Photolithographic Synthesis of High-Density DNA and RNA Arrays on Flexible, Transparent, and Easily Subdivided Plastic Substrates.

The photolithographic fabrication of high-density DNA and RNA arrays on flexible and transparent plastic substrates is reported. The substrates are thin sheets of poly(ethylene terephthalate) (PET) coated with cross-linked polymer multilayers that present hydroxyl groups suitable for conventional phosphoramidite-based nucleic acid synthesis. We demonstrate that by modifying array synthesis procedures to accommodate the physical and chemical properties of these materials, it is possible to synthesize plastic-backed oligonucleotide arrays with feature sizes as small as 14 µm × 14 µm and feature densities in excess of 125 000/cm(2), similar to specifications attainable using rigid substrates such as glass or glassy carbon. These plastic-backed arrays are tolerant to a wide range of hybridization temperatures, and improved synthetic procedures are described that enable the fabrication of arrays with sequences up to 50 nucleotides in length. These arrays hybridize with S/N ratios comparable to those fabricated on otherwise identical arrays prepared on glass or glassy carbon. This platform supports the enzymatic synthesis of RNA arrays and proof-of-concept experiments are presented showing that the arrays can be readily subdivided into smaller arrays (or "millichips") using common laboratory-scale laser cutting tools. These results expand the utility of oligonucleotide arrays fabricated on plastic substrates and open the door to new applications for these important bioanalytical tools.

DNA millichips as a low-cost platform for gene expression analysis.

Our goal was to create a DNA chip that is as easy, convenient, and inexpensive as an agarose gel. For a first-generation solution, we describe a low-cost, easy-to-use de novo synthesis oligonucleotide microarray technology that draws on the inherent flexibility of the maskless array synthesizer for in situ synthesis of thousands of photolithographically produced oligonucleotides covalently attached to a microscope slide. The method involves physically subdividing the slide into 1 × 1 mm millichips that are hybridized to fluorescent RNA or DNA of biological origin, in a microfuge tube at an ordinary laboratory benchtop, rather than in dedicated hybridization chambers. Fluorescence intensity is then measured with a standard microscope rather than sophisticated DNA chip scanners. For proof of principle, we measured changes in the transcriptome of Arabidopsis (Arabidopsis thaliana) plants induced by growth in the presence of three major environmental abiotic stresses (temperature, light, and water status), in all possible combinations. Validation by comparison with quantitative reverse transcription PCR showed a high correlation coefficient and analysis of variance indicated a high technical reproducibility. These experiments demonstrate that low-cost DNA millichips can be made and reliably used at the benchtop in a normal laboratory setting, without assistance of core facilities containing costly specialized instrumentation.

Mass spectrometric based analysis of whole eggs dissolved in formic acid.

We have developed a method for complete dissolution of whole eggs in formic acid that provides a new approach to analyzing egg biomolecules. As expected from prior work with extracted lipids, phosphatidylcholine represents the most abundant 31P NMR signal. A simplified methanol/chloroform partitioning method for separating the dissolved egg solution into metabolites, lipids and protein was performed and after ultra-high mass resolution and tandem MS fragmentation analyses several phosphatidylcholine molecules containing different fatty acid chain lengths as well as number and position of double bonds was detected. The MS based proteomic analysis further revealed 6 Gallus sequences annotated as 'uncharacterized' because they show no sequence homology with any other protein found in nature and thus, may represent proteins uniquely evolved to perform functions specific to chickens. Overall, this procedure is a rapid and facile means of characterizing in a high throughput and comprehensive manner, the molecular components of whole eggs.

Radical-Mediated Covalent Azidylation of Hydrophobic Microdomains in Water-Soluble Proteins.

Hydrophobic microdomains, also known as hydrophobic patches, are essential for many important biological functions of water-soluble proteins. These include ligand or substrate binding, protein-protein interactions, proper folding after translation, and aggregation during denaturation. Unlike transmembrane domains, which are easily recognized from stretches of contiguous hydrophobic sidechains in amino acids via primary protein sequence, these three-dimensional hydrophobic patches cannot be easily predicted. The lack of experimental strategies for directly determining their locations hinders further understanding of their structure and function. Here, we posit that the small triatomic anion N3- (azide) is attracted to these patches and, in the presence of an oxidant, forms a radical that covalently modifies C-H bonds of nearby amino acids. Using two model proteins (BSA and lysozyme) and a cell-free lysate from the model higher plant Arabidopsis thaliana, we find that radical-mediated covalent azidylation occurs within buried catalytic active sites and ligand binding sites and exhibits similar behavior to established hydrophobic probes. The results herein suggest a model in which the azido radical is acting as an "affinity reagent" for nonaqueous three-dimensional protein microenvironments and is consistent with both the nonlocalized electron density of the azide moiety and the known high reactivity of azido radicals widely used in organic chemistry syntheses. We propose that the azido radical is a facile means of identifying hydrophobic microenvironments in soluble proteins and, in addition, provides a simple new method for attaching chemical handles to proteins without the need for genetic manipulation or specialized reagents.

An Asymmetric, bifunctional catalytic approach to non-natural alpha-amino acid derivatives.

A catalytic, asymmetric process for the synthesis of 1,4-benzoxazinones from o-benzoquinone imides and ketene enolates is reported. Addition of Lewis acids (Zn(OTf)2, In(OTf)3, and in particular Sc(OTf)3) creates a bifunctional catalytic system that dramatically increases the reaction rate and the yield of these non-natural amino acid precursors while preserving the remarkable enantioselectivity inherent to the reaction. Cocatalyst Sc(OTf)3 increases the yield by up to 42% while producing products in >99% ee.

Scalable methodology for the catalytic, asymmetric alpha-bromination of acid chlorides.

The optimization of a practical, catalytic, asymmetric process for the alpha-bromination of acid chlorides to produce synthetically versatile, optically active alpha-bromoesters is reported. A range of products is produced in high enantioselectivity and moderate to good chemical yields with retention of both upon scale-up. The reactions herein are catalyzed by cinchona alkaloid derivatives, with the best performance achieved by the use of a proline cinchona alkaloid conjugate designed in a de novo fashion.

Catalytic, enantioselective [4 + 2]-cycloadditions of ketene enolates and o-quinones: efficient entry to chiral, alpha-oxygenated carboxylic acid derivatives.

We report catalytic, enantioselective [4 + 2]-cycloadditions of o-quinones with ketene enolates (derived from readily available acid chlorides) using cinchona alkaloid derivatives as catalysts to produce products in high enantiomeric excess (ee) and good to excellent yields. The thermodynamic driving force for these reactions is due in part to the restoration of aromaticity to the products. The resulting chiral, bicycloadducts can be synthetically manipulated in a variety of useful ways, for example to provide a flexible synthesis of alpha-oxygenated carboxylic acid derivatives.