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公开(公告)号：US20050064435A1
公开(公告)日：2005-03-24
申请号：US10670701
申请日：2003-09-24
申请人： Xing Su , Tae-Woong Koo , Andrew Berlin , Lei Sun , Narayanan Sundararajan , Mineo Yamakawa
发明人： Xing Su , Tae-Woong Koo , Andrew Berlin , Lei Sun , Narayanan Sundararajan , Mineo Yamakawa
CPC分类号： B82Y10/00 , B82Y5/00 , C12Q1/6816 , G06K19/06028 , C12Q2525/161 , C12Q2537/143 , C12Q2565/1025
摘要： 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.
摘要翻译： 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。 绑定的条形码可以通过各种成像模式来检测，例如表面等离子体共振，荧光或拉曼光谱。
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公开(公告)号：US20070054288A1
公开(公告)日：2007-03-08
申请号：US11430612
申请日：2006-05-08
申请人： Xing Su , Tae-Woong Koo , Andrew Berlin , Lei Sun , Narayanan Sundararajan , Mineo Yamakawa
发明人： Xing Su , Tae-Woong Koo , Andrew Berlin , Lei Sun , Narayanan Sundararajan , Mineo Yamakawa
CPC分类号： B82Y10/00 , B82Y5/00 , C12Q1/6816 , G06K19/06028 , C12Q2525/161 , C12Q2537/143 , C12Q2565/1025
摘要： 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.
摘要翻译： 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。
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公开(公告)号：US20060199216A1
公开(公告)日：2006-09-07
申请号：US11430590
申请日：2006-05-08
申请人： Xing Su , Tae-Woong Koo , Andrew Berlin , Lei Sun , Narayanan Sundararajan , Mineo Yamakawa
发明人： Xing Su , Tae-Woong Koo , Andrew Berlin , Lei Sun , Narayanan Sundararajan , Mineo Yamakawa
IPC分类号： C12Q1/68 , G01N33/551
CPC分类号： B82Y10/00 , B82Y5/00 , C12Q1/6816 , G06K19/06028 , C12Q2525/161 , C12Q2537/143 , C12Q2565/1025
摘要： 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.
摘要翻译： 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。 绑定的条形码可以通过各种成像模式来检测，例如表面等离子体共振，荧光或拉曼光谱。
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公开(公告)号：US20060166243A1
公开(公告)日：2006-07-27
申请号：US11329693
申请日：2006-01-10
申请人： Xing Su , Andrew Berlin , Selena Chan , Steven Kirch , Tac-Woong Koo , Gabi Neubauer , Valluri Rao , Narayanan Sundararajan , Mineo Yamakawa
发明人： Xing Su , Andrew Berlin , Selena Chan , Steven Kirch , Tac-Woong Koo , Gabi Neubauer , Valluri Rao , Narayanan Sundararajan , Mineo Yamakawa
CPC分类号： C12Q1/6869 , C12Q2565/632 , C12Q2563/155 , C12Q2521/319
摘要： The methods and apparatus disclosed herein concern nucleic acid sequencing by enhanced Raman spectroscopy. In certain embodiments of the invention, nucleotides are covalently attached to Raman labels before incorporation into a nucleic acid. In other embodiments, unlabeled nucleic acids are used. Exonuclease treatment of the nucleic acid results in the release of labeled or unlabeled nucleotides that are detected by Raman spectroscopy. In alternative embodiments of the invention, nucleotides released from a nucleic acid by exonuclease treatment are covalently cross-linked to nanoparticles and detected by surface enhanced Raman spectroscopy (SERS), surface enhanced resonance Raman spectroscopy (SERRS) and/or coherent anti-Stokes Raman spectroscopy (CARS). Other embodiments of the invention concern apparatus for nucleic acid sequencing.
摘要翻译： 本文公开的方法和装置涉及通过增强拉曼光谱进行的核酸测序。 在本发明的某些实施方案中，在掺入核酸之前，核苷酸与拉曼标记物共价连接。 在其它实施方案中，使用未标记的核酸。 核酸外切核酸处理导致通过拉曼光谱法检测的标记或未标记的核苷酸的释放。 在本发明的替代实施方案中，通过外切核酸酶处理从核酸释放的核苷酸与纳米颗粒共价交联，并通过表面增强拉曼光谱（SERS），表面增强共振拉曼光谱（SERRS）和/或相干反斯托克斯拉曼 光谱学（CARS）。 本发明的其它实施方案涉及用于核酸测序的装置。
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15.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图案生产碳纳米管的方法公开(公告)号：US20050151126A1
公开(公告)日：2005-07-14
申请号：US10750141
申请日：2003-12-31
申请人： Mineo Yamakawa , Yeugang Zhang , Xing Su , Lei Sun , Andrew Berlin , Narayanan Sundararajan
发明人： Mineo Yamakawa , Yeugang Zhang , Xing Su , Lei Sun , Andrew Berlin , Narayanan Sundararajan
CPC分类号： B82Y40/00 , B82Y10/00 , B82Y30/00 , C01B32/162 , C01B2202/08 , C01B2202/36 , D01F9/127 , H01L51/0048 , H01L51/0052
摘要： 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 can be attached to the substrate in ordered patterns, using self-assembly or molecular 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.
摘要翻译： 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连接到聚合物120,210分子，将聚合物120,210分子连接到基底上的方法形成，除去聚合物120,210分子并产生碳 催化剂纳米颗粒140,230上的纳米管。聚合物120,210分子可以使用自组装或分子对准技术以有序图案附着到基底上。 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。
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公开(公告)号：US20050181383A1
公开(公告)日：2005-08-18
申请号：US10897190
申请日：2004-07-21
申请人： Xing Su , Narayanan Sundararajan , Tae-Woong Koo
发明人： Xing Su , Narayanan Sundararajan , Tae-Woong Koo
CPC分类号： G01N33/54353 , B01L3/5027 , C12N15/1006 , C12Q1/6869 , C12Q2565/629 , C12Q2521/319 , C12Q2565/518
摘要： Devices and methods for isolating, detecting, and positioning single polymeric molecules without the need for expensive equipment are provided. The disclosed devices and methods allow for a molecule to be quickly and efficiently transported to a specific sub-micron area. Such devices are useful, for instance, for performing analyses in which the sequence of a polymer of interest is determined.
摘要翻译： 提供了用于隔离，检测和定位单个聚合物分子的装置和方法，而不需要昂贵的设备。 所公开的装置和方法允许将分子快速有效地运送到特定的亚微米区域。 这样的装置例如用于进行其中确定感兴趣聚合物序列的分析是有用的。
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17.发明申请Method and device for isolating and positioning single nucleic acid molecules 审中-公开用于分离和定位单个核酸分子的方法和装置公开(公告)号：US20050181379A1
公开(公告)日：2005-08-18
申请号：US10781238
申请日：2004-02-18
申请人： Xing Su , Narayanan Sundararajan , Tae-Woong Koo
发明人： Xing Su , Narayanan Sundararajan , Tae-Woong Koo
CPC分类号： C12N15/1006 , B01L3/5027 , C12Q1/6869 , C12Q2565/518
摘要： The disclosed methods and devices provides a method and device for isolating and positioning a single polymer molecule, such as a nucleic acid strand, for sequencing, and a method for manufacturing such a device. The method and device can be used for sequencing individual polymer molecules, such as ribonucleic acid (RNA) or deoxyribonucleic acid (DNA).
摘要翻译： 所公开的方法和装置提供了用于分离和定位用于测序的单个聚合物分子例如核酸链的方法和装置，以及用于制造这种装置的方法。 该方法和装置可用于测序单个聚合物分子，例如核糖核酸（RNA）或脱氧核糖核酸（DNA）。
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公开(公告)号：US07238477B2
公开(公告)日：2007-07-03
申请号：US10660902
申请日：2003-09-12
申请人： Xing Su , Andrew A. Berlin , Selena Chan , Steven J. Kirch , Tac-Woong Koo , Gabi Neubauer , Valluri Rao , Narayanan Sundararajan , Mineo Yamakawa
发明人： Xing Su , Andrew A. Berlin , Selena Chan , Steven J. Kirch , Tac-Woong Koo , Gabi Neubauer , Valluri Rao , Narayanan Sundararajan , Mineo Yamakawa
CPC分类号： C12Q1/6869 , C12Q2565/632 , C12Q2563/155 , C12Q2521/319
摘要： The methods and apparatus disclosed herein concern nucleic acid sequencing by enhanced Raman spectroscopy. In certain embodiments of the invention, nucleotides are covalently attached to Raman labels before incorporation into a nucleic acid. In other embodiments, unlabeled nucleic acids are used. Exonuclease treatment of the nucleic acid results in the release of labeled or unlabeled nucleotides that are detected by Raman spectroscopy. In alternative embodiments of the invention, nucleotides released from a nucleic acid by exonuclease treatment are covalently cross-linked to nanoparticles and detected by surface enhanced Raman spectroscopy (SERS), surface enhanced resonance Raman spectroscopy (SERRS) and/or coherent anti-Stokes Raman spectroscopy (CARS). Other embodiments of the invention concern apparatus for nucleic acid sequencing.
摘要翻译： 本文公开的方法和装置涉及通过增强拉曼光谱进行的核酸测序。 在本发明的某些实施方案中，在掺入核酸之前，核苷酸与拉曼标记物共价连接。 在其它实施方案中，使用未标记的核酸。 核酸外切核酸处理导致通过拉曼光谱法检测的标记或未标记的核苷酸的释放。 在本发明的替代实施方案中，通过外切核酸酶处理从核酸释放的核苷酸与纳米颗粒共价交联，并通过表面增强拉曼光谱（SERS），表面增强共振拉曼光谱（SERRS）和/或相干反斯托克斯拉曼 光谱学（CARS）。 本发明的其它实施方案涉及用于核酸测序的装置。
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19.发明申请Metal coated nanocrystalline silicon as an active surface enhanced raman spectroscopy (SERS) substrate 有权金属涂层纳米晶硅作为活性表面增强拉曼光谱（SERS）底物公开(公告)号：US20060215154A1
公开(公告)日：2006-09-28
申请号：US11264433
申请日：2005-10-31
CPC分类号： C12Q1/6825 , B82Y15/00 , B82Y30/00 , G01J3/44 , G01N21/658 , G01N2021/6439 , G01N2021/653 , G01N2021/655 , G01N2021/656 , C12Q2565/632 , C12Q2563/155
摘要： The disclosed methods and apparatus concern Raman spectroscopy using metal coated nanocrystalline porous silicon substrates. Porous silicon substrates may be formed by anodic etching in dilute hydrofluoric acid. A thin coating of a Raman active metal, such as gold or silver, may be coated onto the porous silicon by cathodic electromigration or any known technique. In certain alternatives, the metal coated porous silicon substrate comprises a plasma-oxidized, dip and decomposed porous silicon substrate. The metal-coated substrate provides an extensive, metal rich environment for SERS, SERRS, hyper-Raman and/or CARS Raman spectroscopy. In certain alternatives, metal nanoparticles may be added to the metal-coated substrate to further enhance the Raman signals. Raman spectroscopy may be used to detect, identify and/or quantify a wide variety of analytes, using the disclosed methods and apparatus. In some disclosed methods, Raman spectroscopy may be used to detect nucleotides, purines or pyrimidines at the single molecule level.
摘要翻译： 所公开的方法和装置涉及使用金属涂覆的纳米晶体多孔硅衬底的拉曼光谱。 多孔硅衬底可以通过在稀氢氟酸中的阳极蚀刻形成。 拉曼活性金属如金或银的薄涂层可以通过阴极电迁移或任何已知技术涂覆在多孔硅上。 在某些替代方案中，金属涂覆的多孔硅衬底包括等离子体氧化的，浸渍和分解的多孔硅衬底。 金属涂层的基底为SERS，SERRS，超拉曼和/或CARS拉曼光谱提供了广泛的金属丰富的环境。 在某些替代方案中，可以将金属纳米颗粒加入到金属涂覆的基底中以进一步增强拉曼信号。 使用所公开的方法和装置，可以使用拉曼光谱来检测，鉴定和/或定量各种分析物。 在一些公开的方法中，可以使用拉曼光谱法在单一分子水平检测核苷酸，嘌呤或嘧啶。
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20.发明申请公开(公告)号：US20060100787A1
公开(公告)日：2006-05-11
申请号：US10985547
申请日：2004-11-09
IPC分类号： G06F19/00
摘要： Methods for making nanocodes that can be detected using scanning probe microscopy are provided, as are nanocodes constructed of two or more polymers, including homogeneous polymers such as nucleic acid molecules and heterogeneous polymers such as peptide nucleic acid polymers, and subunits useful for constructing such nanocodes. Also provided are modified nanocodes such as a nanocode containing one or more linked metals such as gold or iron and/or a linked probe that can specifically bind a target molecule. In addition, systems are provided that include such nanocodes, for example, a system that includes the nanocode and a surface and/or a scanning probe microscope probe. Methods of using such nanocodes, for example, to detect and/or identify a target molecule in a sample (e.g., a biological or environmental sample) using scanning probe microscopy, also are provided.
摘要翻译： 提供了可以使用扫描探针显微镜检测的纳代码的方法，以及由两种或更多种聚合物构成的纳代码，包括均质聚合物，例如核酸分子和非均相聚合物如肽核酸聚合物，以及可用于构建这样的纳代码的亚基 。 还提供了修饰的纳代码，例如包含一种或多种连接的金属如金或铁的纳代码和/或可以特异性结合靶分子的连接的探针。 此外，提供了包括这样的纳代码的系统，例如，包括纳代码和表面和/或扫描探针显微镜探针的系统。 还提供了使用这样的纳代码例如使用扫描探针显微镜检测和/或鉴定样品（例如，生物或环境样品）中的靶分子的方法。
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