Oligonucleotide microarrays, also called "DNA chips," are currently made by a light-directed chemistry that requires a large number of photolithographic masks for each chip. Here we describe a maskless array synthesizer (MAS) that replaces the chrome masks with virtual masks generated on a computer, which are relayed to a digital micromirror array. A 1:1 reflective imaging system forms an ultraviolet image of the virtual mask on the active surface of the glass substrate, which is mounted in a flow cell reaction chamber connected to a DNA synthesizer. Programmed chemical coupling cycles follow light exposure, and these steps are repeated with different virtual masks to grow desired oligonucleotides in a selected pattern. This instrument has been used to synthesize oligonucleotide microarrays containing more than 76,000 features measuring 16 microm 2. The oligonucleotides were synthesized at high repetitive yield and, after hybridization, could readily discriminate single-base pair mismatches. The MAS is adaptable to the fabrication of DNA chips containing probes for thousands of genes, as well as any other solid-phase combinatorial chemistry to be performed in high-density microarrays.

We demonstrate 0.8-dB/cm transmission loss for a single-mode, strip Si/SiO(2) waveguide with submicrometer cross-sectional dimensions. We compare the conventional waveguide-fabrication method with two smoothing technologies that we have developed, oxidation smoothing and anisotropic etching. We observe significant reduction of sidewall roughness with our smoothing technologies, which directly results in reduced scattering losses. The rapid increase in the scattering losses as the waveguide dimension is miniaturized, as seen in conventionally fabricated waveguides, is effectively suppressed in the waveguides made with our smoothing technologies. In the oxidation smoothing case, the loss is reduced from 32 dB/cm for the conventional fabrication method to 0.8 dB/cm for the single-mode waveguide width of 0.5 microm . This is to our knowledge the smallest reported loss for a high-index-difference system such as a Si/SiO(2) strip waveguide.

Microarrays containing 195,000 in situ synthesized oligonucleotide features have been created using a benchtop, maskless photolithographic instrument. This instrument, the Maskless Array Synthesizer (MAS), uses a digital light processor (DLP) developed by Texas Instruments. The DLP creates the patterns of UV light used in the light-directed synthesis of oligonucleotides. This digital mask eliminates the need for expensive and time-consuming chromium masks. In this report, we describe experiments in which we tested this maskless technology for DNA synthesis on glass surfaces. Parameters examined included deprotection rates, repetitive yields, and oligonucleotide length. Custom gene expression arrays were manufactured and hybridized toDrosophila melanogaster and mouse samples. Quantitative PCR was used to validate the gene expression data from the mouse arrays.[The sequence data from this study have been submitted to GEO under accession nos. GPL208, GSM2409, GSM2410, GSM2411, GSM2412, GSM2413, GSM2414, GSE81, GSE82.]

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Self-assembled films of octadecyltrichlorosilane were patterned with regions of different chemical functionality using extreme ultraviolet interferometric lithography. Unexposed regions of the imaging layers remain terminated in methyl groups, and exposed regions are modified so as to be terminated with polar, oxygen-containing terminal groups. Thin films of symmetric poly(styrene-b-methyl methacrylate) were deposited on the substrates and annealed. Unexposed and exposed regions are preferentially wet by the polystyrene block and poly(methyl methacrylate) block of the copolymer, respectively. The dimensions of the grating patterns on the substrate had periods (L s) from 1400 to ∼60 nm. If L s ≫ L o (L o = bulk lamellar period of the block copolymer), then the surface pattern was replicated in the topography of the polymer film with a maximum difference in film thickness of 1/2 L o on adjacent regions. The topographic pattern of the polymer film was a result of lamellae oriented parallel to the substrate with symmetric wetting on unexposed regions (thickness = nL o) and with asymmetric wetting on exposed regions (thickness = (n + 1/2)L o). As the dimension of L s approached L o, the replication of the surface pattern in the topography of the film continued to be observed, but with decreasing difference in thickness over adjacent exposed and unexposed regions. For a surface pattern with L s ≈ L o, the lamellae oriented perpendicular to the substrate and were macroscopically aligned with the surface pattern.

Evaluating the specificity spectra of DNA binding molecules is a nontrivial challenge that hinders the ability to decipher gene regulatory networks or engineer molecules that act on genomes.Here we compare the DNA sequence specificities for different classes of proteins and engineered DNA binding molecules across the entire sequence space. These high-content data are visualized and interpreted using an interactive "specificity landscape" which simultaneously displays the affinity and specificity of a million-plus DNA sequences. Contrary to expectation, specificity landscapes reveal that synthetic DNA ligands match, and often surpass, the specificities of eukaryotic DNA binding proteins. The landscapes also identify differential specificity constraints imposed by diverse structural folds of natural and synthetic DNA binders. Importantly, the sequence context of a binding site significantly influences binding energetics, and utilizing the full contextual information permits greater accuracy in annotating regulatory elements within a given genome. Assigning such context-dependent binding values to every DNA sequence across the genome yields predictive genome-wide binding landscapes (genomescapes). A genomescape of a synthetic DNA binding molecule provided insight into its differential regulatory activity in cultured cells. The approach we describe will accelerate the creation of precision-tailored DNA therapeutics and uncover principles that govern sequence-specificity of DNA binding molecules.

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Focusing of 8 keV x rays to a spot size of 150 and 90 nm full width at half maximum have been demonstrated at the first-and third-order foci, respectively, of a phase zone plate ͑PZP͒. The PZP has a numerical aperture of 1.5 mrad and focusing efficiency of 13% for 8 keV x rays. A flux density gain of 121 000 was obtained at the first-order focus. In this article, the fabrication of the PZP and its experimental characterization are presented and some special applications are discussed.