Photoelectrochemical synthesis of DNA microarrays

Abstract

Optical addressing of semiconductor electrodes represents a powerful technology that enables the independent and parallel control of a very large number of electrical phenomena at the solidelectrolyte interface. To date, it has been used in a wide range of applications including electrophoretic manipulation, biomolecule sensing, and stimulating networks of neurons. Here, we have adapted this approach for the parallel addressing of redox reactions, and report the construction of a DNA microarray synthesis platform based on semiconductor photoelectrochemistry (PEC). An amorphous silicon photoconductor is activated by an optical projection system to create virtual electrodes capable of electrochemically generating protons; these PEC-generated protons then cleave the acid-labile dimethoxytrityl protecting groups of DNA phosphoramidite synthesis reagents with the requisite spatial selectivity to generate DNA microarrays. Furthermore, a thin-film porous glass dramatically increases the amount of DNA synthesized per chip by over an order of magnitude versus uncoated glass. This platform demonstrates that PEC can be used toward combinatorial bio-polymer and small molecule synthesis.combinatorial chemistry ͉ genomics ͉ opto-electronics ͉ phosphoramidite ͉ solid-phase synthesis

Error correction in gene synthesis technology

“…In any case, truncated products could arise from misalignment of printed droplets or from partial deblocking as a result of poor light-source registration and improper sequestering of redox ions. Erroneous products caused by such “edge effects” could be mitigated by employing patterned substrates for synthesis [23, 24]. Studies using the inkjet chip synthesis platformdetermined that the error rate can be reduced from 1 error in ~200 bases to 1 error in ~600 bases by using patterned silica features on a plastic chip [25].…”

Light-addressable Electrodes for Dynamic and Flexible Addressing of Biological Systems and Electrochemical Reactions

“…In another approach, the electrode structure was modified and amorphous silicon was deposited on ITO glass with structured platinum pads on top. To increase the surface area, an additional porous glass layer was deposited [120]. Spatially resolved detritlyation of surface-bounded 4,4-dimethoxytrityl protecting groups by photoelectrochemically generated protons led to a subsequent hybridization of oligonucleotides.…”

“…Polymer Polystyrene TiO 2 [110] Polyaniline WO 3 [111] Polyaniline TiO 2 [111] Polypyrrol TiO 2 [56,111,112,114,115,122] Polypyrrol n-Si [55,92] Polypyrrol ZnO [113] Others Calcium alginate gels a:Si [110] Calcium alginate gels TiOPc [85,86] Chitosan a:Si [87,88] Polyhistidine-tagged proteins TiO 2 [89] DNA oligonucleotids n-Si [119] DNA oligonucleotids a:Si [120]…”

Modern approaches to artificial gene synthesis: aspects of oligonucleotide synthesis, enzymatic assembly, sequence verification and error correction

“…Thus, microchip-based approaches previously used for DNA diagnostics and sequencing have been adopted for multi-parallel synthesis of oligonucleotide arrays. Several constructive implementations such as ink-jet DNA printing (Lausted et al, 2004), microfluidic devices Huang et al, 2009;Lee et al, 2010), light-directed (Richmond et al, 2004) and electrochemical (Egeland, Southern, 2005;Chow et al, 2009) microarray synthesis and LED-controlled capillaries (Blair et al, 2006) synthesis have been independently developed. A conditions modification during the detritylation step of chip-based oligonucleotide synthesis lead to improved quality of oligonucleotides with the possible length up to 150 nt .…”