Parallel production of oligonucleotide arrays using membranes and reagent jet printing

Public consortium efforts in toxicogenomics

Public consortia provide a forum for addressing questions requiring more resources than one organization alone could bring to bear and engaging many sectors of the scientific community. They are particular well suited for tackling some of the questions encountered in the field of toxicogenomics, where the number of studies and microarray analyses would be prohibitively expensive for a single organization to carry out. Five consortia that stand out in the field of toxicogenomics are the Institutional Life Sciences Institute (ILSI) Health and Environmental Sciences Institute (HESI) Committee on the Application of Genomics to Mechanism Based Risk Assessment, the Toxicogenomics Research Consortium, the MicroArray Quality Control (MAQC) Consortium, the InnoMed PredTox effort, and the Predictive Safety Testing Consortium. Collectively, these consortia efforts have addressed issues such as reproducibility of microarray results, standard practice for assays and analysis, relevance of microarray results to conventional end points, and robustness of statistical models on diverse data sets. Their results demonstrate the impact that the pooling of resources, experience, expertise, and insight found in consortia can have.

The dosage of small volumes for chromatographic quantifications using a drop-on-demand dispenser system

A commercially available piezo-driven drop-on-demand dispenser was tested for its suitability for the preparation of analytical calibration standards and in a standard addition approach prior to quantitative ultra performance liquid chromatography (UPLC) analysis of homoserines. The reproducibility of the drop-on-demand dosing system was tested and the verification of the droplet volume was performed by preparing a series of 1.0 mg/L caffeine standard solutions from a 1,000.0 mg/L stock solution and analysis of the concentrations obtained by UPLC. The reproducibility was better than 1% relative standard deviation from measurement to measurement and the highest was 1.6% from day to day. The results were compared with the conventional way of generating standard solutions (pipetting). A gravimetric method and a photography-based method for the determination of the average single droplet volume were compared and found to be in very good agreement. The system was employed for the quantification of N-decanoyl homoserine by standard addition in bacterial culture supernatants containing this analyte. The agreement with conventional quantification techniques was high. The paper shows the feasibility of the approach with advantages in low sample and solvent volume consumption and very good reproducibility and reliability combined with easy usage. Figure Ejected droplet, 60 mus after application of the pulse.

Nanoliter-scale reactor arrays for biochemical sensing

A general approach is described for array-based biochemical sensing that uses contact-free dispersal of compounds into addressable microfabricated reactors. The arrays are composed of 1 to 100 nL volume open reactors that have been microfabricated on quartz substrates using lithography. The open architecture of these reactors allows them to be addressed in parallel or individually with an ink-jet arrayer that is capable of distributing 0.004 to 1 nL volumes of reagents. A seven-step biochemical assay has been conducted on a small array of reactors to demonstrate how they can be integrated with an ink-jet arrayer and optical detector. This nanoreactor assay format appears to overcome several limitations that chip-based microarray technology currently imposes on protein assays: the arrays can be created in a manner that does not expose the biochemical reagents to osmotic stress, independent reactions can be conducted in individual reactors, and the conditions in all of the reactors (e.g., concentration and pH) can be rapidly scanned. We believe that these nanoreactor arrays will be useful for biochemical sensing that involves delicate proteins and protein assemblies.

[8] Printing Your Own Inkjet Microarrays

DNA arrays are now the tools of choice for high-throughput DNA/RNA analysis. While many technologies exist for mass-producing arrays, there are just a few ways to economically produce small batches of custom oligonucleotide arrays for prototyping experiments and specialized applications. Inkjet printing, adapted from the world of office electronics to the world of molecular biology, is one such method. With programmable oligonucleotide synthesizers, scientists can prototype DNA array assays quickly and inexpensively. A benchtop inkjet arrayer-nicknamed POSAM-can be built by most skilled molecular biology laboratories. Inkjet arrays can fulfill the changing needs of those studying the complex network of relationships in systems biology.

Electrochemically directed synthesis of oligonucleotides for DNA microarray fabrication

We demonstrate a new method for making oligonucleotide microarrays by synthesis in situ. The method uses conventional DNA synthesis chemistry with an electrochemical deblocking step. Acid is delivered to specific regions on a glass slide, thus allowing nucleotide addition only at chosen sites. The acid is produced by electrochemical oxidation controlled by an array of independent microelectrodes. Deblocking is complete in a few seconds, when competing side-product reactions are minimal. We demonstrate the successful synthesis of 17mers and discrimination of single base pair mismatched hybrids. Features generated in this study are 40 μm wide, with sharply defined edges. The synthetic technique may be applicable to fabrication of other molecular arrays.

POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer

DNA arrays are valuable tools in molecular biology laboratories. Their rapid acceptance was aided by the release of plans for a pin-spotting microarrayer by researchers at Stanford. Inkjet microarraying is a flexible, complementary technique that allows the synthesis of arrays of any oligonucleotide sequences de novo. We describe here an open-source inkjet arrayer capable of rapidly producing sets of unique 9,800-feature arrays.

A standard operating procedure for assessing liquid handler performance in high-throughput screening

The thrust of early drug discovery in recent years has been toward the configuration of homogeneous miniaturized assays. This has allowed organizations to contain costs in the face of exponential increases in the number of screening assays that need to be run to remain competitive. Miniaturization brings with it an increasing dependence on instrumentation, which over the past several years has seen the development of nanodispensing capability and sophisticated detection strategies. To maintain confidence in the data generated from miniaturized assays, it is critical to ensure that both compounds and reagents have been delivered as expected to the target wells. The authors have developed a standard operating procedure for liquid-handling quality control that has enabled them to evaluate performance on 2 levels. The first level provides for routine daily testing on existing instrumentation, and the second allows for more rigorous testing of new dispensing technologies. The procedure has shown itself to be useful in identifying both method programming and instrumentation performance shortcomings and has provided a means to harmonizing instrumentation usage by assay development and screening groups. The goal is that this type of procedure be used for facilitating the exchange of liquid handler performance data across the industry.

An electrochemical redox couple activitated by microelectrodes for confined chemical patterning of surfaces

Microelectrodes, printed as an array on the surface of a silicon chip, generate chemically active species in a solution of electrolyte held between the electrode array and a glass plate. The active species induce chemical change in molecules coupled to the surface of the glass plate, which is separated from the electrode array by a gap of several micrometers. This paper explores the nature and pattern of the induced chemical change. The patterning is discussed with respect to the electrolyte composition and the magnitude and duration of current applied to the microelectrodes. We show that under suitable conditions the active species is confined to micrometer-sized features and diffusion does not obscure the surface pattern produced.

Real-time measurements of DNA hybridization on microparticles with fluorescence resonance energy transfer

When capture oligonucleotides are tethered on planar surfaces, mass transport limitations influence the kinetics of solid-phase nucleic acid hybridizations. By diffusion theory, however, hybridization of oligonucleotides on microparticles should be reaction-rate limited. In an initial effort to understand the kinetics of microparticle hybridization reactions, we developed a fluorescence resonance energy transfer method for monitoring oligonucleotide hybridization on microparticles. Microparticles were coated with a fluoresceinated oligomer at surface densities of 20, 40, and 80% saturation, hybridized to a complementary oligonucleotide labeled with tetramethylrhodamine, and monitored over time for quenching of the fluorescein signal as hybridization occurred on the particle surface. Association rate constants were compared for microparticle-based hybridization and solution-phase hybridization. Rate constants for hybridizations on the particle surface were about an order of magnitude less than those for hybridization in solution, but decreasing the surface density of the capture oligonucleotide to 20% saturation improved particle hybridization rates. Although a bimolecular reaction model adequately described solution-phase hybridization kinetics, oligonucleotide hybridization on microparticles did not fit this model but exhibited biphasic reaction kinetics. Based on two different lines of reasoning, we argue that microparticle-based oligonucleotide hybridization was indeed reaction-rate limited in our system and not diffusion-rate limited.