays: current status and key technological advances

Antibody-based microarrays are among the novel classes of rapidly evolving proteomic technologies that holds great promise in biomedicine. Miniaturized microarrays (< 1 cm2) can be printed with thousands of individual antibodies carrying the desired specificities, and with biological sample (e.g., an entire proteome) added, virtually any specifically bound analytes can be detected. While consuming only minute amounts (< microL scale) of reagents, ultra- sensitive assays (zeptomol range) can readily be performed in a highly multiplexed manner. The microarray patterns generated can then be transformed into proteomic maps, or detailed molecular fingerprints, revealing the composition of the proteome. Thus, protein expression profiling and global proteome analysis using this tool will offer new opportunities for drug target and biomarker discovery, disease diagnostics, and insights into disease biology. Adopting the antibody microarray technology platform, several biomedical applications, ranging from focused assays to proteome-scale analysis will be rapidly emerging in the coming years. This review will discuss the current status of the antibody microarray technology focusing on recent technological advances and key issues in the process of evolving the methodology into a high-performing proteomic research tool.

DNA-duplexes containing abasic sites: correlation between thermostability and acoustic wave properties

Aldehydic apurinic or apyrimidinic sites that lack a nucleobase moiety are one of the most common forms of toxic lesions in DNA. In the present study, a close structural analog of such a site, the 2-(hydroxymethyl) tetrahydrofuranyl residue, was synthesized in order to act as a model for damaged nucleic acid probes. Prepared oligodeoxyribonucleotides containing one, two or three abasic sites were hybridized to complementary sequences immobilized on a gold surface using the neutravidin-biotin interaction for study by thickness shear mode acoustic wave detector. Measurement of the complex electrical impedance of an AT-cut quartz device with immobilized biotinylated nucleotide allowed the detection of changes of series resonance frequency, Deltafs, and motional resistance, Rm, associated with duplex formation. The changes as detected by the acoustic wave method correlated well with the thermostability of DNA duplexes in solution. With respect to the latter, UV-monitored melting curves indicate that both the number of sites and their localization in the double-stranded structure influence the amount by which a 19 b.p. duplex is destabilized. The presence of 3 abasic sites completely destabilized the DNA duplex.

Carbon nanotube DNA sensor and sensing mechanism

We report the fabrication of single-walled carbon nanotube (SWNT) DNA sensors and the sensing mechanism. The simple and generic protocol for label-free detection of DNA hybridization is demonstrated with random sequence 15mer and 30mer oligonucleotides. DNA hybridization on gold electrodes, instead of on SWNT sidewalls, is mainly responsible for the acute electrical conductance change due to the modulation of energy level alignment between SWNT and gold contact. This work provides concrete experimental evidence on the effect of SWNT-DNA binding on DNA functionality, which will help to pave the way for future designing of SWNT biocomplexes for applications in biotechnology in general and also DNA-assisted nanotube manipulation techniques.

AFM images of short oligonucleotides on a surface of supported lipid films

Atomic force microscopy (AFM) was used to study the topography of lipid films on a gold support with immobilized 19 mer single stranded DNA (ssDNA) chemically modified by oleylamine and after hybridization with complementary DNA. The topography of various surfaces was analyzed, including alkanethiol layer chemisorbed on a gold support, lipid films formed on alkanethiol layer without and with immobilized single or double stranded DNA (dsDNA). The value of root means square roughness (RMS) for each surface was determined. RMS value for sBLM with immobilized ssDNA was 2.98 nm, while slightly higher value of 3.37 nm was typical for dsDNA. The analysis of AFM images revealed that both ssDNA and dsDNA form clusters. The clusters formed by ssDNA are not uniform, but that formed by dsDNA are almost of circular shape with diameter of 13.6+/-0.5 nm. Formation of the clusters could be consequence of lower hydration of lipids and DNA at an air. The water deficit and hence increased ion concentration probably facilitate the attraction between oligonucleotides.

Microarrays meet the Voltaire challenge: Drug discovery on a chip?

The co-emergence of microarray technologies with systems oriented approaches to discovery is testament to the technological and conceptual advancements of recent years. By providing a platform for massively parallelized reductionism, microarrays are enabling us to examine the functional features of diverse classes of bio-system components in a contextually meaningful manner. Yet, to provide economic impact, future development of these technologies demands intimate alignment with the goal of producing safer and more efficacious drugs.:

Emerging tools for real-time label-free detection of interactions on functional protein microarrays

The availability of extensive genomic information and content has spawned an era of high-throughput screening that is generating large sets of functional genomic data. In particular, the need to understand the biochemical wiring within a cell has introduced novel approaches to map the intricate networks of biological interactions arising from the interactions of proteins. The current technologies for assaying protein interactions--yeast two-hybrid and immunoprecipitation with mass spectrometric detection--have met with considerable success. However, the parallel use of these approaches has identified only a small fraction of physiologically relevant interactions among proteins, neglecting all nonprotein interactions, such as with metabolites, lipids, DNA and small molecules. This highlights the need for further development of proteome scale technologies that enable the study of protein function. Here we discuss recent advances in high-throughput technologies for displaying proteins on functional protein microarrays and the real-time label-free detection of interactions using probes of the local index of refraction, carbon nanotubes and nanowires, or microelectromechanical systems cantilevers. The combination of these technologies will facilitate the large-scale study of protein interactions with proteins as well as with other biomolecules.