Agilent Technologies, Inc.

Applied Biosystems, LLC

Mel N Kronick

Eric M Leproust

Douglas A Amorese

Norman M Whiteley

Lincoln J McBride

Douglas H Keith

Gary B Gordon

Carol T Schembri

Andreas N Dorsel

Michael W Hunkapiller

Paul K Wolber

James Alexander Apffel, Jr

Robert H Kincaid

Karen M Hahnenberger

Matthew Marton

John S Hinchcliffe

Dianne Rees

Diane Ilsley-Tyree

Andrew S Atwell

Barnett E Saunders

Martin Verhoef

Methods and compositions for generating mixtures of product molecules from an initial chemical array are provided. In the subject methods, a chemical array of surface immobilized first moieties is subjected to cleavage conditions such that a composition of solution phase first moieties is produced. The resultant composition of solution phase first moieties is then contacted with one or more reactants to produce a mixture of product molecules that are different from the first moieties. Also provided are the arrays employed in the subject methods and kits for practicing the subject methods.

Chemical arrays and methods of using the same

Methods and devices are disclosed for microarray analysis. In one embodiment a method is disclosed for processing a non-standard size slide having an array of chemical compounds attached to a surface of the slide. A sample is exposed to the surface of the non-standard size slide wherein components in the sample bind to the chemical compounds on the surface of the slide. The sample and the slide are incubated under conditions for carrying out the binding reactions, and the surface of the non-standard size slide is examined for the results of the binding reactions. Prior to the exposing step or the incubating step or the examining step, the non-standard size slide is placed into a slide holder comprising a slide-holding section a slide-holding section adapted to dispose the non-standard size slide to a processing instrument in a manner similar to that for a standard size slide. The non-standard size slide may also include an identifier such as a bar code.

Manufacture and use of non-standard size microarray slides

Methods and devices for detecting deposition unit misalignment, e.g., printhead misalignment, of an in situ polymeric, e.g., a nucleic acid, array synthesis device are provided. In accordance with the subject methods, at least one test probe feature is synthesized on a substrate using an in situ polymeric array, e.g., nucleic acid array or protein array, synthesis device. The at least one test probe feature is then contacted with at least two different distinguishably labeled targets, e.g., target nucleic acids. The binding of the targets to the at least one test probe feature is then evaluated to detect any misalignment, e.g., deposition unit or pulse jet misalignments, of the synthesis device. Also provided are substrates having at least one test probe feature and at least one polymeric array, as well as methods of using the substrates in array assays. Also included are kits for use in practicing the subject methods.

Methods and devices for detecting printhead misalignment of an in situ polymeric array synthesis device

A method is provided for the separation of nucleic acid samples. The method includes: providing a test mixture of a plurality of nucleic acid samples, wherein each sample is labeled with a spectrally detectable tag; applying the test mixture to a reversed phase solid support; eluting the mixture under partially denaturing conditions; and detecting spectrally resolved signals produced by the nucleic acid samples labeled with the detectable tags.

Multiplexing methods for identifying nucleic acids using denaturing liquid chromatography

A method for reading out data from microlocations of a microelectronic array involves activating multiple microlocations in parallel and simultaneously detecting the responses from the activated microlocations to determine concentrations of molecular biological material at each microlocation. In a preferred embodiment, the microelectronic array includes electronically addressable electrodes at each microlocation which can be individually activated via a control system. An electrochemiluminescent detection technique is used to detect the presence and determine the concentration of bound molecular biological material that is located at each microlocation. Electrochemiluminescent material is utilized because it gives off light when excited by an applied electrical field. With an addressable microelectronic array, electrical fields can be applied to various combinations of microlocations simultaneously to allow readout of several microlocations in parallel. This is in contrast to the laser-based readout approach which applies activation energy to one microlocation at a time by impacting each microlocation with a single laser system. Reading out multiple microlocations simultaneously in accordance with the invention can produce significant time savings in large arrays.

Readout method for molecular biological electronically addressable arrays

Nucleic acid sequences are detected by a multi-step process, involving labeling sample nucleic acid sequences, duplexing the labeled sample with a probe having a coupling element, immobilizing all of the duplexed probe and target sequence and unduplexed probe, separating specifically immobilized nucleic acid from free and non-specifically immobilized nucleic acid, releasing specifically immobilized nucleic acid, and detecting the presence of the sequence of interest by means of the label. The labeled sequence may be characterized by sizing, e.g. electrophoresis. The method provides for a sensitive and rapid means for accurate detection of sequences of interest in a wide variety of situations.

Nucleic acid detection with separation

Termini of restricted double-stranded DNA fragments are modified by ligating the fragments with terminal phosphate-free double-stranded oligonucleotides having a complementary terminus in the presence of a restriction enzyme and a ligase, where joining of the complementary ends results in loss of the restriction enzyme recognition sequence.

Labeling by simultaneous ligation and restriction

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Palo Alto, CA, United States of America

Mel N Kronick