Simultaneous Light-Directed Synthesis of Mirror-Image Microarrays in a Photochemical Reaction Cell with Flare Suppression

Abstract

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. The reaction cell positions both substrates within the limited depth-of-focus of the optical system while maintaining the necessary reagent flow conditions. The resulting microarrays are mirror images of each other but otherwise essentially identical. The new reaction cell doubles the throughput of microarray synthesis without increasing the consumption of reagents. In addition, a secondary flow chamber behind the reaction cell can be filled with an absorbent and index-matching fluid to eliminate reflections from light exiting the reaction cell assembly, greatly reducing unintended light exposure that reduces the sequence fidelity of the microarray probes.

Nϵ‐Carboxymethyllysine Increases the Expression of miR‐103/143 and Enhances Lipid Accumulation in 3T3‐L1 Cells

“…MicroRNA micorarrays were synthesized using maskless microarray synthesis as described by Agbavwe et al [2011], with a modified reaction chamber allowing for the simultaneous synthesis of microarrays on two independent glass substrates as described by Sack et al [2013]. The customized microarray comprises probes for all known mature mouse miRNA sequences from release 19 of miRBase [Griffiths‐Jones et al, 2006, 2008; Kozomara and Griffiths‐Jones, 2011], as described previously by Rohm et al [2015].…”

High‐Density RNA Microarrays Synthesized In Situ by Photolithography

“…Our MAS setup is equipped with aDMD of 1024 768 mirrors,resulting in amaximal achievable density of 786 432 features per array. [19,20] Thenumber of sequence combinations of nine nucleotides can be expressed as 4 9 (262 144 sequences) and fit comfortably on asingle array,…”

High-Density DNA and RNA microarrays - Photolithographic Synthesis, Hybridization and Preparation of Large Nucleic Acid Libraries

“…We have brought in new light-sensitive 5' protecting groups that can be removed in seconds only, transforming the synthesis of hundreds of thousands of 100mers into a few hours-long process 26 . We have also doubled the throughput of array fabrication by exposing two substrates simultaneously 27 . Finally, we have introduced a dT phosphoramidite containing a base-sensitive succinyl group as a convenient way to cleave, collect and analyze DNA and RNA oligonucleotides, which is central to library preparation 28 .…”