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1. 发明申请

WO2007011903A3 ANALYZING MESSENGER RNA AND MICRO RNA IN THE SAME REACTION MIXTURE 审中-公开
标题翻译：在同一反应混合物中分析信使RNA和微RNA
公开(公告)号：WO2007011903A3
公开(公告)日：2007-07-12
申请号：PCT/US2006027757
申请日：2006-07-17
申请人： APPLERA CORP , LAO KAI QIN , STRAUS NEIL A
发明人： LAO KAI QIN , STRAUS NEIL A
IPC分类号： C12P19/34 , C07K17/00
CPC分类号： C12Q1/686 , C12Q1/6809 , C12Q1/6844 , C12Q1/6848 , C12Q1/6853 , C12Q2549/101 , C12Q2537/143 , C12Q2527/107 , C12Q2525/301 , C12Q2525/207 , C12Q2533/101
摘要： The present teachings provide methods, compositions, and kits for performing primer extension reactions on at least two target polynucleotides in the same reaction mixture. In some embodiments, a reverse transcription reaction is performed on a first target polynucleotide with a hot start primer comprising a self-complementary stem and a loop, and extension products form at high temperatures but extension products form less so at low temperatures since the self-complementary stem of the hot start primer prevents hybridization of the target specific region to the target. However, non-hot start primers with free target specific regions can hybridize to their corresponding targets at the low temperature and extension can happen at the low temperature.
摘要翻译：本教导提供了用于在相同反应混合物中对至少两个靶多核苷酸进行引物延伸反应的方法，组合物和试剂盒。在一些实施方案中，用包含自身互补茎和环的热启动引物对第一靶多核苷酸进行逆转录反应，并且在高温下形成延伸产物，但延伸产物在低温下形成较少，热启动引物的互补茎阻止靶特异性区域与靶标杂交。然而，具有游离靶标特异性区域的非热启动引物可以在低温下与其相应的靶标杂交并且可以在低温下延伸。

2. 发明申请

WO2011123246A3 SOLID-PHASE CLONAL AMPLIFICATION AND RELATED METHODS 审中-公开
标题翻译：固相放大和相关方法
公开(公告)号：WO2011123246A3
公开(公告)日：2013-05-30
申请号：PCT/US2011028644
申请日：2011-03-16
申请人： ILLUMINA INC , STRAUS NEIL A , SHENGRONG LIN , ELTHOUKHY HELMY A , GUNDERSON KEVIN
发明人： STRAUS NEIL A , SHENGRONG LIN , ELTHOUKHY HELMY A , GUNDERSON KEVIN
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q1/6834 , C12Q1/6837 , C12Q2531/125 , C12Q2563/149
摘要： The present invention provides methods and compositions for analyzing nucleic acid sequences. In some aspects, the methods utilize clonal objects, such as DNA balls, that have been captured on beads. Using the methods described here, compositions are fabricated wherein a bead and one clonal object are affinity bound or hybridized to each other through an affinity binding patch or hybridization patch on the surface of the bead. The invention also provides a population of beads having affinity bound or hybridized clonal objects at a ratio of 1:1. The invention additionally provides methods for amplifying a target nucleic acid molecule utilizing the compositions described herein.
摘要翻译：本发明提供了用于分析核酸序列的方法和组合物。在某些方面，该方法利用已被捕获在珠上的克隆物体，例如DNA球。使用本文描述的方法，制备组合物，其中珠粒和一个克隆物体通过珠粒表面上的亲和结合片段或杂交片段彼此亲和地结合或杂交。本发明还提供了以1:1的比例具有亲和结合或杂交的克隆物体的珠群。本发明另外提供了利用本文所述组合物扩增靶核酸分子的方法。

3. 发明申请

WO2006115570A3 SMALL NUCLEIC ACID DETECTION PROBES AND USES THEREOF 审中-公开
标题翻译：小核酸检测探针及其用途
公开(公告)号：WO2006115570A3
公开(公告)日：2007-11-01
申请号：PCT/US2006005828
申请日：2006-02-17
申请人： APPLERA CORP , LAO KAI QIN , STRAUS NEIL A
发明人： LAO KAI QIN , STRAUS NEIL A
IPC分类号： C12Q1/68 , C07H21/02
CPC分类号： C12Q1/6818 , C12Q2563/173 , C12Q2545/114 , C12Q2525/301
摘要： The present teachings are directed to compositions, methods, and kits for detecting and quantitating small nucleic acid molecules, including small DNA molecules and small RNA molecules. The detector probes of the current teachings, including single-loop detector probes, double-loop detector probes, and bimolecular detector probes, are designed to selectively hybridize with a corresponding small nucleic acid target and to produce, under appropriate conditions, a detectable signal or a detectably different signal. The detector complexes of the current teachings comprise a detector probe comprising a first reporter group and a displaceable sequence comprising a second reporter group, wherein the displaceable sequence is hybridized to the detector probe. According to certain methods, detecting a small nucleic acid target comprises the target displacing the displaceable sequence of a detector complex to form a detector probe-small nucleic acid target duplex, illuminating the duplex with light of an appropriate wavelength, and determining the presence of a detectable fluorescent signal or the change in a detectable signal.
摘要翻译：本教导涉及用于检测和定量小核酸分子（包括小DNA分子和小RNA分子）的组合物，方法和试剂盒。目前的教导的检测器探针，包括单环检测器探针，双环检测器探针和双分子检测器探针被设计为与相应的小核酸靶选择性杂交，并在适当条件下产生可检测信号或一个可检测的不同信号。本教导的检测器复合物包括检测器探针，其包括第一报告基团和包含第二报告基团的可置换序列，其中可移位序列与检测器探针杂交。根据某些方法，检测小核酸靶包括靶取代检测器复合物的可置换序列以形成检测器探针 - 小核酸靶双链体，用合适波长的光照亮双链体，并确定可检测的荧光信号或可检测信号的变化。

4. 发明申请

WO2007044066A2 METHODS FOR NORMALIZING AND FOR IDENTIFYING SMALL NUCLEIC ACIDS 审中-公开
标题翻译：用于正常化和鉴定小核酸的方法
公开(公告)号：WO2007044066A2
公开(公告)日：2007-04-19
申请号：PCT/US2006/012025
申请日：2006-03-29
申请人： APPLERA CORPORATION , LAO, Kai Qin , STRAUS, Neil, A. , BURNS, John, W.
发明人： LAO, Kai Qin , STRAUS, Neil, A. , BURNS, John, W.
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6855 , C12Q1/6851 , C12Q2535/138 , C12Q2525/121 , C12Q2525/301
摘要： The present teachings are generally directed to methods for normalizing at least one species of small nucleic acid that is present in a population of small nucleic acid species, wherein the relative concentration of at least one small nucleic acid species is substantially greater than the relative concentration of at least one other small nucleic acid species in the population. At least one small nucleic acid species is normalized using a multiplicity of primers comprising degenerate sequences. In some embodiments, a small nucleic acid species is identified by inserting at least part of an extension product from a normalized population into a vector and subsequently sequencing the insert. In some embodiments, a small nucleic acid species is identified by determining the sequence of at least part of an extension product.
摘要翻译：本教导通常涉及用于归一化存在于小核酸物种群中的至少一种小核酸的方法，其中至少一种小核酸物质的相对浓度基本上大于群体中至少一种其他小核酸物种。使用包含简并序列的多个引物将至少一个小核酸物质归一化。在一些实施方案中，通过将来自标准化群体的至少部分延伸产物插入载体并随后对插入物进行测序来鉴定小核酸物种。在一些实施方案中，通过确定延伸产物的至少一部分的序列来鉴定小核酸物种。

5. 发明申请

WO2006065597A3 ID-TAG COMPLEXES, ARRAYS, AND METHODS OF USE THEREOF 审中-公开
标题翻译： ID-TAG复合物，阵列及其使用方法
公开(公告)号：WO2006065597A3
公开(公告)日：2006-07-27
申请号：PCT/US2005044269
申请日：2005-12-06
申请人： APPLERA CORP , SCHROTH GARY P , LAO KAI QIN , STRAUS NEIL A
发明人： SCHROTH GARY P , LAO KAI QIN , STRAUS NEIL A
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6823 , C12Q1/6816 , C12Q2565/519 , C12Q2537/1373 , C12Q2537/125 , C12Q2565/501 , C12Q2563/131 , C12Q2525/197 , C12Q2563/185
摘要： The present invention relates to the detection of target sequences. Detection can be achieved through the use of ID-tag complexes. These ID-tag complexes are relatively stable in the absence of a target sequence. In the presence of a target sequence, the complexes dissociate and form new complexes or duplexes, which can be purified or eliminated and detected on an ID-tag system.
摘要翻译：本发明涉及靶序列的检测。检测可以通过使用ID-标签复合物来实现。这些ID-标签复合物在不存在靶序列的情况下相对稳定。在靶序列的存在下，复合物解离并形成新的复合物或双链体，其可以在ID-标签系统上纯化或消除并检测。

6. 发明申请

WO2006016978A1 ANALOG PROBE COMPLEXES 审中-公开
标题翻译：模拟探头复合器
公开(公告)号：WO2006016978A1
公开(公告)日：2006-02-16
申请号：PCT/US2005/021906
申请日：2005-06-21
申请人： APPLERA CORPORATION , LAO, Kai, Qin , GEISER, Timothy, G. , STRAUS, Neil, A.
发明人： LAO, Kai, Qin , GEISER, Timothy, G. , STRAUS, Neil, A.
IPC分类号： C12Q1/68
CPC分类号： B82Y10/00 , B82Y5/00 , C12Q1/6832 , C12Q1/6876 , C12Q2525/101
摘要： The present invention relates to the detection of target sequences. The present description discloses compositions and methods involving analog nucleic acids, such as PNA and L-DNA, for the detection of nucleic acids. Additionally, hybrid detectable markers are provided.
摘要翻译：本发明涉及靶序列的检测。本说明书公开了涉及用于检测核酸的类似核酸如PNA和L-DNA的组合物和方法。另外，提供了杂交可检测标记。

7. 发明申请

WO2011123246A2 SOLID-PHASE CLONAL AMPLIFICATION AND RELATED METHODS 审中-公开
标题翻译：固相放大和相关方法
公开(公告)号：WO2011123246A2
公开(公告)日：2011-10-06
申请号：PCT/US2011/028644
申请日：2011-03-16
申请人： ILLUMINA, INC. , STRAUS, Neil, A. , SHENGRONG, Lin , ELTHOUKHY, Helmy, A. , GUNDERSON, Kevin
发明人： STRAUS, Neil, A. , SHENGRONG, Lin , ELTHOUKHY, Helmy, A. , GUNDERSON, Kevin
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q1/6834 , C12Q1/6837 , C12Q2531/125 , C12Q2563/149
摘要： The present invention provides methods and compositions for analyzing nucleic acid sequences. In some aspects, the methods utilize clonal objects, such as DNA balls, that have been captured on beads. Using the methods described here, compositions are fabricated wherein a bead and one clonal object are affinity bound or hybridized to each other through an affinity binding patch or hybridization patch on the surface of the bead. The invention also provides a population of beads having affinity bound or hybridized clonal objects at a ratio of 1:1. The invention additionally provides methods for amplifying a target nucleic acid molecule utilizing the compositions described herein.
摘要翻译：本发明提供了用于分析核酸序列的方法和组合物。在某些方面，该方法利用已被捕获在珠上的克隆物体，例如DNA球。使用本文描述的方法，制备组合物，其中珠粒和一个克隆物体通过珠粒表面上的亲和结合片段或杂交片段彼此亲和地结合或杂交。本发明还提供了以1:1的比例具有亲和结合或杂交的克隆物体的珠群。本发明另外提供了利用本文所述组合物扩增靶核酸分子的方法。

8. 发明申请

WO2008076842A2 SEQUENCING METHODS 审中-公开
标题翻译：测序方法
公开(公告)号：WO2008076842A2
公开(公告)日：2008-06-26
申请号：PCT/US2007/087472
申请日：2007-12-13
申请人： APPLERA CORPORATION , LAO, Kai, Qin , STRAUS, Neil, A.
发明人： LAO, Kai, Qin , STRAUS, Neil, A.
IPC分类号： C12P19/34
CPC分类号： C12Q1/6872 , C12Q2537/143 , C12Q2535/101
摘要： The present teachings provide methods and compositions for sequencing one or more target nucleic acids. High levels of multiplexing are provided by the use of an emulsion PCR comprising primer-immobilized beads. The resulting reaction products can be sequenced by any of a variety of mobility-dependent analytical techniques, such as mass spectrometry. In some embodiments, a first collection of amplification products on a first collection of beads are transferred to a second collection of beads. In some embodiments, a first collection of amplification products on a first collection of beads is amplified in a rolling circle amplification reaction. The present teachings also provide compositions, kits, and devices for performing and sequencing the products of the emulsion amplification reactions as described herein.
摘要翻译：本教导提供了用于对一个或多个靶核酸进行测序的方法和组合物。通过使用包含引物固定珠的乳液PCR提供高水平的多重化。所得到的反应产物可以通过多种依赖于迁移率的分析技术中的任何一种进行测序，例如质谱法。在一些实施方案中，将第一批珠子上的扩增产物的第一批收集物转移至第二批珠子中。在一些实施方案中，第一批珠子上的第一批扩增产物在滚环扩增反应中扩增。本教导还提供了用于执行和测序如本文所述的乳液扩增反应产物的组合物，试剂盒和装置。

9. 发明申请

WO2007117256A1 MULTIPLEXED AMPLIFICATION OF SHORT NUCLEIC ACIDS 审中-公开
标题翻译：短期核酸的多重放大
公开(公告)号：WO2007117256A1
公开(公告)日：2007-10-18
申请号：PCT/US2006/021172
申请日：2006-05-31
申请人： APPLERA CORPORATION , LAO, Kai Qin , LIVAK, Kenneth, J. , STRAUS, Neil, A.
发明人： LAO, Kai Qin , LIVAK, Kenneth, J. , STRAUS, Neil, A.
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12N15/1065 , C12Q1/6851 , C12Q1/686 , C12Q2525/301 , C12Q2525/161 , C12Q2563/179 , C12Q2537/143 , C12Q2525/207
摘要： The present teachings provide methods, compositions, and kits for reverse transcribing and amplifying small nucleic acids such as micro RNAs. High levels of multiplexing are provided by the use of a zip-coded stem-loop reverse transcription primer, along with a PCR- based pre-amplification reaction that comprises a zip-coded forward primer. Detector probes in downstream decoding PCRs can take advantage of the zip-code introduced by the stem-loop reverse transcription primer. In some embodiments, further amplification is achieved by cycling the reverse transcription reaction. The present teachings also provide compositions and kits useful for performing the reverse transcription and amplification reactions described herein.
摘要翻译：本教导提供用于逆转录和扩增小核酸如微RNA的方法，组合物和试剂盒。通过使用zip编码的茎环逆转录引物以及包含经翻译的正向引物的基于PCR的预扩增反应提供了高水平的复用。下游解码PCR中的检测器探针可以利用茎环逆转录引物引入的zip码。在一些实施方案中，通过循环逆转录反应来实现进一步的扩增。本教导还提供可用于进行本文所述的逆转录和扩增反应的组合物和试剂盒。

10. 发明申请

WO2006115570A2 SMALL NUCLEIC ACID DETECTION PROBES AND USES THEREOF 审中-公开
标题翻译：小核酸检测探针及其用途
公开(公告)号：WO2006115570A2
公开(公告)日：2006-11-02
申请号：PCT/US2006/005828
申请日：2006-02-17
申请人： APPLERA CORPORATION , LAO, Kai Qin , STRAUS, Neil A.
发明人： LAO, Kai Qin , STRAUS, Neil A.
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6818 , C12Q2563/173 , C12Q2545/114 , C12Q2525/301
摘要： The present teachings are directed to compositions, methods, and kits for detecting and quantitating small nucleic acid molecules, including small DNA molecules and small RNA molecules. The detector probes of the current teachings, including single-loop detector probes, double-loop detector probes, and bimolecular detector probes, are designed to selectively hybridize with a corresponding small nucleic acid target and to produce, under appropriate conditions, a detectable signal or a detectably different signal. The detector complexes of the current teachings comprise a detector probe comprising a first reporter group and a displaceable sequence comprising a second reporter group, wherein the displaceable sequence is hybridized to the detector probe. According to certain methods, detecting a small nucleic acid target comprises the target displacing the displaceable sequence of a detector complex to form a detector probe-small nucleic acid target duplex, illuminating the duplex with light of an appropriate wavelength, and determining the presence of a detectable fluorescent signal or the change in a detectable signal.
摘要翻译：本教导涉及用于检测和定量小核酸分子（包括小DNA分子和小RNA分子）的组合物，方法和试剂盒。目前的教导的检测器探针，包括单环检测器探针，双环检测器探针和双分子检测器探针被设计为与相应的小核酸靶选择性杂交，并在适当的条件下产生可检测的信号或一个可检测的不同信号。本教导的检测器复合物包括检测器探针，其包括第一报告基团和包含第二报告基团的可置换序列，其中可移位序列与检测器探针杂交。根据某些方法，检测小核酸靶包括靶取代检测器复合物的可置换序列以形成检测器探针 - 小核酸靶双链体，用合适波长的光照亮双链体，并确定可检测的荧光信号或可检测信号的变化。

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