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1. 发明授权

US08999674B2 Methods and apparatus for single molecule sequencing using energy transfer detection 有权
标题翻译：使用能量转移检测的单分子测序的方法和装置
公开(公告)号：US08999674B2
公开(公告)日：2015-04-07
申请号：US13562159
申请日：2012-07-30
申请人： Joseph Beechem , Theo Nikiforov , Vi-En Choong , Xinzhan Peng , Guobin Luo , Cheng-Yao Chen , Michael Previte
发明人： Joseph Beechem , Theo Nikiforov , Vi-En Choong , Xinzhan Peng , Guobin Luo , Cheng-Yao Chen , Michael Previte
IPC分类号： C12P19/34 , C12N9/12 , C07H19/20
CPC分类号： C12Q1/6869 , C07H19/20 , C12N9/1241 , C12N9/1252 , C12N9/96 , C12Q1/6818 , C12Y207/07 , C12Y207/07007 , G01N21/6428 , G01N33/582 , G01N2021/6432
摘要： Provided herein are systems and methods for nucleotide incorporation reactions. The systems comprise polymerases having altered nucleotide incorporation kinetics and are linked to an energy transfer donor moiety, and nucleotide molecules linked with at least one energy transfer acceptor moiety. The donor and acceptor moieties undergo energy transfer when the polymerase and nucleotide are proximal to each other during nucleotide binding and/or nucleotide incorporation. As the donor and acceptor moieties undergo energy transfer, they generate an energy transfer signal which can be associated with nucleotide binding or incorporation. Detecting a time sequence of the generated signals, or the change in the signals, can be used to determine the order of the incorporated nucleotides, and can therefore be used to deduce the sequence of the target molecule.
摘要翻译：本文提供了用于核苷酸掺入反应的系统和方法。该系统包含具有改变的核苷酸掺入动力学并且与能量转移供体部分连接的聚合酶，以及与至少一个能量转移受体部分连接的核苷酸分子。当核苷酸结合和/或核苷酸掺入期间聚合酶和核苷酸彼此接近时，供体和受体部分进行能量转移。当供体和受体部分进行能量转移时，它们产生可与核苷酸结合或掺入相关联的能量转移信号。检测所产生的信号的时间序列或信号的变化可用于确定掺入的核苷酸的顺序，因此可用于推导靶分子的序列。

2. 发明申请

US20110281740A1 Methods for Real Time Single Molecule Sequencing 审中-公开
标题翻译：实时单分子测序方法
公开(公告)号：US20110281740A1
公开(公告)日：2011-11-17
申请号：US13001545
申请日：2009-06-30
申请人： Joseph Beechem , Vi-En Choong , Theo Nikiforov
发明人： Joseph Beechem , Vi-En Choong , Theo Nikiforov
IPC分类号： C40B30/00 , C12Q1/68
CPC分类号： C12Q1/686 , C12Q1/6869 , C12Q2565/629 , C12Q2565/301 , C12Q2565/101
摘要： Provided herein are methods and compositions for real time single molecule sequencing of a polymeric molecule, such as a polynucleotide, by isolating the polymeric molecule in a nanofluidic device, subjecting it in situ to a polymerase reaction wherein various components of the polymerase reaction mixture are labeled, and determining the time-sequence of incorporation of monomeric subunits during the polymerization process.
摘要翻译：本文提供了通过在纳米流体装置中分离聚合物分子来对聚合物分子例如多核苷酸进行实时单分子测序的方法和组合物，将其原位进行聚合酶反应，其中聚合酶反应混合物的各种组分被标记，并确定聚合过程中单体亚单位的掺入时间顺序。

3. 发明申请

US20100035268A1 MATERIALS AND METHODS FOR SINGLE MOLECULE NUCLEIC ACID SEQUENCING 审中-公开
标题翻译：单分子核酸序列的材料与方法
公开(公告)号：US20100035268A1
公开(公告)日：2010-02-11
申请号：US12528311
申请日：2008-02-21
申请人： Joseph Beechem , Vi-En Choong , Theo Nikiforov
发明人： Joseph Beechem , Vi-En Choong , Theo Nikiforov
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6827 , C12Q1/6874 , C12Q2565/518 , C12Q2565/101 , C12Q2563/113
摘要： Provided herein are methods and compositions for real time single molecule sequencing of short nucleotide sequences using nucleotide fluorescent semiconductor nanocrystals-conjugated nucleotide primers.
摘要翻译：本文提供了使用核苷酸荧光半导体纳米晶体共轭核苷酸引物对短核苷酸序列进行实时单分子测序的方法和组合物。

4. 发明授权

US08603792B2 Conjugates of biomolecules to nanoparticles 有权
标题翻译：生物分子与纳米颗粒的结合
公开(公告)号：US08603792B2
公开(公告)日：2013-12-10
申请号：US12748355
申请日：2010-03-26
申请人： Theo Nikiforov , Daniel Mazur , Xinzhan Peng , Tommie Lloyd Lincecum, Jr. , Yuri Belosludtsev , Howard Reese , Dmitriy Gremyachinskiy , Roman Rozhkov , John M. Mauro , Joseph Beechem , Eric Tulsky , Imad Naasani , Kari Haley , Joseph A. Treadway
发明人： Theo Nikiforov , Daniel Mazur , Xinzhan Peng , Tommie Lloyd Lincecum, Jr. , Yuri Belosludtsev , Howard Reese , Dmitriy Gremyachinskiy , Roman Rozhkov , John M. Mauro , Joseph Beechem , Eric Tulsky , Imad Naasani , Kari Haley , Joseph A. Treadway
IPC分类号： C12N9/12
CPC分类号： C12Q1/6869 , C07H19/20 , C12N9/1241 , C12N9/1252 , C12N9/96 , C12Q1/6818 , C12Y207/07 , C12Y207/07007 , G01N21/6428 , G01N33/582 , G01N2021/6432
摘要： Disclosed herein are conjugates comprising a biomolecule linked to a label that have biological activity and are useful in a wide variety of biological applications. For example, provided herein are polymerase-nanoparticle conjugates including a polymerase linked to a nanoparticle, wherein the conjugate has polymerase activity. Such conjugates can exhibit reduced aggregation and improved stochiometries wherein the average biomolecule:nanoparticle ratio approaches or equals 1:1. Also disclosed herein are improved methods for preparing such conjugates, and methods and systems for using such conjugates in biological applications such as nucleotide incorporation, primer extension and single molecule sequencing.
摘要翻译：本文公开了包含连接到具有生物活性并可用于多种生物应用的标签的生物分子的缀合物。例如，本文提供了聚合酶 - 纳米颗粒缀合物，其包括与纳米颗粒连接的聚合酶，其中缀合物具有聚合酶活性。这样的缀合物可以表现出减少的聚集和改进的沉淀物，其中平均生物分子：纳米颗粒比接近或等于1:1。本文还公开了制备这种缀合物的改进方法，以及在生物应用中使用这种缀合物的方法和系统，例如核苷酸掺入，引物延伸和单分子测序。

5. 发明申请

US20110003343A1 CONJUGATES OF BIOMOLECULES TO NANOPARTICLES 有权
标题翻译：生物分子与纳米颗粒的结合
公开(公告)号：US20110003343A1
公开(公告)日：2011-01-06
申请号：US12748355
申请日：2010-03-26
申请人： Theo Nikiforov , Daniel Mazur , Xinzhan Peng , Tommie Lloyd Lincecum, JR. , Yuri Belosludtsev , Howard Reese , Dmitriy Gremyachinskiy , Roman Rozhkov , John M. Mauro , Joseph Beechem , Eric Tulsky , Imad Naasani , Kari Haley , Joseph A. Treadway
发明人： Theo Nikiforov , Daniel Mazur , Xinzhan Peng , Tommie Lloyd Lincecum, JR. , Yuri Belosludtsev , Howard Reese , Dmitriy Gremyachinskiy , Roman Rozhkov , John M. Mauro , Joseph Beechem , Eric Tulsky , Imad Naasani , Kari Haley , Joseph A. Treadway
IPC分类号： C12P19/34 , C12N9/10
CPC分类号： C12Q1/6869 , C07H19/20 , C12N9/1241 , C12N9/1252 , C12N9/96 , C12Q1/6818 , C12Y207/07 , C12Y207/07007 , G01N21/6428 , G01N33/582 , G01N2021/6432
摘要： Disclosed herein are conjugates comprising a biomolecule linked to a label that have biological activity and are useful in a wide variety of biological applications. For example, provided herein are polymerase-nanoparticle conjugates including a polymerase linked to a nanoparticle, wherein the conjugate has polymerase activity. Such conjugates can exhibit reduced aggregation and improved stochiometries wherein the average biomolecule:nanoparticle ratio approaches or equals 1:1. Also disclosed herein are improved methods for preparing such conjugates, and methods and systems for using such conjugates in biological applications such as nucleotide incorporation, primer extension and single molecule sequencing.
摘要翻译：本文公开了包含连接到具有生物活性并可用于多种生物应用的标签的生物分子的缀合物。例如，本文提供了聚合酶 - 纳米颗粒缀合物，其包括与纳米颗粒连接的聚合酶，其中缀合物具有聚合酶活性。这样的缀合物可以表现出减少的聚集和改进的沉淀物，其中平均生物分子：纳米颗粒比接近或等于1:1。本文还公开了制备这种缀合物的改进方法，以及在生物应用中使用这种缀合物的方法和系统，例如核苷酸掺入，引物延伸和单分子测序。

6. 发明授权

US09868945B2 Linking methods, compositions, systems, kits and apparatuses 有权
公开(公告)号：US09868945B2
公开(公告)日：2018-01-16
申请号：US13984346
申请日：2012-02-08
申请人： John Davidson , Theo Nikiforov , Guobin Luo
发明人： John Davidson , Theo Nikiforov , Guobin Luo
IPC分类号： C12N11/10 , C12N9/12 , C12Q1/68
CPC分类号： C12N11/10 , C12N9/1241 , C12Q1/68 , G01N2333/9126
摘要： In some embodiments, the disclosure relates generally to methods as well as related compositions, systems, kits and apparatus comprising linking proteins to target compounds and/or to locations of interest using tethers. For example, the tether can be used to link the protein to a target compound, for example, to link an enzyme to a substrate. Similarly, the tether can be used to link the protein at or near a desired location on a surface. In one group of embodiments, the tether includes a polynucleotide and the target compound or location on the surface includes another polynucleotide that is capable of hybridizing to the tether. In such embodiments, the tether can be used to link the protein to the target compound or location using nucleic acid hybridization.

7. 发明申请

US20070161071A1 Assay methods and systems 审中-公开
标题翻译：测定方法和系统
公开(公告)号：US20070161071A1
公开(公告)日：2007-07-12
申请号：US11595271
申请日：2006-11-10
申请人： Theo Nikiforov
发明人： Theo Nikiforov
IPC分类号： C12Q1/48
CPC分类号： G01N33/542 , C12Q1/37 , C12Q1/42 , C12Q1/48 , C12Q1/485 , C12Q1/6816 , G01N2333/9121 , C12Q2565/107 , C12Q2563/107
摘要： Methods, systems, kits for carrying out a wide variety of different assays that comprise providing a first reagent mixture which comprises a first reagent having a fluorescent label. A second reagent is introduced into the first reagent mixture to produce a second reagent mixture, where the second reagent reacts with the first reagent to produce a fluorescently labeled product having a substantially different charge than the first reagent. A polyion is introduced into at least one of the first and second reagent mixtures, and the fluorescent polarization in the second reagent mixture relative to the first reagent mixture is determined, this fluorescent polarization being indicative of the rate or extent of the reaction.
摘要翻译：用于进行各种不同测定的方法，系统，试剂盒，其包括提供包含具有荧光标记的第一试剂的第一试剂混合物。将第二试剂引入第一试剂混合物中以产生第二试剂混合物，其中第二试剂与第一试剂反应以产生具有与第一试剂基本不同的电荷的荧光标记产物。将聚离子引入第一和第二试剂混合物中的至少一种，并且确定第二试剂混合物中相对于第一试剂混合物的荧光偏振，该荧光偏振指示反应的速率或程度。

8. 发明申请

US20060254503A1 Seed layers, cap layers, and thin films and methods of making thereof 有权
标题翻译：种子层，盖层和薄膜及其制造方法
公开(公告)号：US20060254503A1
公开(公告)日：2006-11-16
申请号：US11433824
申请日：2006-05-15
申请人： Haixia Dai , Khashayar Pakbaz , Michael Spaid , Theo Nikiforov
发明人： Haixia Dai , Khashayar Pakbaz , Michael Spaid , Theo Nikiforov
IPC分类号： C30B23/00
CPC分类号： C23C18/1608 , B82Y30/00 , C23C18/1844 , C23C18/50 , H01L21/288 , H01L21/76814 , H01L21/76843 , H01L21/76849 , H01L21/7685 , H01L21/76861 , H01L21/76864 , H01L21/76867 , H01L21/76868 , H01L21/76871 , H01L21/76874 , H01L21/76879
摘要： A seed layer is formed on a substrate using a first biological agent. The seed layer may comprise densified nanoparticles which are bound to the biological agent. The seed layer is then used for a deposition of a metal layer, such as a barrier layer, an interconnect layer, a cap layer and/or a bus line for a solid state device.
摘要翻译：使用第一生物试剂在基材上形成种子层。种子层可以包含与生物制剂结合的致密化纳米颗粒。然后种子层用于沉积用于固态器件的金属层，例如阻挡层，互连层，盖层和/或总线。

9. 发明申请

US20060068410A1 Methods and systems for monitoring intracellular binding reactions 审中-公开
公开(公告)号：US20060068410A1
公开(公告)日：2006-03-30
申请号：US11070155
申请日：2005-03-01
申请人： H. Wada , Javier Farinas , Theo Nikiforov
发明人： H. Wada , Javier Farinas , Theo Nikiforov
IPC分类号： C12Q1/68 , C12M1/34
CPC分类号： C12Q1/6841 , G01N21/6428 , G01N21/6445 , G01N21/6458 , G01N33/5008 , G01N33/5041 , G01N33/542 , G01N33/582 , G01N33/6872 , C12Q2561/119
摘要： Intracellular binding reactions, and particularly DNA/DNA binding protein reactions are detected in situ, using intracellular fluorescence polarization detection. The methods comprise providing a biological cell having at least a first component of a binding reaction disposed therein. The cell is contacted with a second component of the binding reaction whereby the second component is internalized within the biological cell. At least one of the first and second components has a fluorescent label. The amount of binding between the first and second components within the cell is determined by measuring a level of polarized and/or depolarized fluorescence emitted from within the biological cell.

10. 发明授权

US08632975B2 Nucleotide transient binding for sequencing methods 有权
标题翻译：测序方法的核苷酸瞬变结合
公开(公告)号：US08632975B2
公开(公告)日：2014-01-21
申请号：US12790760
申请日：2010-05-28
申请人： Peter B. Vander Horn , Cheng-Yao Chen , Guobin Luo , Michael Previte , Jamshid Temirov , Theo Nikiforov , Zhaohui Zhou , Hongye Sun , Yufang Wang , Stefanie Yukiko Nishimura , Hongyi Wang , Marian Peris , Barnett B. Rosenblum , Michael Phelan
发明人： Peter B. Vander Horn , Cheng-Yao Chen , Guobin Luo , Michael Previte , Jamshid Temirov , Theo Nikiforov , Zhaohui Zhou , Hongye Sun , Yufang Wang , Stefanie Yukiko Nishimura , Hongyi Wang , Marian Peris , Barnett B. Rosenblum , Michael Phelan
IPC分类号： C12Q1/68
CPC分类号： C12N9/1252 , C12Q1/68 , C12Q1/6804 , C12Q1/6818 , C12Q1/6827 , C12Q1/6869 , C12Q1/6872 , C12Y207/07007 , G01N2500/00 , C12Q2565/632 , C12Q2563/137 , C12Q2563/107 , C12Q2565/30 , C12Q2537/157
摘要： Provided herein are compositions and systems for use in polymerase-dependent, nucleotide transient-binding methods. The methods are useful for deducing the sequence of a template nucleic acid molecule and single nucleotide polymorphism (SNP) analyses. The methods rely on the fact that the polymerase transient-binding time for a complementary nucleotide is longer compared to that of a non-complementary nucleotide. The labeled nucleotides transiently-binds the polymerase in a template-dependent manner, but does not incorporate. The methods are conducted under any reaction condition that permits transient binding of a complementary or non-complementary nucleotide to a polymerase, and inhibits nucleotide incorporation.
摘要翻译：本文提供了用于聚合酶依赖性核苷酸瞬变结合方法的组合物和系统。该方法可用于推导模板核酸分子和单核苷酸多态性（SNP）分析的序列。该方法依赖于与非互补核苷酸相比，互补核苷酸的聚合酶瞬时结合时间更长的事实。标记的核苷酸以模板依赖的方式瞬时结合聚合酶，但不包括在内。所述方法在允许互补或非互补核苷酸与聚合酶短暂结合并且抑制核苷酸掺入的任何反应条件下进行。

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