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    Labeling and non-enzymatic fragmentation of cDNA using a ribonucleoside triphosphate analog
    1.
    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。

    Detection of polynucleotides on nucleic acid arrays using azido-modified triphosphate nucleotide analogs
    3.
    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。

    Nucleic acid labeling methods
    4.
    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.

    Preparation and labeling of polynucleotides for hybridization to a nucleic acid array
    8.
    发明申请
    Preparation and labeling of polynucleotides for hybridization to a nucleic acid array 审中-公开
    用于与核酸阵列杂交的多核苷酸的制备和标记

    公开(公告)号：US20060147966A1

    公开(公告)日：2006-07-06

    申请号：US11314034

    申请日：2005-12-20

    申请人： Anthony Barone ,  Glenn McGall

    发明人： Anthony Barone ,  Glenn McGall

    IPC分类号： C12Q1/68 ,  C07H21/04

    CPC分类号： C12Q1/6806 ,  C12Q1/6846 ,  C12Q2525/119 ,  C12Q2525/101 ,  C12Q2523/319

    摘要： In accordance with the present invention, method are presented for labeling a cDNA strand with a photochemical cleavable reagent which upon exposure to electromagnetic radiation of particular reagent to create abasic DNA sites. According to one aspect of the present invention, DNA at the abasic sites, also known a chemical lactone group, is cleaved with an endonuclease, for example an endonuclease IV, which cleaves the DNA and leaves a free 3′ OH group. This free 3′ OH group is then labeled with a terminal transferase to provide a detectable moiety. In accordance with a preferred aspect of the present invention,

    摘要翻译： 根据本发明，提供了用光化学可切割试剂标记cDNA链的方法，其在暴露于特定试剂的电磁辐射以产生脱碱基DNA位点时。 根据本发明的一个方面，在脱碱基位点上也称为化学内酯基团的DNA用内切核酸酶例如内切核酸酶IV切割，其切割DNA并留下游离的3'OH基团。 然后用末端转移酶标记该游离的3'OH基团以提供可检测的部分。 根据本发明的优选方面，

    Methods for fragmenting DNA
    9.
    发明申请
    Methods for fragmenting DNA 审中-公开
    DNA片段化方法

    公开(公告)号：US20050191682A1

    公开(公告)日：2005-09-01

    申请号：US11061954

    申请日：2005-02-17

    申请人： Anthony Barone ,  Glenn McGall ,  Chuan Chen

    发明人： Anthony Barone ,  Glenn McGall ,  Chuan Chen

    IPC分类号： C12P19/34 ,  C12Q1/68

    CPC分类号： C12Q1/6806 ,  C12Q2600/156 ,  C12Q2600/158 ,  C12Q2525/119 ,  C12Q2521/301 ,  C12Q2523/107

    摘要： Methods for fragmenting and labeling nucleic acids for hybridization analysis are disclosed. In one aspect of the invention, methods and compositions are provided for fragmenting nucleic acid samples by exposure to acidic conditions to generate abasic positions and then cleavage of the abasic sites by, for example, an apurinic/apyrimidinic endonuclease. The resulting fragments may be end labeled and analyzed by hybridization to an array of nucleic acid probes.

    摘要翻译： 公开了用于杂交分析的用于片段化和标记核酸的方法。 在本发明的一个方面，提供了方法和组合物，用于通过暴露于酸性条件来分解核酸样品以产生脱碱基位置，然后通过例如无嘌呤/脱嘧啶核苷酸内切酶裂解无碱基位点。 所得到的片段可以是末端标记的，并通过与核酸探针阵列的杂交进行分析。

    Compounds and methods for post incorporation labeling of nucleic acids
    10.
    发明申请
    Compounds and methods for post incorporation labeling of nucleic acids 审中-公开
    用于后缀合标记核酸的化合物和方法

    公开(公告)号：US20050064479A1

    公开(公告)日：2005-03-24

    申请号：US10916849

    申请日：2004-08-12

    申请人： Glenn McGall ,  Anthony Barone

    发明人： Glenn McGall ,  Anthony Barone

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

    CPC分类号： C12P19/34 ,  C07H21/04

    摘要： Methods are provided for post incorporation labeling of a nucleic acid, including for example cRNA, labeled with nucleotide analogs having a formula selected from the group consisting of wherein A is H or a functional group that permits the attachment of the nucleic acid labeling compound to a nucleic acid; Y and Z are independently H or OH; L is linker group; and P is a connecting group. After incorporation of the nucleic acid (including cRNA) with the above nucleotide analogs, the nucleic acid is labeled with a detectable group reagent wherein said detetable group reagent comprises a chemical moiety which is capable of specifically reacting with said P group to allow coupling of the detectable group to said primed cRNA. Compounds comprising nucleotide analogs are also presented in accordance with the present invention. Methods are also presented for incorporating these compounds into nucleic acids and subsequently labeling the incorporated nucleotide analog with detectable moiety reagent.

    摘要翻译： 提供了用于后缀合标记核酸的方法，包括例如用具有选自以下的式的核苷酸类似物的cRNA标记：其中A是H或允许核酸标记化合物与 核酸; Y和Z独立地为H或OH; L是连接基团; P是连接组。 在将核酸（包括cRNA）与上述核苷酸类似物并入后，用可检测组试剂标记核酸，其中所述可检测组试剂包含能够与所述P基团特异性反应的化学部分，以允许 可检测的组与所述引发的cRNA。 包含核苷酸类似物的化合物也是根据本发明提出的。 还提出了将这些化合物并入核酸中并随后用可检测部分试剂标记掺入的核苷酸类似物的方法。