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    Nucleic Acid Proximity Assay Involving the Formation of a Three-way junction
    1.
    发明申请
    Nucleic Acid Proximity Assay Involving the Formation of a Three-way junction 审中-公开
    涉及形成三向连接点的核酸接近度测定

    公开(公告)号：US20140212869A1

    公开(公告)日：2014-07-31

    申请号：US13750810

    申请日：2013-01-25

    Applicant: AGILENT TECHNOLOGIES, INC.

    Inventor： Nicholas M. Sampas ,  Robert A. Ach ,  Nazumi Alice Yamada ,  Kristin Bernick

    IPC: C12Q1/68

    CPC classification number: C12Q1/6818 ,  C12Q2522/101 ,  C12Q2525/161 ,  C12Q2565/101 ,  C12Q2525/301 ,  C12Q2561/125

    Abstract: Provided herein is a proximity assay that, in certain embodiments, involves: (a) hybridizing a first oligonucleotide and a second oligonucleotide with a target nucleic acid, wherein the first oligonucleotide comprises: i. a region that is complementary to a first sequence in the target nucleic acid and ii. a barcode sequence; and the second oligonucleotide comprises i. a region that is complementary to a second region in the target and ii. the complement of the barcode sequence; and (b) detecting hybridization between the barcode sequence and the complement of the barcode sequence, wherein hybridization between the barcode sequence and the complement of the barcode sequence indicates that the first and second target sequences are proximal to one another in the sample.

    Abstract translation: 本文提供了在某些实施方案中的邻近测定法，其包括：（a）将第一寡核苷酸和第二寡核苷酸与靶核酸杂交，其中所述第一寡核苷酸包含： 与靶核酸中的第一序列互补的区域，和ii。 条形码序列; 并且第二寡核苷酸包括i。 与目标中的第二区域互补的区域，以及ii。 条形码序列的补码; 和（b）检测条形码序列与条形码序列的互补之间的杂交，其中条形码序列与条形码序列的互补之间的杂交表明第一和第二靶序列在样本中彼此靠近。

    NUCLEIC ACID ENRICHMENT USING CAS9
    3.
    发明申请
    NUCLEIC ACID ENRICHMENT USING CAS9 审中-公开

    公开(公告)号：US20170107560A1

    公开(公告)日：2017-04-20

    申请号：US15335139

    申请日：2016-10-26

    Applicant: Agilent Technologies, Inc.

    Inventor： Brian Jon Peter ,  Robert A. Ach

    IPC: C12Q1/68 ,  C12N9/22

    CPC classification number: C12Q1/6806 ,  C12N9/22 ,  C12N15/1003 ,  C12N15/1034 ,  C12Q1/6869 ,  C12Y301/00 ,  Y10T436/143333

    Abstract: A method of enriching for a fragment of a genome, as well as corresponding compositions and kits, are provided. In certain embodiments, the method comprises: (a) contacting a sample comprising fragmented DNA with a Cas9-gRNA complex comprising mutant Cas9 protein that has inactivated nuclease activity and a Cas9-associated guide RNA that is complementary to a site in the DNA, to produce a Cas9-fragment complex that comprises a fragment of the fragmented DNA; and (b) isolating the complex. In addition, other methods and compositions for Cas9/CRISPR-mediated nucleic acid manipulation are also provided.

    HAIRPIN-MEDIATED AMPLIFICATION METHOD
    5.
    发明申请
    HAIRPIN-MEDIATED AMPLIFICATION METHOD 审中-公开

    公开(公告)号：US20180073068A1

    公开(公告)日：2018-03-15

    申请号：US15692215

    申请日：2017-08-31

    Applicant: Agilent Technologies, Inc.

    Inventor： Brian Jon Peter ,  Robert A. Ach

    IPC: C12Q1/68

    CPC classification number: C12Q1/6853 ,  C12Q1/6806 ,  C12Q2521/501 ,  C12Q2525/151 ,  C12Q2525/301

    Abstract: In some embodiments, the amplification method may comprise producing a reaction mix comprising: a nucleic acid sample, a polymerase, nucleotides, a forward primer that hybridizes to a sequence in the bottom strand of a fragment in the sample, and a reverse primer. The reverse primer has a hairpin structure comprising a loop, a stem and a 3′ overhang of at least 8 nucleotides, wherein the 3′ overhang hybridizes to a sequence in the top strand of the fragment. Subjecting the reaction mix at least two rounds of denaturation, renaturation and primer extension conditions results in extension the forward and reverse primers to produce an amplification product that contains: a double stranded region comprising a nick adjacent to the 5′ end of the reverse primer, and the loop of the first hairpin primer. Primer sets and kits for performing the methods are also provided.

    SPATIAL MOLECULAR BARCODING OF IN SITU NUCLEIC ACIDS
    7.
    发明申请
    SPATIAL MOLECULAR BARCODING OF IN SITU NUCLEIC ACIDS 有权
    原子核酸的空间分子束缚

    公开(公告)号：US20150148239A1

    公开(公告)日：2015-05-28

    申请号：US14493127

    申请日：2014-09-22

    Applicant: Agilent Technologies, Inc.

    Inventor： Brian Jon Peter ,  Robert A. Ach ,  Alicia Scheffer-Wong ,  Carolina Caffaro

    IPC: C12Q1/68

    CPC classification number: C12Q1/6841 ,  C12Q2565/513 ,  C12Q2565/514

    Abstract: This disclosure provides, among other things, a method for analyzing a planar cellular sample. In some embodiments, the method comprises: (a) indirectly or directly attaching nucleic acid tags to binding sites in a planar cellular sample; (b) contacting the planar cellular sample with a solid support comprising an array of spatially addressed features that comprise oligonucleotides, wherein each oligonucleotide comprises a molecular barcode that identifies the feature in which the oligonucleotides is present; (c) hybridizing the nucleic acid tags, or a copy of the same, with the oligonucleotides to produce duplexes; and (d) extending the oligonucleotides in the duplexes to produce extension products that each comprises (i) a molecular barcode and (ii) a copy of a nucleic acid tag. Other embodiments, e.g., kits and the like, are also described.

    Abstract translation: 本公开尤其提供了一种用于分析平面细胞样品的方法。 在一些实施方案中，所述方法包括：（a）将核酸标签间接或直接附着于平面细胞样品中的结合位点; （b）使所述平面细胞样品与包含寡核苷酸的空间寻址特征阵列的固体支持物接触，其中每个寡核苷酸包含鉴定存在寡核苷酸的特征的分子条形码; （c）将核酸标签或其拷贝与寡核苷酸杂交以产生双链体; 和（d）在双链体中延伸寡核苷酸以产生延伸产物，其各自包含（i）分子条形码和（ii）核酸标签的拷贝。 还描述了其它实施例，例如套件等。

    NUCLEIC ACID ENRICHMENT USING CAS9
    8.
    发明申请
    NUCLEIC ACID ENRICHMENT USING CAS9 审中-公开
    使用CAS9的核酸增殖

    公开(公告)号：US20140356867A1

    公开(公告)日：2014-12-04

    申请号：US14290901

    申请日：2014-05-29

    Applicant: Agilent Technologies, Inc.

    Inventor： Brian Jon Peter ,  Robert A. Ach

    IPC: C12Q1/68 ,  C12N15/10

    Abstract: A method of enriching for a fragment of a genome, as well as corresponding compositions and kits, are provided. In certain embodiments, the method comprises: (a) contacting a sample comprising fragmented DNA with a Cas9-gRNA complex comprising mutant Cas9 protein that has inactivated nuclease activity and a Cas9-associated guide RNA that is complementary to a site in the DNA, to produce a Cas9-fragment complex that comprises a fragment of the fragmented DNA; and (b) isolating the complex. In addition, other methods and compositions for Cas9/CRISPR-mediated nucleic acid manipulation are also provided.

    Abstract translation: 提供了富集基因组片段的方法，以及相应的组合物和试剂盒。 在某些实施方案中，所述方法包括：（a）使包含片段化DNA的样品与Cas9-gRNA复合物接触，所述Cas9-gRNA复合物包含具有失活的核酸酶活性的突变型Cas9蛋白和与DNA中的位点互补的Cas9相关导向RNA， 产生包含片段化DNA的片段的Cas9片段复合体; 和（b）分离复合物。 此外，还提供了用于Cas9 / CRISPR介导的核酸操作的其它方法和组合物。

    Hairpin-mediated amplification method
    10.
    发明授权
    Hairpin-mediated amplification method 有权

    公开(公告)号：US10697006B2

    公开(公告)日：2020-06-30

    申请号：US15692215

    申请日：2017-08-31

    Applicant: Agilent Technologies, Inc.

    Inventor： Brian Jon Peter ,  Robert A. Ach

    IPC: C12P19/34 ,  C12Q1/6853 ,  C12Q1/6806

    Abstract: In some embodiments, the amplification method may comprise producing a reaction mix comprising: a nucleic acid sample, a polymerase, nucleotides, a forward primer that hybridizes to a sequence in the bottom strand of a fragment in the sample, and a reverse primer. The reverse primer has a hairpin structure comprising a loop, a stem and a 3′ overhang of at least 8 nucleotides, wherein the 3′ overhang hybridizes to a sequence in the top strand of the fragment. Subjecting the reaction mix at least two rounds of denaturation, renaturation and primer extension conditions results in extension the forward and reverse primers to produce an amplification product that contains: a double stranded region comprising a nick adjacent to the 5′ end of the reverse primer, and the loop of the first hairpin primer. Primer sets and kits for performing the methods are also provided.

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