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    METHODS AND COMPOSITIONS FOR DETECTING NUCLEIC ACIDS USING SCANNING PROBE MICROSCOPY AND NANOCODES
    1.
    发明申请
    METHODS AND COMPOSITIONS FOR DETECTING NUCLEIC ACIDS USING SCANNING PROBE MICROSCOPY AND NANOCODES 审中-公开
    使用扫描探针显微镜和纳米孔探测核酸的方法和组合物

    公开(公告)号：WO2005066368A3

    公开(公告)日：2005-11-24

    申请号：PCT/US2004043632

    申请日：2004-12-28

    Applicant: INTEL CORP ,  BERLIN ANDREW ,  YAMAKAWA MINEO

    Inventor： BERLIN ANDREW ,  YAMAKAWA MINEO

    IPC: C12Q1/68 ,  G01Q60/10 ,  G01Q60/50

    CPC classification number: C12Q1/6874 ,  B82Y5/00 ,  B82Y10/00 ,  C12Q2565/601 ,  C12Q2563/155 ,  C12Q2525/179

    Abstract: A method for determining a nucleotide sequence of a nucleic acid is provided that includes contacting the nucleic acid with a series of labeled oligonucleotides for binding to the nucleic acid, wherein each labeled oligonucleotide includes a known nucleotide sequence and a molecular nanocode. The nanocode of an isolated labeled oligonucleotides that binds to the nucleic acid is then detected using SPM. Nanocodes of the present invention in certain aspects include detectable features beyond the arrangement of tags that encode information about the barcoded object, which assist in detecting the tags that encode information about the barcoded object. The detectable features include structures of a nanocode or associated with a nanocode, referred to herein as detectable feature tags, for error checking/error-correction, encryption, and data reduction/compression.

    Abstract translation: 提供了用于确定核酸的核苷酸序列的方法，其包括使核酸与一系列标记的寡核苷酸接触以结合核酸，其中每个标记的寡核苷酸包括已知的核苷酸序列和分子纳代码。 然后使用SPM检测与核酸结合的分离的标记的寡核苷酸的纳代码。 在某些方面，本发明的纳代码包括除了编码关于条形码化对象的信息的标签布置之外的可检测特征，其有助于检测编码关于条形码化对象的信息的标签。 可检测特征包括用于错误检查/错误校正，加密和数据简化/压缩的纳代码的结构或与纳代码关联的结构，在本文中被称为可检测特征标签。

    METHODS OF PRODUCING CARBON NANOTUBES USING PEPTIDE OR NUCLEIC ACID MICROPATTERNING
    3.
    发明申请
    METHODS OF PRODUCING CARBON NANOTUBES USING PEPTIDE OR NUCLEIC ACID MICROPATTERNING 审中-公开
    使用肽或核酸微生物生产碳纳米管的方法

    公开(公告)号：WO2005066367A3

    公开(公告)日：2007-03-01

    申请号：PCT/US2004043364

    申请日：2004-12-24

    Applicant: INTEL CORP ,  SU XING ,  SUNDARARAJAN NARAYAN ,  YAMAKAWA MINEO ,  BERLIN ANDREW ,  SUN LEI ,  ZHANG YUEGANG

    Inventor： SU XING ,  SUNDARARAJAN NARAYAN ,  YAMAKAWA MINEO ,  BERLIN ANDREW ,  SUN LEI ,  ZHANG YUEGANG

    IPC: C01B31/02 ,  C12Q1/68 ,  D01F9/127 ,  H01L51/00 ,  H01L51/30

    CPC classification number: B82Y40/00 ,  B82Y10/00 ,  B82Y30/00 ,  C01B32/162 ,  C01B2202/08 ,  C01B2202/36 ,  D01F9/127 ,  H01L51/0048 ,  H01L51/0052

    Abstract: The methods, apparatus and systems disclosed herein concern ordered arrays of carbon nanotubes. In particular embodiments of the invention, the nanotube arrays are formed by a method comprising attaching catalyst nanoparticles (140, 230) to polymer (120, 210) molecules, attaching the polymer (120, 210) molecules to a substrate, removing the polymer (120, 210) molecules and producing carbon nanotubes on the catalyst nanoparticles (140, 230). The polymer (120, 210) molecules alignment techniques. The nanotube arrays can be attached to selected areas (110, 310) of the substrate. Within the selected areas (110, 310), the nanotubes are distributed non-randomly. Other embodiments disclosed herein concern apparatus that include ordered arrays of nanotubes attached to a substrate and systems that include ordered arrays of carbon nanotubes attached to a substrate, produced by the claimed methods. In certain embodiments, provided herein are methods for aligning a molecular wire, by ligating the molecular wire to a double stranded DNA molecule.

    Abstract translation: 本文公开的方法，装置和系统涉及碳纳米管的有序阵列。 在本发明的具体实施方案中，纳米管阵列通过包括将催化剂纳米颗粒（140,230）附着到聚合物（120,210）分子上的方法形成，将聚合物（120,210）分子附着到基底上，去除聚合物 120,210）分子并在催化剂纳米颗粒（140,230）上产生碳纳米管。 聚合物（120,210）分子对齐技术。 纳米管阵列可以附着到基板的选定区域（110,310）。 在所选择的区域（110,310）内，纳米管是非随机分布的。 本文公开的其它实施方案涉及包括连接到衬底的纳米管的有序阵列和包括通过所要求保护的方法产生的连接到衬底的碳纳米管的有序阵列的系统的装置。 在某些实施方案中，本文提供了通过将分子线连接到双链DNA分子来对齐分子线的方法。

    LASER EXPOSURE OF PHOTOSENSITIVE MASKS FOR DNA MICROARRAY FABRICATION
    5.
    发明申请
    LASER EXPOSURE OF PHOTOSENSITIVE MASKS FOR DNA MICROARRAY FABRICATION 审中-公开
    激光曝光用于DNA微量制备的光敏掩模

    公开(公告)号：WO2004065635A3

    公开(公告)日：2005-02-03

    申请号：PCT/US0337839

    申请日：2003-11-26

    Applicant: INTEL CORP

    Inventor： RAO VALLURI ,  YAMAKAWA MINEO ,  BERLIN ANDREW

    IPC: B01J19/00 ,  B05D3/00 ,  C12M1/34 ,  C12Q1/68 ,  G03F1/00 ,  G03F7/20

    CPC classification number: B82Y30/00 ,  B01J19/0046 ,  B01J2219/00441 ,  B01J2219/00527 ,  B01J2219/00608 ,  B01J2219/0061 ,  B01J2219/00612 ,  B01J2219/00621 ,  B01J2219/00689 ,  B01J2219/00711 ,  B01J2219/00722

    Abstract: A method and apparatus for forming a polymer array on a substrate suitable for synthesizing polymer sequences. This includes forming an array, each location of the array having at least one strand end, forming photosensitive protection on the strand ends, and selectively scanning and modulating at least one energy beam to expose a pattern on the photosensitive protection. In some embodiments, the method further includes removing a protective group from selected strand ends based on the exposed pattern. The method then includes adding a predetermined one or more polymeric subunits to the deprotected strand ends. In some embodiments the photosensitive protection includes a layer of photoresist to cover the strand ends. Some embodiments use an ultra-violet laser.

    Abstract translation: 一种在适于合成聚合物序列的基材上形成聚合物阵列的方法和装置。 这包括形成阵列，阵列的每个位置具有至少一个绞合端，在绞合端上形成感光保护，并且选择性地扫描和调制至少一个能量束以暴露感光保护上的图案。 在一些实施方案中，该方法还包括基于暴露图案从选定的链末端去除保护基团。 该方法然后包括将预定的一个或多个聚合物亚单位加入去保护的末端。 在一些实施例中，感光保护包括一层光致抗蚀剂以覆盖绞合端。 一些实施例使用紫外激光。

    NUCLEIC ACID SEQUENCING BY RAMAN MONITORING OF UPTAKE OF PRECURSORS DURING MOLECULAR REPLICATION
    6.
    发明申请
    NUCLEIC ACID SEQUENCING BY RAMAN MONITORING OF UPTAKE OF PRECURSORS DURING MOLECULAR REPLICATION 审中-公开
    在分子复制过程中拉曼监测前列腺素的核酸序列

    公开(公告)号：WO03027307A2

    公开(公告)日：2003-04-03

    申请号：PCT/US0228443

    申请日：2002-09-05

    Applicant: INTEL CORP

    Inventor： RAO VALLURI ,  NEUBAUER GABI ,  KIRCH STEVEN ,  YAMAKAWA MINEO ,  BERLIN ANDREW

    IPC: B01L3/00 ,  C12M1/00 ,  C12M1/34 ,  C12N15/00 ,  C12N15/09 ,  C12Q1/68 ,  G01J3/44 ,  G01N21/65 ,  G01N33/53 ,  G01N33/566 ,  C12Q

    CPC classification number: G01N21/6428 ,  B01L3/5027 ,  C12Q1/6869 ,  G01J3/4406 ,  G01N21/65 ,  G01N21/658 ,  G01N2021/6441 ,  G01N2021/651 ,  G01N2021/653 ,  G01N2021/655 ,  G01N2021/656 ,  C12Q2565/632 ,  C12Q2565/101 ,  C12Q2533/101 ,  C12Q2565/629 ,  C12Q2565/60

    Abstract: The methods, compositions and apparatus disclosed herein are of use for nucleic acid sequence determination. The methods involve isolation of one or more nucleic acid template molecules and polymerization of a nascent complementary strand of nucleic acid, using a DNA or RNA polymerase or similar synthetic reagent. As the nascent strand is extended one nucleotide at a time, the disappearance of nucleotide precursors from solution is monitored by Raman spectroscopy or FRET. The nucleic acid sequence of the nascent strand, and the complementary sequence of the template strand, may be determined by tracking the order of incorporation of nucleotide precursors during the polymerization reaction. Certain embodiments concern apparatus comprising a reaction chamber and detection unit, of use in practicing the claimed methods. The methods, compositions and apparatus are of use in sequencing very long nucleic acid templates in a single sequencing reaction.

    Abstract translation: 本文公开的方法，组合物和装置用于核酸序列测定。 所述方法包括使用DNA或RNA聚合酶或类似的合成试剂分离一个或多个核酸模板分子和核酸的新生互补链的聚合。 当新生链一次延伸一个核苷酸时，通过拉曼光谱法或FRET监测核苷酸前体从溶液中的消失。 新生链的核酸序列和模板链的互补序列可以通过跟踪聚合反应期间核苷酸前体的掺入顺序来确定。 某些实施例涉及包括在实施所要求保护的方法中使用的反应室和检测单元的装置。 方法，组合物和装置在用于在单次测序反应中测序非常长的核酸模板中有用。

    COMPOSITE ORGANIC-INORGANIC NANOCLUSTERS
    8.
    发明申请
    COMPOSITE ORGANIC-INORGANIC NANOCLUSTERS 审中-公开
    复合有机无机纳米粒子

    公开(公告)号：WO2005090948A3

    公开(公告)日：2006-02-16

    申请号：PCT/US2004043878

    申请日：2004-12-28

    Applicant: INTEL CORP ,  SU XING ,  ZHANG JINGWU ,  SUN LEI ,  BERLIN ANDREW

    Inventor： SU XING ,  ZHANG JINGWU ,  SUN LEI ,  BERLIN ANDREW

    IPC: G01N21/65 ,  G01N33/543

    CPC classification number: G01N33/54346 ,  G01N21/658

    Abstract: Composite organic-inorganic nanoclusters (COINs) are provided that produce surface-enhanced Raman signals (SERS) when excited by a laser. The nanoclusters include metal particles and a Raman-active organic compound. The metal required for achieving a suitable SERS signal is inherent in the nanocluster and a wide variety of Raman-active organic compounds and combinations thereof can be incorporated into the nanocluster. In addition, polymeric microspheres containing the nanoclusters and methods of making them are also provided. The nanoclusters and microspheres can be used, for example, in assays for multiplex detection of biological molecules.

    Abstract translation: 提供了复合有机 - 无机纳米团簇（COINs），当激光激发时产生表面增强拉曼信号（SERS）。 纳米团簇包括金属颗粒和拉曼活性有机化合物。 实现合适的SERS信号所需的金属在纳米簇中是固有的，并且可以将多种拉曼活性有机化合物及其组合掺入纳米团簇中。 此外，还提供了含有纳米簇的聚合物微球及其制备方法。 纳米团簇和微球可用于例如生物分子多重检测的测定。

    PROGRAMMABLE MOLECULAR BARCODES
    9.
    发明申请
    PROGRAMMABLE MOLECULAR BARCODES 审中-公开
    可编程分子杆

    公开(公告)号：WO2005030996A2

    公开(公告)日：2005-04-07

    申请号：PCT/US2004031289

    申请日：2004-09-23

    Applicant: INTEL CORP

    Inventor： SU XING ,  KOO TAE-WOONG ,  BERLIN ANDREW ,  SUN LEI ,  SUNDARARAJAN NARAYANAN ,  YAMAKAWA MINEO

    IPC: C12Q1/68 ,  G06K19/06

    CPC classification number: B82Y10/00 ,  B82Y5/00 ,  C12Q1/6816 ,  G06K19/06028 ,  C12Q2525/161 ,  C12Q2537/143 ,  C12Q2565/1025

    Abstract: The present disclosure concerns methods for producing and/or using molecular barcodes. In certain embodiments of the invention, the barcodes comprise polymer backbones that may contain one or more branch structures. Tags may be attached to the backbone and/or branch structures. The barcode may also comprise a probe that can bind to a target, such as proteins, nucleic acids and other biomolecules or aggregates. Different barcodes may be distinguished by the type and location of the tags. In other embodiments, barcodes may be produced by hybridization of one or more tagged oligonucleotides to a template, comprising a container section and a probe section. The tagged oligonucleotides may be designed as modular code sections, to form different barcodes specific for different targets. In alternative embodiments, barcodes may be prepared by polymerization of monomeric units. Bound barcodes may be detected by various imaging modalities, such as, surface plasmon resonance, fluorescent or Raman spectroscopy.

    Abstract translation: 本公开涉及用于生产和/或使用分子条形码的方法。 在本发明的某些实施方案中，条形码包含可包含一个或多个分支结构的聚合物主链。 标签可以附加到骨干和/或分支结构。 条形码还可以包含可以与靶标结合的探针，例如蛋白质，核酸和其他生物分子或聚集体。 可以通过标签的类型和位置区分不同的条形码。 在其它实施方案中，条形码可以通过将一个或多个标记的寡核苷酸与包含容器部分和探针部分的模板杂交来产生。 标记的寡核苷酸可以被设计为模块代码部分，以形成针对不同靶标的不同条形码。 在替代实施例中，条形码可以通过单体单元的聚合来制备。 可以通过各种成像方式，例如表面等离子体共振，荧光或拉曼光谱来检测结合条形码。

    DETECTING MOLECULAR BINDING BY MONITORING FEEDBACK CONTROLLED CANTILEVER DEFLECTIONS
    10.
    发明申请
    DETECTING MOLECULAR BINDING BY MONITORING FEEDBACK CONTROLLED CANTILEVER DEFLECTIONS 审中-公开
    通过监控反馈控制的CANTILEVER偏差检测分子结合

    公开(公告)号：WO2004029625A2

    公开(公告)日：2004-04-08

    申请号：PCT/US0330192

    申请日：2003-09-24

    Applicant: INTEL CORP

    Inventor： SU XING ,  CHAN SELENA ,  KOO TAE-WOONG ,  YAMAKAWA MINEO ,  BERLIN ANDREW

    IPC: C12Q1/68 ,  G01N33/543 ,  G01B7/34

    CPC classification number: C12Q1/6825 ,  B82Y5/00 ,  G01N33/54373 ,  G01N2800/52 ,  Y10S977/924 ,  C12Q2565/501

    Abstract: The present methods and apparatus concern the detection and/or identification of target analytes using probe molecules. In various embodiments of the invention, the probes or analytes are attached to one or more cantilevers. Binding of a probe to an analyte results in deflection of the cantilever, detected by a detection unit. A counterbalancing force may be applied to restore the cantilever to its original position. The counterbalancing force may be magnetic, electrical or radiative. The detection unit and the mechanism generating the counterbalancing force may be operably coupled to an information processing and control unit, such as a computer. The computer may regulate a feedback loop that maintains the cantilever in a fixed position by balancing the deflecting force and the counterbalancing force. The concentration of analytes in a sample may be determined from the magnitude of the counterbalancing force required to maintain the cantilever in a fixed position.

    Abstract translation: 本方法和装置涉及使用探针分子检测和/或鉴定目标分析物。 在本发明的各种实施方案中，探针或分析物附着到一个或多个悬臂。 将探针与分析物结合导致由检测单元检测到的悬臂的偏转。 可以应用平衡力将悬臂恢复到其原始位置。 平衡力可以是磁性的，电的或辐射的。 生成平衡力的检测单元和机构可以可操作地耦合到诸如计算机的信息处理和控制单元。 计算机可以通过平衡偏转力和平衡力来调节将悬臂维持在固定位置的反馈回路。 样品中分析物的浓度可以从将悬臂维持在固定位置所需的平衡力的大小来确定。

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