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Open Access Research

Efficiency, error and yield in light-directed maskless synthesis of DNA microarrays

Christy Agbavwe1, Changhan Kim24, DongGee Hong2, Kurt Heinrich2, Tao Wang3 and Mark M Somoza1*

Author Affiliations

1 Institute of Inorganic Chemistry, University of Vienna, Währinger Strasse 42, A-1090 Vienna, Austria

2 Center for Nanotechnology, Department of Electrical and Computer Engineering, University of Wisconsin, Madison WI 53706, USA

3 Center for Nano Science and Technology, Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA

4 Current Address: Intel Corporation, 8000 S. Federal Way, Boise ID 83716, USA

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Journal of Nanobiotechnology 2011, 9:57  doi:10.1186/1477-3155-9-57

Published: 8 December 2011

Abstract

Background

Light-directed in situ synthesis of DNA microarrays using computer-controlled projection from a digital micromirror device--maskless array synthesis (MAS)--has proved to be successful at both commercial and laboratory scales. The chemical synthetic cycle in MAS is quite similar to that of conventional solid-phase synthesis of oligonucleotides, but the complexity of microarrays and unique synthesis kinetics on the glass substrate require a careful tuning of parameters and unique modifications to the synthesis cycle to obtain optimal deprotection and phosphoramidite coupling. In addition, unintended deprotection due to scattering and diffraction introduce insertion errors that contribute significantly to the overall error rate.

Results

Stepwise phosphoramidite coupling yields have been greatly improved and are now comparable to those obtained in solid phase synthesis of oligonucleotides. Extended chemical exposure in the synthesis of complex, long oligonucleotide arrays result in lower--but still high--final average yields which approach 99%. The new synthesis chemistry includes elimination of the standard oxidation until the final step, and improved coupling and light deprotection. Coupling Insertions due to stray light are the limiting factor in sequence quality for oligonucleotide synthesis for gene assembly. Diffraction and local flare are by far the largest contributors to loss of optical contrast.

Conclusions

Maskless array synthesis is an efficient and versatile method for synthesizing high density arrays of long oligonucleotides for hybridization- and other molecular binding-based experiments. For applications requiring high sequence purity, such as gene assembly, diffraction and flare remain significant obstacles, but can be significantly reduced with straightforward experimental strategies.

Keywords:
Microarray; phosphoramidite chemistry; NPPOC; gene synthesis