公开(公告)号：US10272409B2

公开(公告)日：2019-04-30

申请号：US12080720

申请日：2008-04-04

申请人： Michael E. Hogan ,  Sergy Lemeshko ,  Yuri Belosludtsev ,  Thomas F. Powdrill ,  Rahul Mitra ,  Joseph G. Utermohlen ,  Frederick H. Eggers

发明人： Michael E. Hogan ,  Sergy Lemeshko ,  Yuri Belosludtsev ,  Thomas F. Powdrill ,  Rahul Mitra ,  Joseph G. Utermohlen ,  Frederick H. Eggers

IPC分类号： C12Q1/68 ,  C12P19/34 ,  B01J19/00

摘要： Provided herein are biomolecular hybridization devices comprising a substrate with a permanently and covalently attached surface of functional groups and an adsorbed monolayer of unmodified, single-stranded oligonucleotides all of which are 10 to about 24 bases in length as a saturated film of constrained oligonucleotides on the surface via direct non-covalent phosphate-surface adsorptive contact of substantially all phosphate groups of each oligonucleotide. The constrained oligonucleotides are effective to dissociably hybridize to a complementary single-stranded nucleic acid with asymmetric, non-helical base pairing and without oligonucleotide dissociation from the surface of the device. Also, provided are methods for hybridizing solution-state target nucleic acids to probe nucleic acids and for identifying a nucleotide sequence to which a nucleotide-binding protein binds using the biomolecular hybridization devices.

公开(公告)号：US20090011949A1

公开(公告)日：2009-01-08

申请号：US12080720

申请日：2008-04-04

申请人： Michael E. Hogan ,  Sergy Lemeshko ,  Yuri Belosludtsev ,  Thomas F. Powdrill ,  Rahul Mitra ,  Joseph G. Utermohlen ,  Frederick H. Eggers

发明人： Michael E. Hogan ,  Sergy Lemeshko ,  Yuri Belosludtsev ,  Thomas F. Powdrill ,  Rahul Mitra ,  Joseph G. Utermohlen ,  Frederick H. Eggers

IPC分类号： C40B40/06 ,  C40B30/04

CPC分类号： B01J19/0046 ,  B01J2219/00376 ,  B01J2219/00497 ,  B01J2219/005 ,  B01J2219/00576 ,  B01J2219/00605 ,  B01J2219/00653 ,  B01J2219/00659 ,  B01J2219/00677 ,  B01J2219/00691 ,  B01J2219/00722

摘要： Provided herein are biomolecular hybridization devices comprising a substrate with a permanently and covalently attached surface of functional groups and an adsorbed monolayer of unmodified, single-stranded oligonucleotides all of which are 10 to about 24 bases in length as a saturated film of constrained oligonucleotides on the surface via direct non-covalent phosphate-surface adsorptive contact of substantially all phosphate groups of each oligonucleotide. The constrained oligonucleotides are effective to dissociably hybridize to a complementary single-stranded nucleic acid with asymmetric, non-helical base pairing and without oligonucleotide dissociation from the surface of the device. Also, provided are methods for hybridizing solution-state target nucleic acids to probe nucleic acids and for identifying a nucleotide sequence to which a nucleotide-binding protein binds using the biomolecular hybridization devices.

摘要翻译： 本文提供的生物分子杂交装置包括具有永久且共价连接的官能团表面的底物和未修饰的单链寡核苷酸的吸附单层，其长度为10至约24个碱基，作为约束寡核苷酸的饱和膜 通过每个寡核苷酸的基本上所有磷酸基团的直接非共价磷酸盐表面吸附接触表面。 受约束的寡核苷酸有效地与具有不对称，非螺旋碱基配对并且没有寡核苷酸与装置表面解离的互补单链核酸解离地杂交。 此外，提供了用于将溶液状态靶核酸杂交以探测核酸并用于鉴定核苷酸结合蛋白使用生物分子杂交装置结​​合的核苷酸序列的方法。

公开(公告)号：US07354710B2

公开(公告)日：2008-04-08

申请号：US10193938

申请日：2002-07-11

申请人： Michael Hogan ,  Sergy Lemeshko ,  Yuri Belosludtsev ,  Tom Powdrill ,  Rahul Mitra

发明人： Michael Hogan ,  Sergy Lemeshko ,  Yuri Belosludtsev ,  Tom Powdrill ,  Rahul Mitra

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6837 ,  B01J19/0046 ,  B01J2219/00376 ,  B01J2219/00387 ,  B01J2219/00497 ,  B01J2219/005 ,  B01J2219/00529 ,  B01J2219/00576 ,  B01J2219/00605 ,  B01J2219/00608 ,  B01J2219/00612 ,  B01J2219/00626 ,  B01J2219/00637 ,  B01J2219/00653 ,  B01J2219/00659 ,  B01J2219/00677 ,  B01J2219/00691 ,  B01J2219/00722 ,  C40B60/14 ,  C12Q2523/308

摘要： The present invention relates to simple method to fabricate DNA hybridization devices based upon adsorptive attachment of oligonucleotides to a positively charged surface. Such adsorbed oligonucleotide probes form a densely packed monolayer, which retains capacity for base-pair specific hybridization with a solution state nucleic acid target strand to form the duplex. However, both strand dissociation kinetics and the rate of DNase digestion suggest on symmetry grounds that solution-state nucleic acid binds to such adsorbed oligonucleotides to form a highly asymmetric and unwound duplex, with structural details that are substantially different from that known for the Watson-Crick DNA duplex. This novel nucleic acid duplex form can serve as the basis for a new class of hybridization device and methods for their use. It is also disclosed that new methods of nucleic acid duplex detection can be developed which are based upon the interaction of enzymes and dye labels with the unique structural characteristics of the non-helical duplex described herein. Preferred implementations of the invention include DNA microarrays, bead-based nucleic acid analysis, microelectronic devices to detect nucleic acid hybridization and more traditional methods of laboratory analysis, including hybridization on membranous and other solid supports.

摘要翻译： 本发明涉及基于将寡核苷酸吸附到带正电的表面上的DNA杂交装置的简单方法。 这种吸附的寡核苷酸探针形成密集填充的单层，其保留与溶液状态核酸靶链的碱基对特异性杂交以形成双链体的能力。 然而，链分解动力学和DNA酶消化速率都表明溶液状态核酸与这些吸附的寡核苷酸结合以形成高度不对称和未解链双链体的对称性，结构细节与Watson- 克里克DNA双链体。 这种新的核酸双相形式可以作为新一类杂交装置及其使用方法的基础。 还公开了可以开发新的核酸双相检测方法，其基于酶和染料标记与本文所述的非螺旋双螺旋的独特结构特征的相互作用。 本发明的优选实施方案包括DNA微阵列，基于珠的核酸分析，用于检测核酸杂交的微电子装置和更传统的实验室分析方法，包括膜质和其它固体支持物上的杂交。

公开(公告)号：US20110165652A1

公开(公告)日：2011-07-07

申请号：US12812952

申请日：2009-01-14

申请人： Susan H. Hardin ,  Tommie Lloyd Lincecum, JR. ,  Norha Deluge ,  Hongyi Wang ,  Yuri Belosludtsev ,  Kristi Kincaid ,  Anelia Kraltcheva ,  Benjamin Stevens ,  Ming Fa ,  Amy Bryant ,  Amy Castillo ,  Hye Eun Kim ,  Uma Nagaswamy ,  Mitsu Sreedhar Reddy ,  Alok N. Bandekar ,  Ivan Pan ,  Andrei Volkov

发明人： Susan H. Hardin ,  Tommie Lloyd Lincecum, JR. ,  Norha Deluge ,  Hongyi Wang ,  Yuri Belosludtsev ,  Kristi Kincaid ,  Anelia Kraltcheva ,  Benjamin Stevens ,  Ming Fa ,  Amy Bryant ,  Amy Castillo ,  Hye Eun Kim ,  Uma Nagaswamy ,  Mitsu Sreedhar Reddy ,  Alok N. Bandekar ,  Ivan Pan ,  Andrei Volkov

IPC分类号： C12N9/12

CPC分类号： C07H19/207 ,  C07H19/10 ,  C12N9/1252 ,  C12Q1/6869

摘要： Compositions, systems and methods of sequencing are disclosed, where the compositions and systems include polymerase enzymes that have been genetically modified to more efficiently incorporate nucleotides including labels having a detectable properties that are released during incorporation, to augment a rate of labeled nucleotide incorporation, to augment a rate of pyrophosphate release, or to augment two or more of these properties and rates. Also disclosed are terminally labeled and dual labeled nucleotides, and click-chemistry based methods of synthesizing the same.

摘要翻译： 公开了组合物，系统和测序方法，其中组合物和系统包括经遗传修饰以更有效地掺入核苷酸的聚合酶，包括在掺入期间释放的具有可检测性质的标记，以增加标记的核苷酸掺入率， 增加焦磷酸盐释放的速率，或增加这些性质和速率中的两种或更多种。 还公开了末端标记和双重标记的核苷酸，以及基于点击化学的合成方法。

公开(公告)号：US20090186343A1

公开(公告)日：2009-07-23

申请号：US12035352

申请日：2008-02-21

申请人： Hongyi Wang ,  Norha Deluge ,  Kristi Kincaid ,  Yuri Belosludtsev ,  Tommie Lincecum, JR. ,  Amy Williams ,  Amy Bryant ,  Ming Fa ,  Benjamin Stevens ,  Susan H. Hardin

发明人： Hongyi Wang ,  Norha Deluge ,  Kristi Kincaid ,  Yuri Belosludtsev ,  Tommie Lincecum, JR. ,  Amy Williams ,  Amy Bryant ,  Ming Fa ,  Benjamin Stevens ,  Susan H. Hardin

IPC分类号： C12Q1/68 ,  C12P19/34

CPC分类号： C07H1/00 ,  C07H19/10 ,  C07H19/20 ,  C07H21/00 ,  C12Q1/6869 ,  C12Q2565/101 ,  C12Q2525/117 ,  C12Q2521/101

摘要： A novel and efficient single pot synthetic schemes are disclosed for preparing modified nucleotides, nucleotide analogs, nucleotide polyphosphates, and nucleotide polyphosphate analogs. The novel method is used to prepare nucleotides, nucleotide analogs, nucleotide polyphosphates, and nucleotide polyphosphate analogs having non-persistent or persistent and non-persistent modifications. Novel biomolecular reactions are also disclosed using the novel modified biomolecules disclosed herein.

摘要翻译： 公开了一种用于制备修饰的核苷酸，核苷酸类似物，核苷酸多磷酸酯和核苷酸多磷酸酯类似物的新型和有效的单锅合成方案。 该新方法用于制备具有非持久性或持久性和非持久性修饰的核苷酸，核苷酸类似物，核苷酸多磷酸酯和核苷酸多磷酸酯类似物。 使用本文公开的新的改性生物分子也公开了新的生物分子反应。

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。

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。

公开(公告)号：US20080091005A1

公开(公告)日：2008-04-17

申请号：US11781160

申请日：2007-07-20

申请人： Hongyi Wang ,  Xiaolian Gao ,  Peilin Yu ,  Mitsu Reddy ,  Susan Hardin ,  Tommie Lincecum ,  Amy Williams ,  Norha Deluge ,  Yuri Belosludtsev ,  Steven Menchen ,  Joe Lam ,  Jer-Kang Chen

发明人： Hongyi Wang ,  Xiaolian Gao ,  Peilin Yu ,  Mitsu Reddy ,  Susan Hardin ,  Tommie Lincecum ,  Amy Williams ,  Norha Deluge ,  Yuri Belosludtsev ,  Steven Menchen ,  Joe Lam ,  Jer-Kang Chen

IPC分类号： C07H21/04

CPC分类号： C07H21/04

摘要： Modified nucleotides are disclosed for use in single molecule sequencing, methods for making the modified nucleotides and method for using the modified nucleotides. Linkers for making the modified nucleotide are also disclosed.

摘要翻译： 公开了用于单分子测序的修饰的核苷酸，用于制备修饰的核苷酸的方法和使用修饰的核苷酸的方法。 还公开了用于制备修饰的核苷酸的接头。

公开(公告)号：US20080076189A1

公开(公告)日：2008-03-27

申请号：US11694605

申请日：2007-03-30

申请人： Yuri Belosludtsev ,  Nasanshargal Battulga ,  Mistu Reddy ,  Anelia Kraltcheva ,  Susan Hardin ,  Tommie Lincecum ,  Hongyi Wang ,  Norha Deluge ,  Uma Nagaswamy ,  Benjamin Stevens ,  Kristi Kincaid

发明人： Yuri Belosludtsev ,  Nasanshargal Battulga ,  Mistu Reddy ,  Anelia Kraltcheva ,  Susan Hardin ,  Tommie Lincecum ,  Hongyi Wang ,  Norha Deluge ,  Uma Nagaswamy ,  Benjamin Stevens ,  Kristi Kincaid

IPC分类号： G01N21/64

CPC分类号： G01N21/6428

摘要： Support surfaces are disclosed that are designed to support molecules or molecular assemblies immobilized thereon so that the molecules or molecular assemblies can be observed in single molecule detections systems, where the support surfaces have reduced background and the fluorescent labels associated with the immobilized molecules or molecular assemblies have longer active lifetimes prior to permanent photo-bleaching or deactivation and have improve fluorescence properties and where the surfaces have more uniform fluorescent properties.

摘要翻译： 公开了支撑表面，其被设计成支持固定在其上的分子或分子组件，使得可以在单分子检测系统中观察分子或分子组件，其中支持表面具有降低的背景，并且与固定化分子或分子组装相关联的荧光标记 在永久性光漂白或去活化之前具有更长的活性寿命，并且具有改善的荧光性能以及其表面具有更均匀的荧光性质。