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    Nucleic acid analysis techniques
    1.
    发明授权
    Nucleic acid analysis techniques 失效
    核酸分析技术

    公开(公告)号：US06344316B1

    公开(公告)日：2002-02-05

    申请号：US08882649

    申请日：1997-06-25

    申请人： David J. Lockhart ,  Mark Chee ,  Kevin Gunderson ,  Lai Chaoqiang ,  Lisa Wodicka ,  Maureen T. Cronin ,  Danny Lee ,  Huu M. Tran ,  Hajime Matsuzaki

    发明人： David J. Lockhart ,  Mark Chee ,  Kevin Gunderson ,  Lai Chaoqiang ,  Lisa Wodicka ,  Maureen T. Cronin ,  Danny Lee ,  Huu M. Tran ,  Hajime Matsuzaki

    IPC分类号： C12Q168

    CPC分类号： C07H19/052 ,  C07H19/12 ,  C07H21/00 ,  C12Q1/6809 ,  C12Q1/6837 ,  C12Q2600/156 ,  C40B40/00 ,  G06F19/20 ,  G06F19/22 ,  C12Q2525/161 ,  C12Q2565/501 ,  C12Q2561/125

    摘要： The present invention provides a simplified method for identifying differences in nucleic acid abundances (e.g., expression levels) between two or more samples. The methods involve providing an array containing a large number (e.g. greater than 1,000) of arbitrarily selected different oligonucleotide probes where the sequence and location of each different probe is known. Nucleic acid samples (e.g. mRNA) from two or more samples are hybridized to the probe arrays and the pattern of hybridization is detected. Differences in the hybridization patterns between the samples indicates differences in expression of various genes between those samples. This invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves providing a nucleic acid, providing a labeled oligonucleotide and then enzymatically ligating the oligonucleotide to the nucleic acid. Thus, for example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase. In another embodiment, the end labeling can be accomplished by providing a nucleic acid, providing labeled nucleoside triphosphates, and attaching the nucleoside triphosphates to the nucleic acid using a terminal transferase.

    摘要翻译： 本发明提供用于鉴定两个或多个样品之间的核酸丰度差异（例如，表达水平）的简化方法。 所述方法包括提供包含大量（例如大于1,000个）任意选择的不同寡核苷酸探针的阵列，其中每个不同探针的序列和位置是已知的。 来自两个或更多个样品的核酸样品（例如mRNA）与探针阵列杂交，并检测杂交模式。 样本之间的杂交模式的差异表明这些样品之间各种基因的表达差异。 本发明还提供了一种终止标记核酸的方法。 在一个实施方案中，该方法包括提供核酸，提供标记的寡核苷酸，然后将寡核苷酸酶连接到核酸上。 因此，例如，当核酸是RNA时，可以使用RNA连接酶连接标记的寡核糖核苷酸。 在另一个实施方案中，末端标记可以通过提供核酸，提供标记的核苷三磷酸和使用末端转移酶将核苷三磷酸与核酸连接来实现。

    Methods of using chemical libraries to search for new kinase inhibitors
    3.
    发明授权
    Methods of using chemical libraries to search for new kinase inhibitors 失效
    使用化学文库搜索新的激酶抑制剂的方法

    公开(公告)号：US06573044B1

    公开(公告)日：2003-06-03

    申请号：US09221406

    申请日：1998-12-22

    申请人： Nathanael S. Gray ,  Peter Schultz ,  Lisa Wodicka ,  Laurent Meijer ,  David J. Lockhart

    发明人： Nathanael S. Gray ,  Peter Schultz ,  Lisa Wodicka ,  Laurent Meijer ,  David J. Lockhart

    IPC分类号： C12Q168

    CPC分类号： A61K31/52 ,  C07D473/16

    摘要： The generation of selective inhibitors for specific protein kinases would provide new tools for analyzing signal transduction pathways and possibly new therapeutic agents. We have invented an approach to the development of selective protein kinase inhibitors based on the unexpected binding mode of 2,6,9-trisubstituted purines to the ATP binding site of human CDK2. The most potent inhibitor, purvalanol B (IC50=6 nM), binds with a 30-fold greater affinity than the known CDK2 inhibitor, flavopiridol. The cellular effects of this class of compounds were examined and compared to those of flavopiridol by monitoring changes in mRNA expression levels for all genes in treated cells of Saccharomyces cerevisiae using high-density oligonucleotide probe arrays.

    摘要翻译： 产生特异性蛋白激酶的选择性抑制剂将为分析信号转导途径和可能的新治疗剂提供新的工具。 我们已经发明了一种基于26,9-三取代嘌呤到人CDK2的ATP结合位点的意想不到的结合模式来开发选择性蛋白激酶抑制剂的方法。 最有效的抑制剂，纯丙醇B（IC50 = 6nM）以比已知的CDK2抑制剂flavopiridol高30倍的亲和力结合。 通过使用高密度寡核苷酸探针阵列监测酿酒酵母的处理细胞中所有基因的mRNA表达水平的变化来检查这类化合物的细胞效应，并与黄曲妥替尔的细胞效应进行比较。

    Genotyping biallelic markers
    5.
    发明授权
    Genotyping biallelic markers 有权
    基因分型双标记

    公开(公告)号：US06638719B1

    公开(公告)日：2003-10-28

    申请号：US09603999

    申请日：2000-06-26

    申请人： Kevin Gunderson ,  David J. Lockhart

    发明人： Kevin Gunderson ,  David J. Lockhart

    IPC分类号： C12Q168

    CPC分类号： C12Q1/6837 ,  C12Q1/6827 ,  C12Q1/6858 ,  C12Q2565/501 ,  C12Q2535/131 ,  C12Q2535/125 ,  C12Q2563/107

    摘要： A method is described for determining the genotype of one or more individuals at a biallelic marker. The method employs amplification of a region of genomic DNA using color tagged, allele-specific primers and hybridization of the products to an array of allele-specific probes. The genotype is identified from the pattern of hybridization.

    摘要翻译： 描述了一种用于确定双重标记物中一个或多个个体的基因型的方法。 该方法使用彩色标记的等位基因特异性引物扩增基因组DNA区域，并将产物与等位基因特异性探针阵列进行杂交。 从杂交模式中鉴定出基因型。

    Expression monitoring by hybridization to high density oligonucleotide arrays
    7.
    发明授权
    Expression monitoring by hybridization to high density oligonucleotide arrays 失效
    通过与高密度寡核苷酸阵列杂交进行表达监测

    公开(公告)号：US06927032B2

    公开(公告)日：2005-08-09

    申请号：US10353792

    申请日：2003-01-28

    申请人： David J. Lockhart ,  Eugene L. Brown ,  Gordon G. Wong ,  Mark Chee ,  Thomas R. Gingeras

    发明人： David J. Lockhart ,  Eugene L. Brown ,  Gordon G. Wong ,  Mark Chee ,  Thomas R. Gingeras

    IPC分类号： G01N33/53 ,  C12N15/09 ,  C12Q1/68 ,  G01N15/14 ,  G01N37/00 ,  C07H21/02 ,  C07H21/04 ,  C12M1/34 ,  C12P19/34

    CPC分类号： C12Q1/6809 ,  C12Q1/6837 ,  G01N15/1475 ,  C12Q2565/507

    摘要： This invention provides methods of monitoring the expression levels of a multiplicity of genes. The methods involve hybridizing a nucleic acid sample to a high density array of oligonucleotide probes where the high density array contains oligonucleotide probes complementary to subsequences of target nucleic acids in the nucleic acid sample. In one embodiment, the method involves providing a pool of target nucleic acids comprising RNA transcripts of one or more target genes, or nucleic acids derived from the RNA transcripts, hybridizing said pool of nucleic acids to an array of oligonucleotide probes immobilized on surface, where the array comprising more than 100 different oligonucleotides and each different oligonucleotide is localized in a predetermined region of the surface, the density of the different oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2, and the olignucleotide probes are complementary to the RNA transcripts or nucleic acids derived from the RNA transcripts; and quantifying the hybridized nucleic acids in the array.

    摘要翻译： 本发明提供监测多种基因的表达水平的方法。 所述方法包括将核酸样品与寡核苷酸探针的高密度阵列杂交，其中高密度阵列含有与核酸样品中靶核酸的子序列互补的寡核苷酸探针。 在一个实施方案中，所述方法包括提供包含一个或多个靶基因的RNA转录物或衍生自RNA转录物的核酸的靶核酸库，将所述核酸库与固定在表面上的寡核苷酸探针阵列杂交，其中 包含超过100种不同寡核苷酸的阵列和每种不同的寡核苷酸被定位在表面的预定区域中，不同寡核苷酸的密度大于每1cm 2大约60个不同的寡核苷酸，并且寡核苷酸 探针与衍生自RNA转录物的RNA转录物或核酸互补; 并定量阵列中的杂交核酸。

    Methods of identifying nucleic acid probes to quantify the expression of a target nucleic acid
    10.
    发明授权
    Methods of identifying nucleic acid probes to quantify the expression of a target nucleic acid 有权
    鉴定核酸探针以量化靶核酸的表达的方法

    公开(公告)号：US06548257B2

    公开(公告)日：2003-04-15

    申请号：US09935365

    申请日：2001-08-22

    申请人： David J. Lockhart ,  Eugene L. Brown ,  Gordon G. Wong ,  Mark Chee ,  Thomas R. Gingeras

    发明人： David J. Lockhart ,  Eugene L. Brown ,  Gordon G. Wong ,  Mark Chee ,  Thomas R. Gingeras

    IPC分类号： C12Q168

    CPC分类号： C12Q1/6809 ,  C12Q1/6837 ,  G01N15/1475 ,  C12Q2565/507

    摘要： This invention provides methods of monitoring the expression levels of a multiplicity of genes. The methods involve hybridizing a nucleic acid sample to a high density array of oligonucleotide probes where the high density array contains oligonucleotide probes complementary to subsequences of target nucleic acids in the nucleic acid sample. In one embodiment, the method involves providing a pool of target nucleic acids comprising RNA transcripts of one or more target genes, or nucleic acids derived from the RNA transcripts, hybridizing said pool of nucleic acids to an array of oligonucleotide probes immobilized on surface, where the array comprising more than 100 different oligonucleotides and each different oligonucleotide is localized in a predetermined region of the surface, the density of the different oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2, and the olignucleotide probes are complementary to the RNA transcripts or nucleic acids derived from the RNA transcripts; and quantifying the hybridized nucleic acids in the array.

    摘要翻译： 本发明提供监测多种基因的表达水平的方法。 所述方法包括将核酸样品与寡核苷酸探针的高密度阵列杂交，其中高密度阵列含有与核酸样品中靶核酸的子序列互补的寡核苷酸探针。 在一个实施方案中，所述方法包括提供包含一个或多个靶基因的RNA转录物或衍生自RNA转录物的核酸的靶核酸库，将所述核酸库与固定在表面上的寡核苷酸探针阵列杂交，其中 包含超过100种不同寡核苷酸的阵列和每种不同的寡核苷酸被定位在表面的预定区域中，不同寡核苷酸的密度大于每1cm 2大约60个不同的寡核苷酸，并且寡核苷酸探针与RNA转录物互补 衍生自RNA转录物的核酸; 并定量阵列中的杂交核酸。