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(12) United States Patent (10) Patent No.: US 7,618,777 B2 Myerson Et Al

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(12) United States Patent (10) Patent No.: US 7,618,777 B2 Myerson Et Al US007618777B2 (12) United States Patent (10) Patent No.: US 7,618,777 B2 Myerson et al. (45) Date of Patent: Nov. 17, 2009 (54) COMPOSITION AND METHOD FOR ARRAY 4,364,837. A 12/1982 Pader HYBRDIZATION 4,380,451 A 4, 1983 Steinberger et al. 4.427,958 A 1/1984 Charlesworth et al. (75) Inventors: Joel Myerson,y Berkeley,y CA (US); 4,728.457 A 3, 1988 Fieler et al. Michael Barrett, Mountain View, CA 5,137,765 A 8, 1992 Farnsworth (US) 5,156,834. A 10/1992 Beckmeyer et al. 5,266.222 A 11, 1993 Willis et al. (73) Assignee: Agilent Technologies, Inc., Santa Clara, 5,624,711 A 4/1997 Sundberg et al. CA (US) 5,639,626 A * 6/1997 Kiaei et al. ................ 435,792 5,650,543 A 7, 1997 Medina (*) Notice: Subject to any disclaimer, the term of this 5,985,793 A 11/1999 Sandbrink et al. patent is extended or adjusted under 35 6,186,659 B1 2/2001 Schembri U.S.C. 154(b) by 550 days. 6,313, 182 B1 1 1/2001 Lassila et al. 6,420,114 B1* 7/2002 Bedilion et al. ................ 435/6 (21) Appl. No.: 11/082,476 6,503,413 B2 1/2003 Uchiyama et al. 6,543,968 B2 4/2003 Robinson (22) Filed: Mar 16, 2005 2002/0011584 A1 1/2002 Uchiyama et al. O O 2003, OO 13092 A1 1/2003 Holcomb et al. (65) Prior Publication Data 2005/0.142563 A1* 6/2005 Haddad et al. ................. 435/6 US 2006/0210997 A1 Sep. 21, 2006 (51) Int. Cl. FOREIGN PATENT DOCUMENTS CI2O I/68 (2006.01) CO7H 2 1/00 (2006.01) EP A 0633018 1, 1995 CO7H 2 1/02 (2006.01) (52) U.S. Cl. ........................ 435/6:536/24.3: 536/24.33 (Continued) (58) Field of Classification Search ..................... 435/6; 536/24.3, 24.33 OTHER PUBLICATIONS See application file for complete search history. Product Data Sheet, Tego Wet 206, Substrate wetting additive, Issue (56) References Cited date of Jan. 2004, Tego Chemie Service GmbH. U.S. PATENT DOCUMENTS (Continued) 2,826,551 A 3, 1958 Green Primary Examiner Jezia Riley 3,268,593. A 3, 1958 Green 2,846,458 A 8, 1958 Halluska (57) ABSTRACT 3,234,252 A 2, 1966 Pater 3.427,271 A 2f1969 McKellar The present disclosure relates to a system, composition, and 3,964,500 A 6, 1976 Drakoff method for hybridizing a microarray. The composition 4,047,958 A 9/1977 Yoneyama et al. 4,117,249 A 9, 1978 De Simone et al. includes a Superwetting agent. The method includes contact 4,152,416 A 5/1979 Spitzer ing the microarray with an aqueous mixture including the 4, 160,776 A 7, 1979 Scardera et al. Superwetting agent. 4,226,794. A 10, 1980 Scardera et al. 4,337,168 A 6, 1982 Scardera et al. 16 Claims, 1 Drawing Sheet o 1 10? 1o 10' FEATURE INTENSITY (WITHBUBBLESCAR(S)) US 7,618,777 B2 Page 2 FOREIGN PATENT DOCUMENTS Array-Based CGH Procedures for Genomic DNA Analysis, Version 1.00, Jan. 2005, Part No. G44 10-90010. EP 1186 671 A2 3, 2002 Nimblegen Chip Protocol optimized by Christopher Wong, GIS, GB 849433 9, 1960 NimbleGen Systems, Inc. and A Star Genome Institute of Singapore, WO WOO3 (010338 A 2, 2003 Christopher Wong, Aug. 2003; pp. 1-4. Bauer Center for Genomics Research, Preparation of Affymetrix GeneChips and Target Hybridization Cocktail, Jennifer A. Couget, OTHER PUBLICATIONS Aug. 26, 2003; pp. 1-4. Array Hybridization Procedures, A Concise Guide to cDNA Microar EnviroGem AE Surfactants Readily Biodegradable, Antifoaming ray Anaylsis, Priti Hegde, Rong Qi, Kristie Abernathy, Cheryl Gay, Wetting Agents, Air Products, Air Products and Chemicals, Inc., Sonia Dharap, Renee Gaspard, Julie Earle-Hughes, Erik Snesrud, 2004. Norman Lee, and John Quackenbush. The Institute for Genomic Dynol 604 Surfactant, Air Products, Air Products and Chemicals, Research, Rockville, MD 20850. Inc., 1998. DuPont Zonyl Fluoroadditives, Technical Information, Dupont ApplicationInformation, 3MNovec Fluorosurfactants For Paints and Chemical Solutions Enterprise, Copyright 2002 E.I. du Pont de Coatings, Issued Oct. 2003. Nemours and Company. A new generation of flurosurfactants, Dr. Michael Terrazas ind Dr. 3M Novec Fluorosurfactant FC-4432, Product Information, 3M Per Rudi Dams introduce two new products from 3M, Speciality Chemi formance Materials Division, Issued Oct. 2003. cals Magazine, Mar. 2004; vol. 24 No. 3. 3M Novec Fluorosurfactant FC-4430, Product Information, 3M Per Masurf FS-Fluorosurfactants-Industrial, Mason Chemical Company, formance Materials Division, Issued Oct. 2003. file:/C:\IE Temp\OLK77\Masurf.620%20FS-Fluorosurfactants1. Laying the Foundation for New Technologies, 3M creates a new htm. Copyright 2003 Mason Chemical Company, pp. 1-3. building block for its fluorosurfactants, Darlene Brezinski. Reprinted Novel Fluorinated Materials Replace Long Chain Surfactants, Dr. with permission from the Jan. 2003 issue of Paint & Coatings Indus Barry Rosenbaum/Omnova Solutions, Inc., Posted on May 31, 2002. try Magazine. Agilent 60-mer oligo microarray processing protocol, Part No. EnviroGem AD01 Surfactant Defoaming Wetting Agent, Air Prod G4140-90030, Apr. 2004, Version 4.1. ucts, Air Products and Chemicals, Inc., 2002. Agilent 60-mer oligo microarray procesing protocol, Part No. F4140 Partial European Search Report EP06251406 dated May 23, 2006. 90050, Version 2.1, Apr. 2004. * cited by examiner U.S. Patent Nov. 17, 2009 US 7,618,777 B2 Sp ?& * ((S)>IVOSETggngHLINN)ALISNELNIEHnLVEH FEATURE INTENSITY (WITH TEGO NOSCARS)„01„01.0?,0?, US 7,618,777 B2 1. 2 COMPOSITION AND METHOD FOR ARRAY be observed using conventional hybridization conditions at HYBRDIZATION hybridization temperatures of for example, about 66°C. and a hybridization time of about 14 to 18 hours. The poor per BACKGROUND formance characteristics can be observed in as little as 6 hours of incubation time at high temperature in conventional buffer Microarrays of DNA or RNA polynucleotides or oligo Solutions. nucleotides are state-of-the-art biological tools used in the Thus, there remains a need for materials, conditions and investigation and evaluation of genes for analytical, diagnos methods for hybridizing surfaces, such as DNA microarrays tic, and therapeutic purposes. Microarrays typically comprise on siliceous substrates, that have improved hybridization a plurality of oligomers, synthesized or deposited on a glass 10 assay performance and uniformity. Support or Substrate in an array pattern. The Support-bound oligomers are called “probes’, which function to bind or SUMMARY hybridize with a sample of DNA or RNA material under test, called a “target' in hybridization experiments. Some investi In general terms, the disclosure relates to a system, com gators also use the reverse definition, referring to the Surface 15 position, and method for associating molecules with a Sur bound oligonucleotides as targets and the solution sample of face, for example, hybridizing a first oligonucleotide bound to nucleic acids as probes. Further, some investigators bind the a Surface with a second unbound oligonucleotide. target sample under test to the microarray Substrate and put One possible aspect of the disclosure is a method of hybrid the oligomer probes in solution for hybridization. Either of izing a first oligonucleotide bound to a Surface with a second the “target' or “probes' may be the one that is to be evaluated unbound oligonucleotide, comprising: contacting the Surface by the other. Thus, either one could be an unknown mixture of with an aqueous mixture comprising a Superwetting agent. polynucleotides to be evaluated by binding with the other. All Another possible aspect of the disclosure is a buffer con of these iterations are within the scope of the present disclo centrate comprising: a Superwetting agent and a buffer. Sure. In use, the array Surface is contacted with one or more Still another possible aspect of the disclosure is a product targets under conditions that promote specific, high-affinity 25 of mixing comprising: a Superwetting agent; an organosulfate binding of the target to one or more of the probes. The targets Surfactant or salt thereof a water Soluble organosulfonic acid are typically labeled with an optically detectable label, such or salt thereof an organopolyalkoxylate; a chelator or salt as a fluorescent tag, so that the hybridized targets and probes thereof: a source of a monovalent cation; and optionally an are detectable with scanning equipment. DNA array technol aqueous carrier. ogy offers the potential of using a multitude (e.g., hundreds of 30 Yet another possible aspect of the disclosure is a kit for thousands) of different oligonucleotides to analyze changing hybridizing an oligonucleotide material comprising: a buffer mRNA populations. concentrate comprising a Superwetting agent, an optional Hybridization of DNA microarrays typically employs a microarray having a siliceous Substrate, wherein a surface of target solution having a suitable buffer. Such buffers often the Substrate is optionally derivatized, and optionally having include anionic detergents such as sodium dodecyl Sulfate, 35 a plurality of oligonucleotides attached to the Surface in an lithium lauryl sulfate, N-lauryl sarcoside, or non-ionic deter array pattern of features; and instructions for using the buffer gents such as Tween 20R or Triton X-102(R). Known hybrid concentrate to hybridize the oligonucleotide attached to a ization buffers provide at least some wetting and flow char microarray. acteristics. Wetting and flow characteristics of the buffer, the target Solution, or combinations thereof, can be significant 40 BRIEF DESCRIPTION OF THE DRAWINGS(S) when, for example, the DNA microarray slides that are used are hydrophobic. Appropriate flow characteristics can also be FIG. 1 shows a comparative scatter plot of observed feature advantageous when, for example, it is desirable to use mixing intensity for two arrays, one with scar defects and without or agitation to help distribute the target Solution uniformly scar defects, in embodiments of the present disclosure.
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