PI: Dr. Jay Shendure
Location: University of Washington, Genome Sciences
Methods for Programmable Gene Synthesis and Allelic Series
The Shendure Lab, located in the Department of Genome Sciences at the University of Washington, is broadly interested in developing broadly enabling technologies for human genetics and molecular biology. The areas in which we are working include the development of methods that facilitate protein synthesis and engineering. Although next-generation sequencing can be used to efficiently ‘read’ DNA, there is a strong need for ‘write’ methods that enable the ultra-cheap and highly accurate synthesis of kilobase-scale or megabase-scale DNA constructs of arbitrary sequence. We are therefore developing generalized protocols for multiplex, error-free gene synthesis that rely on oligonucleotides from programmable microarrays as raw material (as the per-base cost of these oligonucleotides is <1/20th that of conventionally synthesized oligonucleotides, with the potential to be much cheaper). We are concurrently developing cost-effective, high-throughput methods for programmable mutagenesis, e.g. to facilitate the efficient construction of complex allelic series of proteins or regulatory elements. These allelic series can be subjected to multiplex functional analysis to facilitate deeper understanding of biochemical function as well as for rapid, empirical protein engineering.
Patwardhan RP, Lee C, Litvin O, Young DL, Pe’er D, Shendure J. High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nature Biotechnology 2009 Dec;27(12):1173-5.
Hiatt JB, Patwardhan RP, Turner EH, Lee C, Shendure J. Parallel, tag-directed assembly of locally derived short sequence reads. Nature Methods 2010 Feb;7(2):119-22.
Patwardhan RP, Hiatt JB, Witten DM, Kim MJ, Smith RP, May D, Lee C, Andrie JM, Lee SI, Cooper GM, Ahituv N, Pennacchio LA, Shendure J. Massively parallel functional dissection of mammalian enhancers in vivo. Nature Biotechnology 2012 Feb 26;30(3):265-70.
Schwartz JJ, Lee C, Shendure J. Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules. Nature Methods 2012 Sep;9(9):913-5.