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1. 发明专利

JP2006055177A Template-dependent ligation using pna-dna chimeric probe 审中-公开
标题翻译：使用PNA-DNA CHIMERIC PROBE的模板依赖关系
公开(公告)号：JP2006055177A
公开(公告)日：2006-03-02
申请号：JP2005329510
申请日：2005-11-14
申请人： Applera Corp , アプレラコーポレイション
发明人： EGHOLM MICHAEL , CHEN CAIFU
IPC分类号： C12N15/09 , G01N21/78 , C12Q1/68
CPC分类号： C12Q1/6862
摘要： PROBLEM TO BE SOLVED: To provide chimeric molecules of PNA (peptide nucleic acid) and DNA monomer units, and their use in ligation methods to generate ligation products. SOLUTION: Disclosed is a method for producing a template-dependent ligation product, wherein the method comprises a process of enzymatically linking a PNA-DNA chimeric probe to a second probe in the presence of a template nucleic acid and ligase, wherein the chimeric probe has a PNA part and a DNA part and the DNA part has at least two nucleotides and 3' hydroxy terminus or 5' hydroxy terminus, wherein the chimeric probe and the second probe are respectively hybridized to the template nucleic acid and are adjacent each other, and wherein at least one part of the PNA part is hybridized to a template and the second probe is a PNA-DNA chimera or oligonucleotide. COPYRIGHT: (C)2006,JPO&NCIPI
摘要翻译：要解决的问题：提供PNA（肽核酸）和DNA单体单元的嵌合分子，以及它们在连接方法中的用途以产生连接产物。解决方案：公开了一种制备模板依赖性连接产物的方法，其中该方法包括在模板核酸和连接酶存在下将PNA-DNA嵌合探针酶催化连接到第二探针的方法，其中嵌合探针具有PNA部分和DNA部分，DNA部分具有至少两个核苷酸和3'羟基末端或5'羟基末端，其中嵌合探针和第二探针分别与模板核酸杂交并与每个并且其中至少一部分PNA部分与模板杂交，第二探针是PNA-DNA嵌合体或寡核苷酸。版权所有（C）2006，JPO＆NCIPI

2. 发明申请

WO2005098040A8 LIGATION AND AMPLIFICATION REACTIONS FOR DETERMINING TARGET MOLECULES 审中-公开
标题翻译：用于确定目标分子的放射反应和放大反应
公开(公告)号：WO2005098040A8
公开(公告)日：2005-12-01
申请号：PCT/US2005010184
申请日：2005-03-24
申请人： APPLERA CORP , ANDERSEN MARK R , LIVAK KENNETH J , BROOMER ADAM , CHEN CAIFU
发明人： ANDERSEN MARK R , LIVAK KENNETH J , BROOMER ADAM , CHEN CAIFU
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6869 , C12Q1/6851 , C12Q2525/191 , C12Q2525/185 , C12Q2521/501 , C12Q2525/155 , C12Q2521/313 , C12Q2537/143 , C12Q2525/161
摘要： The present invention is directed to methods, reagents, and kits for detecting the presence or absence of (or quantifying) target polynucleotide sequences and proteins in at least one sample using encoding and decoding reactions. When a particular target polynucleotide is present in a sample for example, a reaction product is formed in the encoding reaction that includes addressable primer portions. At least one labeling probe and at least one address primer can be employed in the decoding amplification reaction thereby providing a detectable signal value depending upon whether a sequence is present or absent. In some embodiments, the encoding comprises a ligation reaction with linker probes, and single nucleotide polymorphisms (SNPs) are analyzed.
摘要翻译：本发明涉及用于使用编码和解码反应检测至少一个样品中靶多核苷酸序列和蛋白质的存在或不存在（或定量）的方法，试剂和试剂盒。当特定靶多核苷酸例如存在于样品中时，在包含可寻址引物部分的编码反应中形成反应产物。可以在解码扩增反应中使用至少一个标记探针和至少一个地址引物，从而根据序列是否存在提供可检测的信号值。在一些实施方案中，编码包含与接头探针的连接反应，并分析单核苷酸多态性（SNP）。

3. 发明申请

WO0194638A3 ASYNCHRONOUS PRIMED PCR 审中-公开
标题翻译：异步PRIMED PCR
公开(公告)号：WO0194638A3
公开(公告)日：2003-07-10
申请号：PCT/US0118464
申请日：2001-06-06
申请人： APPLERA CORP
发明人： CHEN CAIFU , EGHOLM MICHAEL , HAFF LAWRENCE
IPC分类号： G01N33/53 , C12N15/09 , C12Q1/68 , G01N33/566
CPC分类号： C12Q1/686 , C12Q2561/101 , C12Q2527/113 , C12Q2527/107
摘要： An asynchronous thermal cycling protocol for nucleic acid amplification uses two primers with thermal melting temperatures different by about 10 to 30 DEG C. After the higher melting primer has annealed and polymerase mediated extension, the uncopied, single-stranded target sequence may be hybridized and detected by a probe. DNA probes may be cleaved by the exonuclease activity of a polymerase. The probe may be a non-cleaving analog such as PNA. When a probe is labelled with a reporter dye and a quencher selected to undergo energy transfer, e.g. FRET, fluorescence from the reporter dye may be effectively quenched when the probe is unbound. Upon hybridization of the probe to complementary target or upon cleavage while bound to target, the reporter dye is no longer quenched, resulting in a detectable amount of fluorescence. The second, lower-melting primer may be annealed and extended to generate a double-stranded nucleic acid. Amplification may be monitored in real time, including each cycle, or at the end point. The asynchronous PCR thermal cycling protocol can generate a preponderance of the PCR amplicon in single-stranded form by repetition at the end of the protocol of annealing and extension of the higher melting primer.
摘要翻译：用于核酸扩增的异步热循环方案使用两种引物，其热解温度不同于约10至30℃。在较高熔点的引物退火和聚合酶介导的延伸之后，未结合的单链靶序列可能被杂交和检测通过探针。 DNA探针可能被聚合酶的外切核酸酶活性切割。探针可以是非断裂的类似物，例如PNA。当探针用报告染料和选择进行能量转移的猝灭剂标记时，例如，当探针未结合时，来自报告染料的荧光可以被有效地淬灭。当探针与互补靶物杂交时或在与靶标结合时进行切割时，报道染料不再猝灭，导致可检测量的荧光。可以将第二种较低熔点的引物退火并延伸以产生双链核酸。可以实时监测放大，包括每个周期，或在终点。异构PCR热循环方案可以在退火和延伸较高熔点引物的方案结束时通过重复生成单链形式的PCR扩增子的优势。

4. 发明申请

WO0194638A8 ASYNCHRONOUS PRIMED PCR 审中-公开
标题翻译：异步PRIMED PCR
公开(公告)号：WO0194638A8
公开(公告)日：2002-04-11
申请号：PCT/US0118464
申请日：2001-06-06
申请人： APPLERA CORP
发明人： CHEN CAIFU , EGHOLM MICHAEL , HAFF LAWRENCE
IPC分类号： G01N33/53 , C12N15/09 , C12Q1/68 , G01N33/566
CPC分类号： C12Q1/686 , C12Q2561/101 , C12Q2527/113 , C12Q2527/107
摘要： An asynchronous thermal cycling protocol for nucleic acid amplification uses two primers with thermal melting temperatures different by about 10 to 30 DEG C. After the higher melting primer has annealed and polymerase mediated extension, the uncopied, single-stranded target sequence may be hybridized and detected by a probe. DNA probes may be cleaved by the exonuclease activity of a polymerase. The probe may be a non-cleaving analog such as PNA. When a probe is labelled with a reporter dye and a quencher selected to undergo energy transfer, e.g. FRET, fluorescence from the reporter dye may be effectively quenched when the probe is unbound. Upon hybridization of the probe to complementary target or upon cleavage while bound to target, the reporter dye is no longer quenched, resulting in a detectable amount of fluorescence. The second, lower-melting primer may be annealed and extended to generate a double-stranded nucleic acid. Amplification may be monitored in real time, including each cycle, or at the end point. The asynchronous PCR thermal cycling protocol can generate a preponderance of the PCR amplicon in single-stranded form by repetition at the end of the protocol of annealing and extension of the higher melting primer.
摘要翻译：用于核酸扩增的异步热循环方案使用两种引物，其热解温度不同于约10至30℃。在较高熔点的引物退火和聚合酶介导的延伸之后，未结合的单链靶序列可能被杂交和检测通过探针。 DNA探针可能被聚合酶的外切核酸酶活性切割。探针可以是非断裂的类似物，例如PNA。当探针用报告染料和选择进行能量转移的猝灭剂标记时，例如，当探针未结合时，来自报告染料的荧光可以被有效地淬灭。当探针与互补靶物杂交时或在与靶标结合时进行切割时，报道染料不再猝灭，导致可检测量的荧光。可以将第二种较低熔点的引物退火并延伸以产生双链核酸。可以实时监测放大，包括每个周期，或在终点。异构PCR热循环方案可以在退火和延伸较高熔点引物的方案结束时通过重复生成单链形式的PCR扩增子的优势。

5. 发明申请

WO2007025281A3 A METHOD TO QUANTIFY SIRNAS, MIRNAS AND POLYMORPHIC MIRNAS 审中-公开
标题翻译：量化SIRNAS，MIRNAS和多态MIRNAS的方法
公开(公告)号：WO2007025281A3
公开(公告)日：2007-11-01
申请号：PCT/US2006033642
申请日：2006-08-24
申请人： APPLERA CORP , TAN RUOYING , CHEN CAIFU , GUEGLER KARL
发明人： TAN RUOYING , CHEN CAIFU , GUEGLER KARL
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6855 , C12Q1/6851 , C12Q2525/301 , C12Q2525/207 , C12Q2521/501 , C12Q2537/143
摘要： The present teachings provide methods, compositions, and kits for quantifying target polynucleotides. In some embodiments, a reverse stem-loop ligation probe is ligated to the 3' end of a target polynucleotide, using a ligase that can ligate the 3' end of RNA to the 5' end of DNA using a DNA template, such as T4 DNA ligase. Following digestion to form an elongated target polynucleotide with a liberated end, a reverse transcription reaction can be performed, followed by a PCR. In some embodiments, the methods of the present teachings can discriminate between polymorphic polynucleotides that vary by as little as one nucleotide.
摘要翻译：本教导提供了用于定量靶多核苷酸的方法，组合物和试剂盒。在一些实施方案中，使用连接酶将反向茎环连接探针连接至靶多核苷酸的3'末端，所述连接酶可使用DNA模板如T4将DNA的3'末端连接至DNA的5'末端 DNA连接酶。消化形成具有释放末端的延长的靶多核苷酸后，可以进行逆转录反应，然后进行PCR。在一些实施方案中，本教导的方法可以区分变化少至一个核苷酸的多态性多核苷酸。

6. 发明公开

EP1924713A4 A METHOD TO QUANTIFY SIRNAS, MIRNAS AND POLYMORPHIC MIRNAS 有权转让
标题翻译：方法的的siRNA，miRNA的miRNA和多晶型的定量分析
公开(公告)号：EP1924713A4
公开(公告)日：2009-01-14
申请号：EP06802531
申请日：2006-08-24
申请人： APPLERA CORP
发明人： TAN RUOYING , CHEN CAIFU , GUEGLER KARL
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6855 , C12Q1/6851 , C12Q2525/301 , C12Q2525/207 , C12Q2521/501 , C12Q2537/143
摘要： The present teachings provide methods, compositions, and kits for quantifying target polynucleotides. In some embodiments, a reverse stem-loop ligation probe is ligated to the 3' end of a target polynucleotide, using a ligase that can ligate the 3’ end of RNA to the 5’ end of DNA using a DNA template, such as T4 DNA ligase. Following digestion to form an elongated target polynucleotide with a liberated end, a reverse transcription reaction can be performed, followed by a PCR. In some embodiments, the methods of the present teachings can discriminate between polymorphic polynucleotides that vary by as little as one nucleotide.

7. 发明专利

DE60016947T2 未知
公开(公告)号：DE60016947T2
公开(公告)日：2005-12-15
申请号：DE60016947
申请日：2000-10-06
申请人： APPLERA CORP
发明人： EGHOLM MICHAEL , CHEN CAIFU
IPC分类号： G01N21/78 , C12N15/09 , C12Q1/68 , C07K14/00
摘要： The invention provides methods, kits, and compositions for ligation of PNA-DNA chimeric probes and oligonucleotides when they are hybridized adjacently to template nucleic acids using ligases and ligation reagents. Structural requirements of the chimeras for ligation include 5 to 15 contiguous PNA monomer units, 2 or more contiguous nucleotides, and a 3' hydroxyl or 5' hydroxyl terminus. The chimera and/or oligonucleotide may be labelled with fluorescent dyes or other labels. The methods include, for example, oligonucleotide-ligation assays (OLA) and single nucleotide polymorphism detection.

8. 发明专利

AU2003233495A1 UNIVERSAL-TAGGED OLIGONUCLEOTIDE PRIMERS AND METHODS OF USE 未知
公开(公告)号：AU2003233495A1
公开(公告)日：2003-12-02
申请号：AU2003233495
申请日：2003-05-07
申请人： APPLERA CORP
发明人： LAO KAI QIN , CHEN CAIFU , KOEHLER RYAN T , SCAFE CHARLES , SCHROTH GARY
IPC分类号： C07H21/00 , C12Q1/68
摘要： The present invention relates to universal-tagged oligonucleotide primers, and to methods of using the primers for amplifying the genome.

9. 发明专利

AU2002366947A1 METHODS FOR QUANTITATING NUCLEIC ACIDS USING COUPLED LIGATION AND AMPLIFICATION 未知
公开(公告)号：AU2002366947A1
公开(公告)日：2003-07-09
申请号：AU2002366947
申请日：2002-12-05
申请人： APPLERA CORP
发明人： SCHROTH GARY P , CHEN CAIFU , WENZ H MICHAEL
IPC分类号： C12Q1/68 , C12Q1/6844 , C12Q1/6858
摘要： The present invention relates to methods and kits for quantitating target nucleic acid sequences using coupled ligation and amplification. The invention also relates to methods, reagents, and kits that employ addressable-support specific portions.

10. 发明专利

AU6823501A Asynchronous primed pcr 未知
公开(公告)号：AU6823501A
公开(公告)日：2001-12-17
申请号：AU6823501
申请日：2001-06-06
申请人： APPLERA CORP
发明人： CHEN CAIFU , EGHOLM MICHAEL , HAFF LAWRENCE
IPC分类号： G01N33/53 , C12N15/09 , C12Q1/68 , G01N33/566

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