Wisconsin Alumni Research Foundation

Nimblegen Systems Gmbh

Other

Roche Nimblegen, Inc.

Francesco Cerrina

Roland D Green

Michael Richard Sussman

Peter Jeremy Belshaw

Frederick R Blattner

Paul Franklin Nealey

Harun Solak

Sangeet Singh-Gasson

Juan J Depablo

Wei Huang

Michael J Sussman

Qiang Wang

Richard D Peters

XiaoMin Yang

Shane T Flickinger

Alan Pitas

Adam R Pawloski

J Leon Shohet

James Welch Taylor

Kathryn E Richmond

Lin Wang

Mo-Huang Li

James Howard Kaysen

Chang-Han Kim

Cristian Cismaru

Lei Yang

Jasjit J Singh

Roland Green

The synthesis of arrays of DNA probes sequences, polypeptides, and the like is carried out using a patterning process on an active surface of a substrate. An image is projected onto the active surface of the substrate utilizing reflective projection optics. The projection optics project a light image onto the active surface of the substrate to deprotect linker molecules thereon. A first level of bases may then be applied to the substrate, followed by development steps, and subsequent exposure of the substrate utilizing a different light image, with further repeats until the elements of a two dimensional array on the substrate surface have an appropriate base bound thereto.

Methods for the synthesis of arrays of DNA probes

During the light illumination period of a monomer addition cycle in synthesizing an DNA microarray, undesirable reflections of illumination light from various interfaces that the illumination light passes through near the synthesis surface of the substrate may reduce the light-dark contrast, and negatively affect the precision and resolution of the microarray synthesis. The present invention provides an flow cell that reduces the undesired reflections by constructing certain flow cell structures with materials that have similar refractive indexes as that of the solution that is in the oligomer synthesis chamber during the illumination period and/or constructing certain flow cell structures or covering the structures with a layer of a material that has a high extinction coefficient.

Microarray synthesis instrument and method

A method is disclosed for the direct synthesis of double stranded DNA molecules of a variety of sizes and with any desired sequence. The DNA molecule to be synthesis is logically broken up into smaller overlapping DNA segments. A maskless microarray synthesizer is used to make a DNA microarray on a substrate in which each element or feature of the array is populated by DNA of a one of the overlapping DNA segments. The DNA segments are released from the substrate and held under conditions favoring hybridization of DNA, under which conditions the segments will spontaneously hybridize together to form the desired DNA construct. This method makes possible the remote assembly of DNA sequence, through a process analogous to facsimile transmission of documents, since the information on DNA to be made can be transmitted remotely to an instrument which can then synthesize any needed DNA sequence from the information.

Method for the synthesis of DNA sequences

Synthesis of chain molecules such as DNA is carried out in a conduit having an interior channel with an inlet end and an outlet end. At least one wall of the conduit is substantially transparent to selected wavelengths of light. Solid carrier particles are contained within the interior channel of the conduit. A plurality of controllable light sources are mounted at spaced locations along the length of the transparent wall of the conduit to allow selective illumination of separated sections of the particles within the conduit. When a light source is turned on, a photodeprotecting group is removed from the carrier particles in the section that is illuminated by the light source. A reagent containing a selected base is flowed through the conduit so that the base will attach to the carrier particles in those sections which have been exposed to light and deprotected. Reagents may be applied which subsequently again protect the bases followed by selective application of light to certain sections, removal of the deprotection group, and attachment of a new base, with the process repeated until desired sequences have been formed on the carrier particles at each of the separated sections in the conduit. The synthesized molecules may then be removed for direct use or further processing.

Method and apparatus for parallel synthesis of chain molecules such as DNA

The present invention provides an apparatus and a method for the synthesis of arrays of oligomers that have tight illumination intensity requirement. The apparatus and the method contains a mechanism to correct for illumination nonuniformity during the oligomer array synthesis process. To correct for illumination nonuniformity, the illumination intensity of different oligomer synthesis positions across an area in which oligomers are synthesized are determined first. Then, the difference in illumination intensity among the positions are evaluated mathematically. Next, any nonuniformity in illumination intensity is corrected by either reducing the intensity of the light for the brighter positions before the light reaches the illumination area or reducing the illumination time of the brighter positions during one protection group deprotection period.

Correction for illumination non-uniformity during the synthesis of arrays of oligomers

A method is disclosed for the direct synthesis of double stranded DNA molecules of a variety of sizes and with any desired sequence. The DNA molecule to be synthesis is logically broken up into smaller overlapping DNA segments. A maskless microarray synthesizer is used to make a DNA microarray on a substrate in which each element or feature of the array is populated by DNA of a one of the overlapping DNA segments. The complement of each segment is also made in the microarray. The DNA segments are released from the substrate and held under conditions favoring hybridization of DNA, under which conditions the segments will hybridize to form duplexes. The duplexes are then separated using a DNA binding agent which binds to improperly formed DNA helixes to remove errors from the set of DNA molecules. The segments can then be hybridized to each other to assemble the larger target DNA sequence.

Method of error reduction in nucleic acid populations

A dark-field imaging method for detecting defects in reflective lithography masks (e.g., extreme ultraviolet (EUV) masks) used, e.g., in processes for the fabrication of microelectronic devices. A mask blank is coated with a photoresist layer having a fluorescent dye incorporated therein. The photoresist layer is exposed to a source of radiation (e.g., EUV radiation or glancing soft X-rays). In areas of the mask blank having defects the combined direct and reflected radiation will be insufficient fully to expose the photoresist layer. After development, photoresist will remain on the mask blank surface in areas corresponding to defects. Illumination with the excitation wavelength of the fluorescent dye reveals the location of any remaining photoresist, which can be detected using an optical microscope, thereby to detect defects in the mask blank.

Defect inspection of extreme ultraviolet lithography masks and the like

An optical alignment system for a device for synthesizing DNA polymers provides for a patterned substrate for simple alignment of the system. The substrate may also be used for synthesis allowing precise alignment of the synthesis substrate during each synthesis operation. The patterning of the substrate may be used to promote separation of reaction sites.

Prepatterned substrate for optical synthesis of DNA probes

An image locking system for DNA micro-array synthesis provides a feedback system to stabilize or lock the image with respect to an image capture device, such as a camera and/or microscope. The image locking system includes the use of detection or reference marks. When a shift in image position is detected, a correction signal is sent to one of two mirrors, moving the image to correct for the shift in image position. The system comprises a first light beam directed towards a micromirror device that forms an alignment pattern on a reaction cell and a second light beam directed towards the micromirror device that forms a micro-array image on an active surface of the reaction cell. A camera captures the alignment pattern and an alignment mark. A computer calculates a correction signal to realign the alignment pattern with the alignment mark when movement is detected.

Image locking system for DNA micro-array synthesis

The present invention provides an apparatus for constructing arrays of DNA sequences using the image of a micromirror array projected on a reaction site using a highly uniform beam of light produced by a homogenizer formed of a prismatic refractive element followed by a kaleidoscopic element.

Apparatus for constructing DNA probes having a prismatic and kaleidoscopic light homogenizer

Copolymer structures are formed by exposing a substrate with an imaging layer thereon to two or more beams of selected wavelengths to form interference patterns at the imaging layer to change the wettability of the imaging layer in accordance with the interference patterns. A layer of a selected block copolymer is deposited onto the exposed imaging layer and annealed to separate the components of the copolymer in accordance with the pattern of wettability and to replicate the pattern of the imaging layer in the copolymer layer. Stripes or isolated regions of the separated components may be formed with periodic dimensions in the range of 100 nm or less.

Guided self-assembly of block copolymer films on interferometrically nanopatterned substrates

A method and apparatus for reducing plasma-induced charging damage in a semiconducting device are provided. The method includes exposing an article having a dielectric material susceptible to plasma-induced charging, to vacuum-ultraviolet (VUV) radiation of an energy greater than the bandgap energy of the dielectric material during or after plasma processing of the device. The plasma-induced charge is conducted from, or recombined at, the charging site.

Growing community of inventors

Madison, WI, United States of America

Francesco Cerrina