公开(公告)号：US20080032297A1

公开(公告)日：2008-02-07

申请号：US11704231

申请日：2007-02-09

申请人： Xing Su ,  Andrew Berlin ,  Selena Chan ,  Steven Kirch ,  Tae-Woong Koo ,  Gabi Neubauer ,  Valluri Rao ,  Narayanan Sundararajan ,  Mineo Yamakawa

发明人： Xing Su ,  Andrew Berlin ,  Selena Chan ,  Steven Kirch ,  Tae-Woong Koo ,  Gabi Neubauer ,  Valluri Rao ,  Narayanan Sundararajan ,  Mineo Yamakawa

IPC分类号： C12Q1/68

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。

公开(公告)号：US07270952B2

公开(公告)日：2007-09-18

申请号：US10254201

申请日：2002-09-24

申请人： Xing Su ,  Selena Chan ,  Tae-Woong Koo ,  Mineo Yamakawa ,  Andrew A. Berlin

发明人： Xing Su ,  Selena Chan ,  Tae-Woong Koo ,  Mineo Yamakawa ,  Andrew A. Berlin

IPC分类号： C12Q1/68

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

摘要： 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.

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

IPC分类号： C12Q1/68 ,  C12P19/34

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。

公开(公告)号：US06970239B2

公开(公告)日：2005-11-29

申请号：US10171357

申请日：2002-06-12

申请人： Selena Chan ,  Andrew A. Berlin ,  Mineo Yamakawa

发明人： Selena Chan ,  Andrew A. Berlin ,  Mineo Yamakawa

IPC分类号： C12Q1/68 ,  G01J3/44 ,  G01N21/65 ,  G01N33/53 ,  G01N33/543 ,  G01N33/553

CPC分类号： C12Q1/6825 ,  G01J3/44 ,  G01N21/658 ,  G01N2021/653 ,  C12Q2565/632 ,  C12Q2563/155

摘要： The methods and apparatus 300 disclosed herein concern Raman spectroscopy using metal coated nanocrystalline porous silicon substrates 240, 340. In certain embodiments of the invention, porous silicon substrates 110, 210 may be formed by anodic etching in dilute hydrofluoric acid 150. A thin coating of a Raman active metal, such as gold or silver, may be coated onto the porous silicon 110, 210 by cathodic electromigration or any known technique. The metal-coated substrate 240, 340 provides an extensive, metal rich environment for SERS, SERRS, hyper-Raman and/or CARS Raman spectroscopy. In certain embodiments of the invention, metal nanoparticles may be added to the metal-coated substrate 240, 340 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 300.

摘要翻译： 本文公开的方法和装置300涉及使用金属涂覆的纳米晶体多孔硅衬底240,340的拉曼光谱。 在本发明的某些实施例中，多孔硅衬底110,210可以通过在稀氢氟酸150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110,210上。 金属涂覆的基底240,340为SERS，SERRS，超拉曼和/或CARS拉曼光谱提供了广泛的金属富集环境。 在本发明的某些实施方案中，可以将金属纳米颗粒加入到金属涂覆的基底240,340中以进一步增强拉曼信号。 使用所公开的方法和装置300，可以使用拉曼光谱来检测，鉴定和/或定量各种各样的分析物。

公开(公告)号：US20050250159A1

公开(公告)日：2005-11-10

申请号：US11083418

申请日：2005-03-17

申请人： Xing Su ,  Lei Sun ,  Mineo Yamakawa ,  Tae-Woong Koo ,  Selena Chan ,  Andrew Berlin ,  Narayanan Sundararajan

发明人： Xing Su ,  Lei Sun ,  Mineo Yamakawa ,  Tae-Woong Koo ,  Selena Chan ,  Andrew Berlin ,  Narayanan Sundararajan

IPC分类号： G01N21/65 ,  G01N33/58 ,  G01N33/68 ,  G01N33/53 ,  G01N33/00

CPC分类号： G01N21/658 ,  G01N33/6803 ,  G01N2021/653 ,  G01N2021/655 ,  G01N2021/656

摘要： The invention provides methods for analyzing the protein content of a biological sample, for example to obtain a protein profile of a sample provided by a particular individual. The proteins and protein fragments in the sample are separated on the basis of chemical and/or physical properties and maintained in a separated state at discrete locations on a solid substrate or within a stream of flowing liquid. Raman spectra are then detected as produced by the separated proteins or fragments at the discrete locations such that a spectrum from a discrete location provides information about the structure or identity of one or more particular proteins or fragments at the discrete location. The proteins or fragments at discrete locations can be coated with a metal, such as gold or silver, and/or the separated proteins can be contacted with a chemical enhancer to provide SERS spectra. Method and kits for practicing the invention are also provided.

摘要翻译： 本发明提供了用于分析生物样品的蛋白质含量的方法，例如获得由特定个体提供的样品的蛋白质谱。 样品中的蛋白质和蛋白质片段基于化学和/或物理性质分离，并在固体基质上或流动液体流中的离散位置保持分离状态。 然后检测拉曼光谱，由离散位置处的分离的蛋白质或片段产生，使得离散位置的光谱提供关于在离散位置处的一种或多种特定蛋白质或片段的结构或身份的信息。 离散位置处的蛋白质或片段可以用金属（例如金或银）涂覆，和/或分离的蛋白质可与化学增强剂接触以提供SERS光谱。 还提供了用于实施本发明的方法和试剂盒。

公开(公告)号：US20090262994A1

公开(公告)日：2009-10-22

申请号：US12359637

申请日：2009-01-26

申请人： Horst Haussecker ,  Andrew A. Berlin ,  Selena Chan ,  Eric Hannah ,  Narayanan Sundararajan ,  Mineo Yamakawa

发明人： Horst Haussecker ,  Andrew A. Berlin ,  Selena Chan ,  Eric Hannah ,  Narayanan Sundararajan ,  Mineo Yamakawa

IPC分类号： G06K9/00

CPC分类号： G01Q30/04 ,  B82Y35/00

摘要： In certain embodiments of the invention, a plurality of images of one or more subjects may be captured using different imaging techniques, such as different modalities of scanning probe microscopy. Parameters may be estimated from the plurality of images, using one or more models of known molecular structures to provide a model-based analysis. The estimated parameters may be fused, with further input from physical models of known molecular structures. The fused parameters may be used to characterize the subjects. Such characterization may include the detection and/or identification of specific molecular structures, such as proteins, peptides and/or nucleic acids of known sequence and/or structure. In some embodiments of the invention the structural characterizations may be used to identify previously unknown properties of a subject molecule.

摘要翻译： 在本发明的某些实施例中，可以使用不同的成像技术（例如扫描探针显微镜的不同方式）捕获一个或多个受试者的多个图像。 可以使用已知分子结构的一个或多个模型从多个图像估计参数以提供基于模型的分析。 估计的参数可以与已知分子结构的物理模型的进一步输入融合。 融合参数可用于表征受试者。 这种表征可以包括具体分子结构的检测和/或鉴定，例如已知序列和/或结构的蛋白质，肽和/或核酸。 在本发明的一些实施方案中，结构表征可用于鉴定受试者分子的先前未知的性质。

公开(公告)号：US07606403B2

公开(公告)日：2009-10-20

申请号：US10685867

申请日：2003-10-14

申请人： Horst Haussecker ,  Andrew A. Berlin ,  Selena Chan ,  Eric Hannah ,  Narayanan Sundararajan ,  Mineo Yamakawa

发明人： Horst Haussecker ,  Andrew A. Berlin ,  Selena Chan ,  Eric Hannah ,  Narayanan Sundararajan ,  Mineo Yamakawa

IPC分类号： G06K9/00

CPC分类号： G01Q30/04 ,  B82Y35/00

摘要： In certain embodiments of the invention, a plurality of images of one or more subjects may be captured using different imaging techniques, such as different modalities of scanning probe microscopy. Parameters may be estimated from the plurality of images, using one or more models of known molecular structures to provide a model-based analysis. The estimated parameters may be fused, with further input from physical models of known molecular structures. The fused parameters may be used to characterize the subjects. Such characterization may include the detection and/or identification of specific molecular structures, such as proteins, peptides and/or nucleic acids of known sequence and/or structure. In some embodiments of the invention the structural characterizations may be used to identify previously unknown properties of a subject molecule.

摘要翻译： 在本发明的某些实施例中，可以使用不同的成像技术（例如扫描探针显微镜的不同方式）捕获一个或多个受试者的多个图像。 可以使用已知分子结构的一个或多个模型从多个图像估计参数以提供基于模型的分析。 估计的参数可以与已知分子结构的物理模型的进一步输入融合。 融合参数可用于表征受试者。 这种表征可以包括具体分子结构的检测和/或鉴定，例如已知序列和/或结构的蛋白质，肽和/或核酸。 在本发明的一些实施方案中，结构表征可用于鉴定受试者分子的先前未知的性质。

公开(公告)号：US07400395B2

公开(公告)日：2008-07-15

申请号：US11264433

申请日：2005-10-31

申请人： Selena Chan ,  Andrew A. Berlin ,  Sunghoon Kwon ,  Narayanan Sundararajan ,  Mineo Yamakawa

发明人： Selena Chan ,  Andrew A. Berlin ,  Sunghoon Kwon ,  Narayanan Sundararajan ,  Mineo Yamakawa

IPC分类号： G01J3/44

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（例如金或银）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。

公开(公告)号：US07291466B2

公开(公告)日：2007-11-06

申请号：US11111308

申请日：2005-04-20

申请人： Xing Su ,  Selena Chan ,  Tae-Woong Koo ,  Mineo Yamakawa ,  Andrew A. Berlin

发明人： Xing Su ,  Selena Chan ,  Tae-Woong Koo ,  Mineo Yamakawa ,  Andrew A. Berlin

IPC分类号： C12Q1/68

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

摘要： 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.

摘要翻译： 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悬臂的偏转，由检测单元检测。 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。

公开(公告)号：US20060281119A1

公开(公告)日：2006-12-14

申请号：US11446273

申请日：2006-06-02

申请人： Selena Chan ,  Xing Su ,  Mineo Yamakawa

发明人： Selena Chan ,  Xing Su ,  Mineo Yamakawa

IPC分类号： C12Q1/68 ,  C12M1/34

CPC分类号： C12Q1/6816 ,  Y10S977/704 ,  Y10S977/728 ,  Y10S977/734 ,  Y10S977/742 ,  Y10S977/773 ,  Y10S977/774 ,  C12Q2565/601 ,  C12Q2563/155 ,  C12Q2537/143

摘要： The methods, apparatus and compositions disclosed herein concern the detection, identification and/or sequencing of biomolecules, such as nucleic acids or proteins. In certain embodiments of the invention, coded probes comprising a probe molecule attached to one or more nano-barcodes may be allowed to bind to one or more target molecules. After binding and separation from unbound coded probes, the bound coded probes may be aligned on a surface and analyzed by scanning probe microscopy. The nano-barcodes may be any molecule or complex that is distinguishable by SPM, such as carbon nanotubes, fullerenes, submicrometer metallic barcodes, nanoparticles or quantum dots. Where the probes are oligonucleotides, adjacent coded probes hybridized to a target nucleic acid may be ligated together before alignment and SPM analysis. Compositions comprising coded probes are also disclosed herein. Systems for biomolecule analysis may comprise an SPM instrument and at least one coded probe attached to a surface.

摘要翻译： 本文公开的方法，装置和组合物涉及生物分子如核酸或蛋白质的检测，鉴定和/或测序。 在本发明的某些实施方案中，包含与一个或多个纳米条形码连接的探针分子的编码探针可以被允许与一个或多个靶分子结合。 在结合和分离未结合的编码探针之后，结合编码的探针可以在表面上对准并通过扫描探针显微镜进行分析。 纳米条形码可以是通过SPM可区分的任何分子或复合物，例如碳纳米管，富勒烯，亚微米金属条形码，纳米粒子或量子点。 当探针是寡核苷酸时，与靶核酸杂交的相邻编码探针可以在对准和SPM分析之前连接在一起。 包含编码探针的组合物也在本文中公开。 用于生物分子分析的系统可以包括SPM仪器和附接到表面的至少一个编码探针。