NimbleGen

NimbleGen uniquely produces high-density arrays of long oligo probes that provide great information content and high data quality for studying the full diversity of genomic and epigenomic variation.

NimbleGen's Maskless Array Synthesis (MAS) technology combines digital light processing and rapid, high-yield photochemistry to shorten array fabrication time from months to hours. NimbleGen's long isothermal probes high-density arrays of that provide superior can be used for a wide rangeof of micoarray applications:

• Sequence Capture - Enrich thousands of targeted loci from complex genomic DNA for high-throughput sequencing with programmable Sequence Capture microarrays.
• Array CGH - Identify genomic insertions and deletions and copy number changes at ultra-high resolution, genome wide or focused fine tiling, with high-definition CGH.
• ChIP-chip - Map regulatory protein binding sites genome wide for transcription factors, polymerases and histones, or target promoter regions with ChIP-chip analysis.
• DNA Methylation - Find methylated regions genome-wide or within targeted promoters or CpG islands with NimbleGen's high-resolution DNA methylation analysis technology.
• Gene Expression - Determine differentially expressed genes and map transcription activity with prokaryotic or eukaryotic whole-genome expression analysis.
• Comparative Genome Sequencing - Survey microbial genomes and identify and categorize all SNPs in a single experiment with Comparative Genome Sequencing.

Array Synthesis

NimbleGen manufactures custom, high-density DNA arrays based on its proprietary Maskless Array Synthesizer (MAS) technology. The MAS system is a bench top, solid-state, high-density DNA array fabrication instrument comprised of a maskless light projector, a reaction chamber, a personal computer, and a DNA synthesizer. NimbleGen builds its arrays using photo-mediated synthesis chemistry with its MAS system.

At the heart of the system is a Digital Micromirror Device (DMD), similar to Texas Instruments' Digital Light Processor (DLP), employing a solid-state array of miniature aluminum mirrors to pattern 786,000 to 4.2 million individual pixels of light. The DMD creates "virtual masks" that replace the physical chromium masks used in traditional arrays.

These "virtual masks" reflect the desired pattern of UV light with individually addressable aluminum mirrors controlled by the computer. The DMD controls the pattern of UV light projected on the microscope slide in the reaction chamber, which is coupled to the DNA synthesizer. The UV light selectively cleaves a UV-labile protecting group at the precise location where the next nucleotide will be coupled. The patterns are coordinated with the DNA synthesis chemistry in a parallel, combinatorial manner such that 385,000 to 2.1 million unique probe features are synthesized in a single array.

The synthesis of microarrays using NimbleGen System's MAS technology is very similar to traditional oligonucleotide synthesis with some important exceptions. Unlike conventional oligo synthesis, arrays are synthesized on glass slides rather than controlled pore glass supports. Another key difference is that the deprotection steps are performed by photodeprotection rather than by acid deprotection. The illustration here depicts digital micromirrors reflecting a pattern of UV light, which deprotects the nascent oligonucleotide and allows addition of the next base.

The Digital Micromirror Device's (DMD) micromirrors are displayed in comparison to the tip of a pin. Each of the 786,000 micromirrors is individually addressable, giving unparalleled precision and control over DNA array fabrication chemistry and structure.

 

  Hybridization

Hybridization of NimbleGen arrays performed on MAUI Hybridization Station with precision controlled temperature and active mixing.

The Hybridization Mixer adheres to the microarray slide via an adhesive gasket forming a uniform, low volume, sealed hybridization chamber. This chamber is clamped into one of the heated slide bays in the base unit, where hybridization takes place.