In vitro combinatory effects of the Alternaria mycotoxins alternariol and altertoxin II and potentially involved miRNAs.

Alternariol (AOH) and altertoxin II (ATX II) are mycotoxins formed by Alternaria spp. Since they are expected to co-occur in Alternaria-infested food and feed, we addressed the question of combinatory effects. In addition, potentially involved regulatory microRNAs were surveyed in an exploratory approach.

Express photolithographic DNA microarray synthesis with optimized chemistry and high-efficiency photolabile groups.

Background: DNA microarrays are a core element of modern genomics research and medical diagnostics, allowing the simple and simultaneous determination of the relative abundances of hundreds of thousands to millions of genomic DNA or RNA sequences in a sample. Photolithographic in situ synthesis, using light projection from a digitally-controlled array of micromirrors, has been successful at both commercial and laboratory scales. The advantages of this synthesis method are its ability to reliably produce high-quality custom microarrays with a very high spatial density of DNA features using a compact device with few moving parts.

Sequence-Dependent Fluorescence of Cy3- and Cy5-Labeled Double-Stranded DNA.

The fluorescent intensity of Cy3 and Cy5 dyes is strongly dependent on the nucleobase sequence of the labeled oligonucleotides. Sequence-dependent fluorescence may significantly influence the data obtained from many common experimental methods based on fluorescence detection of nucleic acids, such as sequencing, PCR, FRET, and FISH. To quantify sequence dependent fluorescence, we have measured the fluorescence intensity of Cy3 and Cy5 bound to the 5' end of all 1024 possible double-stranded DNA 5mers.

Base-cleavable microarrays for the characterization of DNA and RNA oligonucleotides synthesized in situ by photolithography.

Assessing synthesis efficiency, errors, failed deprotections, and chemical and enzymatic degradation of oligonucleotides on microarrays is essential for improving existing in situ synthesis methods, and for the development of new chemistries. We describe the use of LC-MS to analyse DNA and RNA oligonucleotides deprotected and cleaved under basic conditions from microarrays fabricated using light-directed in situ chemistry. The data yield essential information on array quality and sequence identity.

Simultaneous light-directed synthesis of mirror-image microarrays in a photochemical reaction cell with flare suppression.

The use of photolabile protecting groups is a versatile and well-established means of synthesizing high complexity microarrays of biopolymers, such as nucleic acids and peptides, for high-throughput analysis. The synthesis takes place in a photochemical reaction cell which positions the microarray substrate at the focus of the optical system delivering the light and which can be connected to a fluidics system which delivers appropriate reagents to the surface in synchrony with the light exposure. Here we describe a novel photochemical reaction cell which allows for the simultaneous synthesis of microarrays on two substrates.