Progress in gene assembly from a MAS-driven DNA microarray

Kim, C.; Kaysen, James H.; Richmond, K.; Rodesch, Matthew J.; Binkowski, Brock F.; Chu, L.L.; Li, M.; Heinrich, K.; Blair, Sarah L.; Belshaw, Peter J.; Sussman, Michael R.; Cerrina, F.

doi:10.1016/j.mee.2006.01.143

Cited by 13 publications

(19 citation statements)

References 9 publications

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“…The 93% stepwise yield is in line with previous first reports, which have ranged from 91-98% (21)(22)(23)(24)(25). Future studies will aim to optimize system parameters by constructing an improved optical projection system, examining other suitable semiconductors and device architectures (e.g., nanoparticle-based films, n-i-p diodes, microfabricated fluidic channels), and altering the coupling cycles (16,26).…”

Section: Resultssupporting

confidence: 85%

“…The large synthesis capacity of the porous glass film may greatly benefit applications that use custom microarrays to drive down the cost per base for genomic research, such as multiplexed gene synthesis (16,26,36), library construction (37,38), and genomic selection for targeted sequencing (39)(40)(41). It effectively further lowers the cost per base by reducing the spot redundancy required to obtain biologically relevant quantities of each sequence, and also limits the need for amplification protocols.…”

Section: Discussionmentioning

confidence: 99%

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Photoelectrochemical synthesis of DNA microarrays

Chow

Emig

Jacobson

2009

Proc. Natl. Acad. Sci. U.S.A.

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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

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Section: Resultssupporting

confidence: 85%

Section: Discussionmentioning

confidence: 99%

Photoelectrochemical synthesis of DNA microarrays

Chow

Emig

Jacobson

2009

Proc. Natl. Acad. Sci. U.S.A.

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“…8,9 Arrays synthesized using in situ methods, such as those produced commercially by Nimblegen, Agilent, or Affymetrix, are also now routinely used as sources for complex oligonucleotide pools for gene synthesis. 10-12 Such arrays are fabricated using phosphoramidite chemistry to build oligonucleotides base-by-base, enabling the synthesis of specific sequences up to ∼150 nucleotides in length. 13 …”

mentioning

confidence: 99%

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

Holden

Carter

et al. 2015

Anal. Chem.

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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 crosslinked polymer multilayers that present hydroxyl groups suitable for conventional phosphoramidite-based nucleic acid synthesis. We demonstrate that by modifying MAS 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 × 14 μm and feature densities in excess of 125 000/cm2, 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 sub-divided 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 potential applications for these important bioanalytical tools.

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“…Previous efforts have demonstrated the ability to synthesize genes from DNA microchips3,4,5,14. These approaches have thus far failed to scale for at least three reasons.…”

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confidence: 99%

Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips

Eroshenko²,

et al. 2010

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Development of cheap, high-throughput, and reliable gene synthesis methods will broadly stimulate progress in biology and biotechnology1. Currently, the reliance on column-synthesized oligonucleotides as a source of DNA limits further cost reductions in gene synthesis2. Oligonucleotides from DNA microchips can reduce costs by at least an order of magnitude3,4,5, yet efforts to scale their use have been largely unsuccessful due to the high error rates and complexity of the oligonucleotide mixtures. Here we use high-fidelity DNA microchips, selective oligonucleotide pool amplification, optimized gene assembly protocols, and enzymatic error correction to develop a highly parallel gene synthesis platform. We tested our platform by assembling 47 genes, including 42 challenging therapeutic antibody sequences, encoding a total of ~35 kilo-basepairs of DNA. These assemblies were performed from a complex background containing 13,000 oligonucleotides encoding ~2.5 megabases of DNA, which is at least 50 times larger than previously published attempts.

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Progress in gene assembly from a MAS-driven DNA microarray

Cited by 13 publications

References 9 publications

Photoelectrochemical synthesis of DNA microarrays

Photoelectrochemical synthesis of DNA microarrays

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

Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips

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