NimbleGen will refine its proprietary technology and manufacturing system into the Maskless Array Synthesizer System (MAS Systems). The MAS System will permit owners to rapidly produce inexpensive High Density Custom DNA Arrays (CDAs) in their own facilities to their own specifications. NimbleGen builds its arrays using photo deposition chemistry with its proprietary Maskless UV Light Projector. Texas Instruments Digital Light Processor (DLP) is at the heart of the NimbleGen Projector. The DLP employs a solid-state array of miniaturized aluminum mirrors to pattern up to 780,000 individual pixels of light. Next generation systems will produce up to 1.3 million pixels of light. The computer controlled fabricatoin process requires no human interaction once the glass substrate is placed into NimbleGen's proprietary reaction chamber. Fabrication occurs base-by-base inside the reaction chamber, eliminating the need for the clean rooms common to other array production processes. By using the Maskless UV Projector to control the patterning of UV light on the glass in the reaction chamber, NimbleGen achieves unparalleled precision and control over CDA fabrication. The MAS technology also permits unsurpassed speed - a cycle time of less than four hours - in the production of CDAs, thereby substantially reducing development time and costs.

Proposed Commercial Applications

There is a clear need for an inexpensive, rapid, and reliable method of generating and analyzing custom DNA arrays. There are strong indiciations of the proposed project's potential for commercialization, as follows: The market for DNA arrays and DNA array fabrication equipment is projected to be $318 million in 2001, growing to $1.7 billion in 2005, a CAGR of 49%.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Small Business Innovation Research Grants (SBIR) - Phase II (R44)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-SSS-Y (10))
Program Officer
Feingold, Elise A
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Nimblegen Systems, Inc.
United States
Zip Code
Haugen, Brian J; Pellett, Shahaireen; Redford, Peter et al. (2007) In vivo gene expression analysis identifies genes required for enhanced colonization of the mouse urinary tract by uropathogenic Escherichia coli strain CFT073 dsdA. Infect Immun 75:278-89
Steinmetz, Eric J; Warren, Christopher L; Kuehner, Jason N et al. (2006) Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol Cell 24:735-46
Anderson, Bradley D; Gilson, Michael C; Scott, Abigail A et al. (2006) CGHScan: finding variable regions using high-density microarray comparative genomic hybridization data. BMC Genomics 7:91
Snyder, Jennifer A; Haugen, Brian J; Lockatell, C Virginia et al. (2005) Coordinate expression of fimbriae in uropathogenic Escherichia coli. Infect Immun 73:7588-96
Winterberg, Kelly M; Luecke, John; Bruegl, Amanda S et al. (2005) Phenotypic screening of Escherichia coli K-12 Tn5 insertion libraries, using whole-genome oligonucleotide microarrays. Appl Environ Microbiol 71:451-9
Ulijasz, Andrew T; Andes, David R; Glasner, Jeremy D et al. (2004) Regulation of iron transport in Streptococcus pneumoniae by RitR, an orphan response regulator. J Bacteriol 186:8123-36
Rajashekara, Gireesh; Glasner, Jeremy D; Glover, David A et al. (2004) Comparative whole-genome hybridization reveals genomic islands in Brucella species. J Bacteriol 186:5040-51
Snyder, Jennifer A; Haugen, Brian J; Buckles, Eric L et al. (2004) Transcriptome of uropathogenic Escherichia coli during urinary tract infection. Infect Immun 72:6373-81
Bockhorst, Joseph; Qiu, Yu; Glasner, Jeremy et al. (2003) Predicting bacterial transcription units using sequence and expression data. Bioinformatics 19 Suppl 1:i34-43
Tobler, J B; Molla, M N; Nuwaysir, E F et al. (2002) Evaluating machine learning approaches for aiding probe selection for gene-expression arrays. Bioinformatics 18 Suppl 1:S164-71