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    Detection of polynucleotides on nucleic acid arrays using azido-modified triphosphate nucleotide analogs
    1.
    发明申请
    Detection of polynucleotides on nucleic acid arrays using azido-modified triphosphate nucleotide analogs 审中-公开
    使用叠氮基修饰的三磷酸核苷酸类似物检测核酸阵列上的多核苷酸

    公开(公告)号：US20060147963A1

    公开(公告)日：2006-07-06

    申请号：US11313480

    申请日：2005-12-20

    申请人： Anthony Barone ,  Handong Li ,  Glenn McGall

    发明人： Anthony Barone ,  Handong Li ,  Glenn McGall

    IPC分类号： C12Q1/68

    CPC分类号： C12Q1/6816 ,  C12N15/1096 ,  C12Q1/6806 ,  C12Q1/6837 ,  C12Q2600/158 ,  C12Q2525/113 ,  C12Q2565/501 ,  C12Q2521/107 ,  C12Q2525/143 ,  C12Q2525/117

    摘要： Methods are provided for detecting hybridization of a polynucleotide to a nucleic acid array by chemically modifying the polynucleotide to contain a detectable label. According to one aspect of the present invention, a method is provided for detecting the presence of a mRNA in a nucleic acid sample, the method having the steps of providing a mRNA sample and azido modified nucleotides, hybridizing a primer to the mRNA, reversed transcribing the mRNA to provide azido modified DNA, followed by reacting the azido groups with a detectable label, hybridizing the labeled RNA to a nucleic acid array and detecting the presence of the mRNA. Still other methods are provided for detecting the presence or absence of a polynucleotide of interest on a nucleic acid array, the method having the steps of providing a nucleic acid sample comprising a polynucleotide; providing an enzyme to amplify the polynucleotide using an azido nucleotide derivative; amplifying said polynucleotide to provide azido labeled amplified nucleic acids; reacting the azido groups on said nucleic acids with a detectable label to provide labeled nucleic acids; hybridizing said amplified nucleic acids to a nucleic acid array; and detecting the presence or absence of said polynucleotide. Still other methods are presented for detecting polynucleotides on a nucleic acid array using ligases and terminal transferases to end label polynucleotides.

    摘要翻译： 提供了通过化学修饰多核苷酸以含有可检测标记物来检测多核苷酸与核酸阵列的杂交的方法。 根据本发明的一个方面，提供了一种用于检测核酸样品中mRNA的存在的方法，该方法具有以下步骤：提供mRNA样品和叠氮基修饰的核苷酸，将引物与mRNA杂交，逆转录 mRNA以提供叠氮基修饰的DNA，然后使叠氮基与可检测标记反应，将标记的RNA与核酸阵列杂交并检测mRNA的存在。 还提供了用于在核酸阵列上检测感兴趣的多核苷酸的存在或不存在的其它方法，所述方法具有提供包含多核苷酸的核酸样品的步骤; 提供使用叠氮基核苷酸衍生物扩增多核苷酸的酶; 扩增所述多核苷酸以提供叠氮基标记的扩增核酸; 使所述核酸上的叠氮基与可检测标记物反应以提供标记的核酸; 将所述扩增的核酸与核酸阵列杂交; 并检测所述多核苷酸的存在或不存在。 还提出了使用连接酶和末端转移酶终止标记多核苷酸检测核酸阵列上的多核苷酸的其它方法。

    Methods and compositions for monitoring polymer array synthesis
    2.
    发明申请
    Methods and compositions for monitoring polymer array synthesis 审中-公开
    监测聚合物阵列合成的方法和组成

    公开(公告)号：US20060147985A1

    公开(公告)日：2006-07-06

    申请号：US11369628

    申请日：2006-03-07

    申请人： Anthony Barone ,  Glenn McGall ,  Evelyn Chai ,  Nam Ngo

    发明人： Anthony Barone ,  Glenn McGall ,  Evelyn Chai ,  Nam Ngo

    IPC分类号： C40B40/08 ,  C12Q1/68 ,  C07H21/04

    CPC分类号： G01N33/54366 ,  C07H21/04 ,  C12Q1/6837 ,  C12Q2565/137 ,  C12Q2545/114 ,  C12Q2523/107

    摘要： VLSIPS™ manufacturing processes are of increasing commercial importance. The present invention provides methods and compositions for monitoring the efficiency and quality of polymer synthesis in VLSIPS™ arrays. Methods for monitoring polymer synthesis in an array on a substrate are provided. Mono-isomeric labels for the labeling of synthetic polymer arrays are provided. Methods and compositions for post-synthetically labeling polymers in polymer arrays are also provided.

    摘要翻译： VLSIPS（TM）制造工艺在商业上的重要性日益增加。 本发明提供了用于监测VLSIPS TM阵列中聚合物合成的效率和质量的方法和组合物。 提供了在基板上阵列中监测聚合物合成的方法。 提供了用于标记合成聚合物阵列的单异构体标记。 还提供了聚合物阵列中后合成标记聚合物的方法和组合物。

    Nucleic acid analysis techniques
    4.
    发明申请
    Nucleic acid analysis techniques 审中-公开
    核酸分析技术

    公开(公告)号：US20050191646A1

    公开(公告)日：2005-09-01

    申请号：US10961341

    申请日：2004-10-07

    申请人： David Lockhart ,  Mark Chee ,  Kevin Gunderson ,  Lai Chaoqiang ,  Lisa Wodicka ,  Maureen Cronin ,  Danny Lee ,  Huu Tran ,  Hajime Matsuzaki ,  Glenn McGall ,  Anthony Barone

    发明人： David Lockhart ,  Mark Chee ,  Kevin Gunderson ,  Lai Chaoqiang ,  Lisa Wodicka ,  Maureen Cronin ,  Danny Lee ,  Huu Tran ,  Hajime Matsuzaki ,  Glenn McGall ,  Anthony Barone

    IPC分类号： C07B61/00 ,  C07H19/052 ,  C07H19/12 ,  C07H21/00 ,  C12Q1/00 ,  C12Q1/68

    CPC分类号： C07H19/052 ,  C07H19/12 ,  C07H21/00 ,  C12Q1/6809 ,  C12Q1/6837 ,  C12Q2600/156 ,  C40B40/00 ,  G16B25/00 ,  G16B30/00 ,  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。

    Nucleic acid labeling compounds
    6.
    发明申请
    Nucleic acid labeling compounds 有权
    核酸标记化合物

    公开(公告)号：US20050003496A1

    公开(公告)日：2005-01-06

    申请号：US10745916

    申请日：2003-12-23

    申请人： Glenn McGall ,  Anthony Barone ,  Handong Li

    发明人： Glenn McGall ,  Anthony Barone ,  Handong Li

    IPC分类号： C12P17/00 ,  C07

    CPC分类号： C12P17/00

    摘要： Nucleic acid labeling compounds containing heterocyclic derivatives are disclosed. Methods for making such heterocyclic compounds are also disclosed. The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.

    摘要翻译： 公开了含有杂环衍生物的核酸标记化合物。 还公开了制备这种杂环化合物的方法。 标记化合物适合于在末端或内部酶促附着于核酸，以提供核酸检测机制。

    Labeling and non-enzymatic fragmentation of cDNA using a ribonucleoside triphosphate analog
    7.
    发明申请
    Labeling and non-enzymatic fragmentation of cDNA using a ribonucleoside triphosphate analog 审中-公开
    使用核糖核苷三磷酸酯类似物进行cDNA的标记和非酶切片段化

    公开(公告)号：US20070154894A1

    公开(公告)日：2007-07-05

    申请号：US11323068

    申请日：2005-12-30

    申请人： Glenn McGall ,  Handong Li ,  Anthony Barone

    发明人： Glenn McGall ,  Handong Li ,  Anthony Barone

    IPC分类号： C12Q1/68 ,  C12P19/34 ,  C07H21/04

    CPC分类号： C12N15/1096 ,  C12Q1/6806 ,  C12Q2523/107

    摘要： In accordance with the present invention, methods are presented for labeling a cDNA strand with a labeled ribonucleotide base precursor which upon exposure to Mg2+, heat and base cleaves the cDNA at each place of incorporation of an RNA. In accordance with an aspect of the present invention, compounds selected from the group consisting of are incorporated into the growing strand of a cDNA by a reverse transcriptase or a mutant reverse transcriptase. After subject the strands to Mg2+, base and heat, the 3′ OH causes cleavage of the cDNA leaving a 2′OH phosphate with a biotin label. The biotin provides a label which may be bound to streptavidin and thereafter hybridized to a nucleic acid array.

    摘要翻译： 根据本发明，提供了用标记的核糖核苷酸碱基前体标记cDNA链的方法，其在暴露于Mg 2+时，加热和碱基在每个引入RNA的位置切割cDNA。 根据本发明的一个方面，选自组合的化合物通过逆转录酶或突变逆转录酶掺入cDNA的生长链中。 在将基因经过碱基和加热后，3'OH引起用生物素标记物离开2'OH磷酸酯的cDNA的切割。 生物素提供可以与链霉抗生物素蛋白结合的标记，然后与核酸阵列杂交。

    Nucleic acid labeling methods
    9.
    发明申请
    Nucleic acid labeling methods 有权

    公开(公告)号：US20060160096A1

    公开(公告)日：2006-07-20

    申请号：US10983046

    申请日：2004-11-04

    申请人： Kyle Cole ,  Vivi Truong ,  Glenn McGall ,  Anthony Barone

    发明人： Kyle Cole ,  Vivi Truong ,  Glenn McGall ,  Anthony Barone

    IPC分类号： C12Q1/68 ,  C12P19/34

    CPC分类号： C07H19/20 ,  C07H19/10 ,  C07H21/00

    摘要： In one aspect of the invention, a method is provided for end-labeling RNA (total RNA, mRNA, cRNA or fragmented RNA). In one aspect of the present invention, T4 RNA ligase is used to attach a 3′-labeled AMP or CMP donor to an RNA acceptor molecule. In another embodiment, a pyrophosphate molecule 3′-AppN-3′-linker-detectable moiety is used as donor molecule. In another aspect of the present invention, a method of detecting the presence of an RNA of interest in a sample is provided, the method having the following steps: providing the sample comprising RNA which may or may not have said RNA of interest; treating the sample with a fragmenting reagent to provide RNA fragments; removing phosphate groups from said fragments to provide fragments with free 3′ OH groups; ligating said fragment with a labeling reagent according to the instant invention; providing a nucleic acid array having probes directed to said RNA of interest; hybridizing the labeled nucleic acid fragments to said nucleic acid array; and determining the extent of hybridization to said probes to determine the presence of said RNA of interest.