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(12) United States Patent (10) Patent No.: US 8,652,778 B2 Bowman Et Al

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(12) United States Patent (10) Patent No.: US 8,652,778 B2 Bowman Et Al US008652778B2 (12) United States Patent (10) Patent No.: US 8,652,778 B2 BOWman et al. (45) Date of Patent: *Feb. 18, 2014 (54) USE OF PHOTOPOLYMERIZATION FOR 5.449,602 A 9, 1995 Royer et al. AMPLIFICATION AND DETECTION OFA 5: A 3: Nilsen al MOLECULAR RECOGNITION EVENT 5,545,730I w A 8, 1996 UrdeaSee et al.all. 5,571,670 A 11/1996 Urdea et al. (75) Inventors: Christopher N. Bowman, Boulder, CO 5,573,907 A 11, 1996 A. al. (US); Kathy Rowlen, Boulder, CO (US); 5,580,731 A 12/1996 Chang et al. Hadley Sikes, Pasadena, CA (US); Ryan 3. A 3. s al Hansen, Golden, CO (US); Heather 5,594,118.-- I A 1/1997 UrdeaOCa, etCa. al. Jean Avens, Lafayette, CO (US) 5,597,909 A 1/1997 Urdea et al. 5,624,802 A 4/1997 Urdea et al. (73) Assignee: The Regents of the University of 5,635,352 A 6/1997 Urdea et al. Colorado, A Body Corporate, Denver, 5,637.460 A 6/1997 Swan et al. DE (US) 5,660,988 A 8/1997 Duck et al. 5,681,697 A 10, 1997 Urdea et al. 5,681,702 A 10, 1997 Collins et al. (*) Notice: Subject to any disclaimer, the term of this 5,710,264 A 1, 1998 E. al. patent is extended or adjusted under 35 5,770,722 A 6/1998 Lockhart et al. U.S.C. 154(b) by 0 days. 6,096,369 A 8, 2000 Anders et al. - - - - - 6,361,944 B1 3/2002 Mirkin et al. inplent is Subject to a terminal dis- (Continued) (21) Appl. No.: 13/082,814 FOREIGN PATENT DOCUMENTS y x- - - 9 EP O 383 126 8, 1990 (22) Filed: Apr. 8, 2011 WO WOOOf 43539 T 2000 O O Continued) (65)65 PriorO PublicationDO Dat OTHER( PUBLICATIONS US 2011 FO25.1092A1 Oct. 13, 2011 Tan et al. Bionanotechnology Based on Silica Nanoparticles. 2004. Medicinal Research Reviews, vol. 24, No. 5, pp. 621-638.* Related U.S. Application Data Taton et al. Scanometric DNA Array Detection with Nanoparticle (63) Continuation of application No. 12/099.560, filed on Probes. Sep 8, 2000. Science. vol. 289, p. 1757-1760.* Apr. 8, 2008, now abandoned, which is a Andras et al. (2001) "Strategies for Signal Amplification in Nucleic - - - - s Acid Detection.” Mol. Biotechnol. 19:29-44. continuation-in-part of application No. 11/372.485, Anthony et al. (2000) “Rapid Diagnosis of Bacteria by Universal filed on Mar. 9, 2006, now Pat. No. 7.354,706, which is Amplification of 23S Ribosomal DNA Followed by Hybridization to a continuation-in-part of application No. an Oligonucleotide Array.” J. Clin. Microbiol. 38:781-788. PCT/US2004/029733, filed on Sep. 9, 2004. Avens et al. (Sep. 2008) “Polymerization Behavior and Polymer Properties of Eosin-Mediated Surface Modification Reactions.” (60) Provisional application No. 60/988,563, filed on Nov. Polymer 49:4762-4768. 16, 2007, provisional application No. 60/982,992, Avens et al. (2009) “Mechanism of Cyclic Dye Regeneration During filed on Oct. 26, 2007, provisional application No. Eosin-Sensitivity Photoinitiation in the Presence of Polymerization 60/662,313, filed on Mar. 16, 2005, provisional Inhibitors. J. Polym. Sci. Polym. Chen. 47:6083-6094. application No. 60/501,755, filed on Sep. 9, 2003. (Continued) (51) Int. Cl. Primary Examiner — Anne Gussow CI2O I/68 (2006.01) Assistant Examiner — Channing S Mahatan C4OB 30/04 (2006.01) (74) Attorney, Agent, or Firm — Lathrop & Gage LLP: B82/30/00 (2011.01) Tamala R. Jonas; Sally Sullivan (52) U.S. Cl. (57) ABSTRACT USPC ................................. 435/6.1: 506/9; 977/773 The invention provides methods to detect molecular recogni (58) Field of Classification Search tion events. The invention also provides methods to detect the None presence of or identify a target species based on its interaction S ee appl1cauonlication fileIlle fIor completelet searcnh historv.n1Story withare based one or on more amplification probespecies. of the The signal methods due to ofeach the molecular invention (56) References Cited recognition event. The amplification is achieved through pho topolymerization, with the polymer formed being associated with the molecular recognition event. In one aspect, a fluo U.S. PATENT DOCUMENTS rescent polymer, a magnetic polymer, a radioactive polymer 4,749,647 A * 6/1988 Thomas et al. ................... 435/5 or an electrically conducting polymer can form the basis of 4,876, 187 A 10, 1989 Ducket al. detection and amplification. In another aspect, a polymer gel 5,011,769 A 4, 1991 Ducket al. Swollen with a fluorescent Solution, a magnetic solution, a 5,019,496 A 5, 1991 Oster et al. radioactive Solution oran electrically conducting Solution can 5,124,246 A 6, 1992 Urdea et al. form the basis of detection and amplification. In another 5,175.270 A 12/1992 Nilsen et al. aspect, detectable particles can be included in the polymer 5,185,243 A 2f1993 Ullman et al. formed. In another aspect, sufficient polymer forms to be 5,196,306 A 3, 1993 Bobrow et al. 5,359,100 A 10, 1994 Urdea et al. detectable by visual inspection. 5,403,711 A 4/1995 Walder et al. 34 Claims, 16 Drawing Sheets US 8,652.778 B2 Page 2 (56) References Cited Collins et al. (1997) 'A Branched DNA Signal Amplification Assay for Quantification of Nucleic Acid Targets Below 100 Molecules/ U.S. PATENT DOCUMENTS ml.” Nuc. Acids Res. 25(15):2979-2984. Cruise et al. (Mar. 20, 1998) “A Sensitivity Study of the Key Param 6,372,937 B1 4/2002 Bobrow et al. eters in the Interfacial Photopolymerization of Poly(ethylene glycol) 6,406,845 B1* 6/2002 Walt et al. .................... 435/6.11 Diacrylate Upon Porcine Islets.” Biotechnol. Bioeng. 57(6):655-665. 6,417.340 B1 7/2002 Mirkin et al. Csako et al. (Web Release Aug. 2005) “Present and Future of Rapid 6,485,703 B1 1 1/2002 Cote et al. 6,495,324 B1 12/2002 Mirkin et al. and/or High-Throughput Methods for Nucleic Acid Testing.” Clinica 6,506,564 B1 1/2003 Mirkin et al. Chimica Acta 363:6-31. 6,582,921 B2 6, 2003 Mirkin et al. Daubendieketal. (1997)"Generation of Catalytic RNA's by Rolling 6,593,100 B2 7/2003 Bobrow et al. Transcription of Synthetic DNA Nanocircles.” Nat. Biotech. 15:273 6,602,669 B2 8/2003 Letsinger et al. 277. 6,610,491 B2 8, 2003 Mirkin et al. Ding etal. (Jan. 2004) “Quantitative Analysis of Nucleic Acids. The 6,645,721 B2 11/2003 Mirkin et al. Last Few Years of Progress,” J. Biochem. Mol. Biol. 37(1): 1-10. 6,667,122 B2 12/2003 Kaufmann Do et al. (Feb. 2007) “cDNA Labeling Strategies for Microarrays 6,673,548 B2 1/2004 Mirkin et al. Using Fluorescent Dyes.” Eng. Life Sci. 7(1):26-34. 6,682,895 B2 1/2004 Mirkin et al. Elghanian et al. (Aug. 22, 1997)"Selective Colorimetric Detection of 6,709,825 B2 3, 2004 Mirkin et al. Polynucleotides Based on the Distance—Dependent Optical Proper 6,720,147 B2 4/2004 Mirkin et al. 6,720,411 B2 4/2004 Mirkin et al. ties of Gold Nanoparticles.” Science 277: 1078-1081. 6,730.269 B2 5, 2004 Mirkin et al. Englisch et al. (Jun. 1991) “Chemically Modified Oligonucleotides 6,740,491 B2 5, 2004 Mirkin et al. as Probes and Inhibitors.” Angew. Chem. Int. Ed, Eng. 30(6):613-629. 6,750,016 B2 6, 2004 Mirkin et al. Epstein et al. (2002) “Fluorescence-Based Nucleic Acid Detection 6,759,199 B2 7/2004 Mirkin et al. and Microarrays.” Anaytica. Chimica Acta 469:3-36. 6,767,702 B2 7/2004 Mirkin et al. Gaylord etal. (Aug. 20, 2002) “DNA Detection Using Water-Soluble 6,773,884 B2 8, 2004 Mirkin et al. Conjugated Polymers and Peptide Nucleic Acid Probes.” Proc. Nat. 6,777, 186 B2 8, 2004 Mirkin et al. Acad. Sci. USA99(17): 10954-10957. 6,806,047 B2 10/2004 Goldberg et al. Hansen etal. (Jul. 2008)"Quantitative Evaluation of Oligonucleotide 7.354,706 B2 * 4/2008 Rowlen et al. .................... 435.5 Surface Concentrations Using Polymerization-Based Amplifica 2002/0001853 A1 1/2002 Obremski et al. 2002, 0071943 A1 6, 2002 Hawker et al. tion.” Anal. Bioanal. Chem. 392: 167-175. 2003/0236425 A1 12, 2003 Herr et al. Hansen et al. (2009) “Visual, Base-Specific Detection of Nucleic 2004, OO63146 A1 4/2004 Sayre et al. Acid Hybridization Using Polymerization-Based Amplification.” 2006/0286570 A1 12/2006 Rowlen et al. Anal. Biochen. 386:285-287. 2009,0005263 A1 1/2009 Kuck Hansen et al. (Dec. 1, 2007) “Visual Detection of Labeled 2009.0137405 A1 5/2009 Bowman et al. Oligonucleotides Using Visible Light-Polymerization-Based Ampli 2009/O163375 A1 6, 2009 Bowman et al. fication. Biomacromolecules, DOI 10.1021/bm7006727. 2012, 0071338 A1 3/2012 Bowman et al. Hardiman, G. (2004) “Microarray Platforms-Comparisons and Con trasts.” Pharmacogenomics 5:487-502. FOREIGN PATENT DOCUMENTS Hoheisel et al. (Mar. 2006) “Microarray Technology: Beyond Tran scription Profiling and Genotype Analysis.” Nat. Rev. Genet. 7:200 WO WO 2004/093845 11, 2004 210. WO WO 2005/024386 3, 2005 Husemann et al. (1999)"Surface Initiated Polymerization for Ampli WO WO 2006/031248 3, 2006 fication of Self-Assembled Monolayers Patterned by Microcontact WO WO 2007/095464 8, 2007 Printing.” Angew: Chem. Int. Ed. 38(5):647-649. International Search Report Corresponding to International Applica OTHER PUBLICATIONS tion No. PCT/US04/029733, Mailed Mar.
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