Source: http://www.google.com/patents/US7575902?dq=5251294
Timestamp: 2016-07-30 09:18:00
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Patent US7575902 - Universal bases for nucleic acid analyses, methods for using universal bases ... - Google PatentsSearch Images Maps Play YouTube News Gmail Drive More »Sign inPatentsCompounds, methods and kits for making and analyzing primer extension products incorporating one or more universal bases are described, including methods and kits for nucleic acid sequencing and microsatellite analysis....http://www.google.com/patents/US7575902?utm_source=gb-gplus-sharePatent US7575902 - Universal bases for nucleic acid analyses, methods for using universal bases, and kits comprising universal basesAdvanced Patent SearchPublication numberUS7575902 B2Publication typeGrantApplication numberUS 11/796,555Publication dateAug 18, 2009Filing dateApr 27, 2007Priority dateNov 7, 2001Fee statusLapsedAlso published asEP1442137A2, EP1442137A4, US7169557, US7214783, US20030119040, US20050037396, US20070190564, US20080274462, US20100184074, WO2003040395A2, WO2003040395A3Publication number11796555, 796555, US 7575902 B2, US 7575902B2, US-B2-7575902, US7575902 B2, US7575902B2InventorsGeun-sook Jeon, Shaheer H. Khan, Barnett B. RosenbaumOriginal AssigneeApplied Biosystems, LlcExport CitationBiBTeX, EndNote, RefManPatent Citations (42), Non-Patent Citations (64), Classifications (16), Legal Events (8) External Links: USPTO, USPTO Assignment, EspacenetUniversal bases for nucleic acid analyses, methods for using universal bases, and kits comprising universal bases
wherein R5 and R6 are the same or different, and are independently selected from the group consisting of H, Cl, F, —R, —OR, —NR2 or halogen groups, where each R is independently H, C1-C6 alkyl or C5-C14 aryl, and wherein R7 is selected from the group consisting of H, Cl, F, —R′, —OR′, —NR′12 or halogen groups, where each R′ is independently H, monophosphate, diphosphate, triphosphate, C1-C6 alkyl or C5-C14 aryl. In some embodiments, the 2′-carbon atom is substituted with one or more of the same or different Cl, F, —R, —OR, —NR2 or halogen groups, where each R is independently H, C1-C6 alkyl or C5-C14 aryl. Exemplary riboses include, but are not limited to, 2′-(C1-C6)alkoxyribose, 2′-(C5-C14)aryloxyribose, 2′,3′-didehydroribose, 2′-deoxy-3′-haloribose, 2′-deoxy-3′-fluororibose, 2′-deoxy-3′-chlororibose, 2′-deoxy-3′-aminoribose, 2′-deoxy-3′-(C1-C6)alkyl ribose, 2′-deoxy-3′-(C1-C6)alkoxyribose and 2′-deoxy-3′-(C5-C14)aryloxyribose, ribose, 2′-deoxyribose, 2′,3′-dideoxyribose, 2′-haloribose, 2′-fluororibose, 2′-chlororibose, and 2′-alkylribose, e.g., 2′-O-methyl, 4′-α-anomeric nucleotides, 1′-α-anomeric nucleotides, 2′-4′- and 3′-4′-linked and other 3�7 locked” or “LNA,” bicyclic sugar modifications (see, e.g., PCT published application nos. WO 98/22489, WO 98/39352, and WO 99/14226). Exemplary LNA sugar analogs within a polynucleotide include, but are not limited to, the structures:
Asymmetric PCR (A-PCR) according to the present invention comprises an amplification reaction composition wherein (i) at least one primer set comprises only a forward primer or only a reverse primer; (ii) there is an excess of one primer (relative to the other primer in a primer set); or (iii) at least one primer set wherein the Tm50 of the first primer is at least 6-8� C. different from the Tm50 of the second primer. In some embodiments, the Tm50 of the first primer is at least 10-12� C. different from the Tm50 of the second primer. Consequently, following a primer extension reaction, an excess of products that are complementary to at least a portion of one strand of the template are generated relative to products that are complementary to at least a portion of the other strand of the template.
To a solution of 4 (1.1 g, 1.9 mmol) in CH3CN (20 mL) was added 1.0 M TBAF (tetrabutylammonium fluoride) dropwise at −20� C., followed by stirring at r.t. for 2 h. The reaction mixture was partitioned between CH2Cl2 and water. The organic layer was dried over MgSO4 and evaporated to dryness. The organic residue was purified by silica gel column chromatography with hexane/CH2Cl2 (100-0%) and then MeOH/CH2Cl2 (0-5%) to give a mixture of 5 and 6 (690 mg, 1.4 mmol, 73%) in a ratio of 1:1. Data for compound 5 is consistent with the literature (J. Am. Chem. Soc. (2000) 122: 7621-7632). Data for compound 6: 1H NMR (CDCl3, 300 MHz) δ 2.41 (s, 3 H, CH3), 2.43 (s, 3 H, CH3), 2.62-2.80 (m, 2H, H2), 4.56-4.65 (m, 3 H, H4′, and 2 H5′), 5.15 (d, terminal allenyl 2 H, J=6.9 Hz), 5.74-5.77 (m, 1 H, H3′), 6.16 (t, internal allenyl H, J=6.9 Hz), 6.94 (dd, 1 H, H1′, J=6.3 and 8.7 Hz), 7.14 (dd, 1 H, H5, J=4.5 and 7.8 Hz), 7.26-7.28 (m, 4 H, C6H4), 7.50 (s, 1H, H2), 7.96-8.00 (m, 5 H, H4 and C6H4), 8.33 (dd, 1 H, H6, J=1.5 and 4.5 Hz).
To a solution of 7 and 8 (50 mg, 0.19 mmol) in trimethylphosphate (500 μL) was added POCl3 ((35 μL, 0.38 mmol) at −10� C., followed by stirring at 10� C. for 2 h. Additional POCl3 (35 μL, 0.38 mmol) was added to the reaction mixture at −10� C., followed by stirring at 10� C. for 2 h. A solution of TBAPP (tributylammonium pyrophosphate, 495 mg, 1.13 mmol) and tributylamine (0.53 mL, 2.27 mmol) in DMF (1 mL) was added to the above mixture at 10� C., followed by stirring for 2 h. 0.1 M TEAB (triethylammonium bicarbonate) was added to the reaction mixture with stirring for 1 h. After evaporating solvents, the residue was purified by preparative RP HPLC with the gradient of 0.1 M TEAA/CH3CN to give two major peaks separated, the faster running compound 9 and the slower running compound 10. Data for compound 9 is consistent with the literature (J. Am. Chem. Soc. (2000) 122: 7621-7632). Data for compound 10: 1H NMR (D2O, 300 MHz) δ 2.26-2.34 (m, 1 H, H2′), 2.55-2.65 (m, 1 H, H2′), 3.90-4.02 (m, 2 H, H5′), 4.04-4.08 (m, 1 H, H4′), 4.60-4.64 (m, 1H, H3′), 5.11 (d, terminal allenyl 2 H, J=6.9 Hz), 6.16 (t, internal allenyl H, J=6.9 Hz), 6.62 (dd, 1 H, H1′, J=6.3 and 8.7 Hz), 7.07 (dd, 1 H, H5, J=4.8 and 8.1 Hz), 7.56 (s, 1H, H2), 8.10 (dd, 1 H, H6, J=1.5 and 4.5 Hz), 8.28 (dd, 1 H, H4, J=1.5 and 7.8 Hz); 31P NMR (D2O, 300 MHz) δ −10.40 (d, J=21.2 Hz), −10.79 (d, J=21.4 Hz), −22.88 (t, J=21.3 Hz).
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Soc., 122(32):7621-7632 (2000).64Zhang et al., "Peptide Nucleic Acid-DNA Duplexes Containing the Universal Base 3- Nitropyrrole," Methods, 23:132-140 (2001).Classifications U.S. Classification435/91.1, 536/24.33, 536/23.1, 536/24.3, 435/6.11International ClassificationC07H21/00, C07H21/04, C07D471/02, C07H19/22, C12N15/09, C12P19/34, C12Q1/68, C07H21/02Cooperative ClassificationY10S435/975, C12Q1/6869European ClassificationC12Q1/68ELegal EventsDateCodeEventDescriptionDec 5, 2008ASAssignmentOwner name: BANK OF AMERICA, N.A, AS COLLATERAL AGENT, WASHINGFree format text: SECURITY AGREEMENT;ASSIGNOR:APPLIED BIOSYSTEMS, LLC;REEL/FRAME:021976/0001Effective date: 20081121Owner name: BANK OF AMERICA, N.A, AS COLLATERAL AGENT,WASHINGTFree format text: SECURITY AGREEMENT;ASSIGNOR:APPLIED BIOSYSTEMS, LLC;REEL/FRAME:021976/0001Effective date: 20081121Mar 17, 2009ASAssignmentOwner name: APPLIED BIOSYSTEMS INC., CALIFORNIAFree format text: CHANGE OF NAME;ASSIGNOR:APPLERA CORPORATION;REEL/FRAME:022417/0802Effective date: 20080630Owner name: APPLIED BIOSYSTEMS, LLC, CALIFORNIAFree format text: MERGER;ASSIGNOR:APPLIED BIOSYSTEMS INC.;REEL/FRAME:022417/0825Effective date: 20081121Owner name: APPLIED BIOSYSTEMS INC., CALIFORNIAFree format text: MERGER;ASSIGNOR:APPLIED BIOSYSTEMS INC.;REEL/FRAME:022417/0818Effective date: 20081121Jun 30, 2009ASAssignmentOwner name: APPLIED BIOSYSTEMS, LLC, CALIFORNIAFree format text: ASSIGNMENT OF ASSIGNORS INTEREST;ASSIGNOR:ROSENBLUM, BARNETT B.;REEL/FRAME:022895/0693Effective date: 20090429Feb 26, 2010ASAssignmentOwner name: APPLIED BIOSYSTEMS, LLC,CALIFORNIAFree format text: MERGER;ASSIGNOR:APPLIED BIOSYSTEMS INC.;REEL/FRAME:023985/0801Effective date: 20081121Owner name: APPLIED BIOSYSTEMS, LLC, CALIFORNIAFree format text: MERGER;ASSIGNOR:APPLIED BIOSYSTEMS INC.;REEL/FRAME:023985/0801Effective date: 20081121Apr 1, 2013REMIMaintenance fee reminder mailedApr 9, 2013ASAssignmentOwner name: APPLIED BIOSYSTEMS, INC., CALIFORNIAFree format text: LIEN RELEASE;ASSIGNOR:BANK OF AMERICA, N.A.;REEL/FRAME:030182/0677Effective date: 20100528Aug 18, 2013LAPSLapse for failure to pay maintenance feesOct 8, 2013FPExpired due to failure to pay maintenance feeEffective date: 20130818RotateOriginal ImageGoogle Home - Sitemap - USPTO Bulk Downloads - Privacy Policy - Terms of Service - About Google Patents - Send FeedbackData provided by IFI CLAIMS Patent Services