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1. 发明申请

US20060035275A1 Nucleic acid diagnostic reagents and methods for detecting nucleic acids, polynucleotides and oligonucleotides 审中-公开
公开(公告)号：US20060035275A1
公开(公告)日：2006-02-16
申请号：US11264859
申请日：2005-11-02
申请人： David Ward , Ronald Breaker
发明人： David Ward , Ronald Breaker
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6811 , C12Q1/6816 , C12Q2521/337 , C12Q2521/343 , C12Q2563/125
摘要： Methods for generating nucleic acid reagents useful for detecting nucleic acids, polynucleotides, and oligonucleotides are disclosed. Selection techniques, enzymatic nucleic acid molecules, allozymes (allosteric nucleic acid sensor molecules), ribozymes, and DNAzymes used as diagnostic reagents and tools are described.

2. 发明申请

US20050227331A1 Conjoined polynucleotide catalysts 审中-公开
标题翻译：连接的多核苷酸催化剂
公开(公告)号：US20050227331A1
公开(公告)日：2005-10-13
申请号：US11054106
申请日：2005-02-09
申请人： Ronald Breaker
发明人： Ronald Breaker
IPC分类号： C12N9/12 , C12N15/62 , C07H21/02 , C07H21/04 , C12P19/28
CPC分类号： C12N9/1205 , C07K2319/00 , C12N15/62
摘要： Conjoined polynucleotides are linked RNA and/or DNA that comprise at least tow catalytic domains which function in concert to provide a chemical transformation involving multiple sequential or component reactions. In many embodiments, the domains are fused together, typically by means of conventional 3′→5′ phosphodiester bonds, with or without intervening nucleotides which are not part of the catalytic domains per se, to form conjoined polynucleotides using standard ligation procedures. Conjoined DNA comprising kinase and adenylase domains and conjoined polynucleotides comprising kinase; adenylase, and ligase domains are useful in DNA cloning.
摘要翻译：连接的多核苷酸是连接的RNA和/或DNA，其包含至少两个催化结构域，其一起起作用以提供涉及多个连续或组分反应的化学转化。在许多实施方案中，通常使用常规的3' - > 5'磷酸二酯键将结构域融合在一起，具有或不具有不属于催化结构域本身的中间核苷酸，以使用标准连接方法形成结合的多核苷酸。包含激酶和腺苷酸结构域的结合的DNA和包含激酶的结合的多核苷酸; 腺苷酸酶和连接酶结构域可用于DNA克隆。

3. 发明申请

US20050053951A1 Riboswitches, methods for their use, and compositions for use with riboswitches 有权
标题翻译：核糖开关，其使用方法和用于核糖开关的组合物
公开(公告)号：US20050053951A1
公开(公告)日：2005-03-10
申请号：US10669162
申请日：2003-09-22
申请人： Ronald Breaker , Ali Nahvi , Narasimhan Sudarsan , Margaret Ebert , Wade Winkler , Jeffrey Barrick , John Wickiser
发明人： Ronald Breaker , Ali Nahvi , Narasimhan Sudarsan , Margaret Ebert , Wade Winkler , Jeffrey Barrick , John Wickiser
IPC分类号： C12N15/113 , C12N15/115 , C12N15/67 , C12Q1/68 , C07H21/02
CPC分类号： C12N15/113 , A61K31/00 , C07D415/00 , C07D473/18 , C07D473/34 , C12N15/115 , C12N15/67 , C12N2310/53
摘要： It has been discovered that certain natural mRNAs serve as metabolite-sensitive genetic switches wherein the RNA directly binds a small organic molecule. This binding process changes the conformation of the mRNA, which causes a change in gene expression by a variety of different mechanisms. Modified versions of these natural “riboswitches” (created by using various nucleic acid engineering strategies) can be employed as designer genetic switches that are controlled by specific effector compounds. Such effector compounds that activate a riboswitch are referred to herein as trigger molecules. The natural switches are targets for antibiotics and other small molecule therapies. In addition, the architecture of riboswitches allows actual pieces of the natural switches to be used to construct new non-immunogenic genetic control elements, for example the aptamer (molecular recognition) domain can be swapped with other non-natural aptamers (or otherwise modified) such that the new recognition domain causes genetic modulation with user-defined effector compounds. The changed switches become part of a therapy regimen-turning on, or off, or regulating protein synthesis. Newly constructed genetic regulation networks can be applied in such areas as living biosensors, metabolic engineering of organisms, and in advanced forms of gene therapy treatments.
摘要翻译：已经发现某些天然mRNA用作代谢物敏感的遗传开关，其中RNA直接结合小的有机分子。这种结合过程改变mRNA的构象，其通过各种不同的机制引起基因表达的改变。这些天然“核糖开关”（通过使用各种核酸工程策略产生）的修饰版本可被用作由特异性效应子化合物控制的设计者遗传开关。激活核糖开关的这种效应化合物在本文中称为触发分子。天然开关是抗生素和其他小分子治疗的靶标。此外，核糖开关的结构允许使用自然开关的实际部分来构建新的非免疫原性遗传控制元件，例如适配子（分子识别）结构域可以与其他非天然适体（或以其它方式修饰）交换，使得新的识别域引起用户定义的效应子化合物的遗传调节。改变的开关成为治疗方案的一部分 - 打开或关闭或调节蛋白质合成。新建的遗传调控网络可以应用于生物传感器，生物体的代谢工程和基因治疗治疗的先进形式等领域。

4. 发明授权

US06831171B2 Nucleic acid catalysts with endonuclease activity 有权
标题翻译：具有核酸内切酶活性的核酸催化剂
公开(公告)号：US06831171B2
公开(公告)日：2004-12-14
申请号：US09780929
申请日：2001-02-08
申请人： Ronald Breaker , Leonid Beigelman
发明人： Ronald Breaker , Leonid Beigelman
IPC分类号： C07H2104
CPC分类号： A61K31/7115 , A61K31/7105 , A61K31/711 , A61K31/712 , A61K31/7125
摘要： The present invention relates to novel Nucleic acid catalysts, methods of synthesis, and uses thereof.
摘要翻译：本发明涉及新型的核酸催化剂，其合成方法及其应用。

5. 发明申请

US20060121510A1 Multidomain polynucleotide molecular sensors 审中-公开
标题翻译：多域多核苷酸分子传感器
公开(公告)号：US20060121510A1
公开(公告)日：2006-06-08
申请号：US11288869
申请日：2005-11-28
申请人： Ronald Breaker , Garrett Soukup
发明人： Ronald Breaker , Garrett Soukup
IPC分类号： C12Q1/68 , C07H21/02
CPC分类号： G01N33/5308 , G01N2333/9005
摘要： Multidomain polynucleotides responsive to signalling agents are designed and constructed to have at least three domains which can be partially or completely overlapping or nonoverlapping: an actuator (catalytic or reporter) domain, a bridging domain, and a receptor domain. In a typical embodiment, a signalling agent such as a chemical ligand interacts with the receptor domain, which changes conformation or otherwise influences the bridging domain so that the activity, catalytic, or reporter function of the actuator domain is stimulated or inhibited. In some ribozyme embodiments, for example, ligand-specific molecular sensors composed of RNA are created by coupling pre-existing catalytic and receptor domains via novel structural bridges which function such that binding of a ligand to the receptor domain triggers a conformational change within the bridge, and this structural reorganization dictates the activity of the adjoining ribozyme. Processes for allosterically selecting other multidomain polynucleotides typically involve mixing and matching domains to optimize binding or other signal response and/or reporter activity.
摘要翻译：响应于信号传导剂的多结构域多核苷酸被设计和构建为具有至少三个结构域，其可以部分或完全重叠或不重叠：致动器（催化或报告分子）结构域，桥连结构域和受体结构域。在典型的实施方案中，诸如化学配体的信号传导剂与受体结构域相互作用，其改变构象或以其它方式影响桥接结构域，从而刺激或抑制致动器结构域的活性，催化或报道分子功能。在一些核酶实施方案中，例如，由RNA组成的配体特异性分子传感器是通过经由新的结构桥连接先前存在的催化剂和受体结构域而产生的，其功能是使配体与受体结构域结合触发桥内的构象变化，这种结构重组决定了邻接核酶的活性。用于变构选择其他多结构域多核苷酸的方法通常涉及混合和匹配结构域以优化结合或其它信号应答和/或报道活性。

6. 发明申请

US20070219365A1 ENZYMATIC NUCLEIC ACID MOLECULES 有权
标题翻译：酶的核酸分子
公开(公告)号：US20070219365A1
公开(公告)日：2007-09-20
申请号：US11605177
申请日：2006-11-28
申请人： Gerald Joyce , Ronald Breaker
发明人： Gerald Joyce , Ronald Breaker
IPC分类号： C07H21/04
CPC分类号： C07H21/02 , C07H21/04 , C12Q1/6806 , C12Q2521/337
摘要： The present invention discloses nucleic acid enzymes and deoxyribonucleic acid enzymes capable of cleaving nucleic acid sequences or molecules, particularly RNA, in a site-specific manner, as well as compositions including same. Methods of making and using the disclosed enzymes and compositions are also disclosed.
摘要翻译：本发明公开了能够以位点特异性方式切割核酸序列或分子，特别是RNA的核酸酶和脱氧核糖核酸酶，以及包含其的组合物。还公开了制备和使用所公开的酶和组合物的方法。

7. 发明申请

US20050176017A1 Bioreactive allosteric polynucleotides 审中-公开
标题翻译：生物反应性变构多核苷酸
公开(公告)号：US20050176017A1
公开(公告)日：2005-08-11
申请号：US10680067
申请日：2003-10-06
申请人： Ronald Breaker
发明人： Ronald Breaker
IPC分类号： C12N15/09 , C12M1/00 , C12N15/10 , C12N15/113 , C12Q1/68 , C07H21/04 , C12N9/00
CPC分类号： C12N15/113 , C07K2319/00 , C12N15/101 , C12N2310/111 , C12N2310/12 , C12N2310/121 , C12N2310/322 , C12Q1/6811 , C12Q1/6825 , C12Q2521/337 , C12Q2525/205
摘要： Polynucleotides having allosteric properties that modify a function or configuration of the polynucleotide with a chemical effector and/or physical signal are employed primarily as biosensors and/or enzymes for diagnostic and catalytic purposes. In some preferred embodiments, the polynucleotides are DNA enzymes that are used in solution/suspension or attached to a solid support as biosensors to detect the presence or absence of a compound, its concentration, or physical change in a sample by observation of self-catalysis. Chemical effectors include organic compounds such as amino acids, amino acid derivatives, peptides, nucleosides, nucleotides, steroids, and mixtures of these with each other and with metal ions, cellular metabolites or blood components obtained from biological samples, steroids, pharmaceuticals, pesticides, herbicides, food toxins, and the like. Physical signals include radiation, temperature changes, and combinations thereof.
摘要翻译：具有修饰具有化学效应物和/或物理信号的多核苷酸的功能或构型的变构性质的多核苷酸主要用作用于诊断和催化目的的生物传感器和/或酶。在一些优选的实施方案中，多核苷酸是在溶液/悬浮液中使用的DNA酶，或者作为生物传感器连接到固体支持物上，以通过观察自身催化来检测样品中是否存在化合物，其浓度或物理变化。化学效应剂包括有机化合物，例如氨基酸，氨基酸衍生物，肽，核苷，核苷酸，类固醇，以及它们彼此之间的混合物，以及与生物样品，类固醇，药物，杀虫剂，金属离子，细胞代谢物或血液成分的有机化合物，除草剂，食物毒素等。物理信号包括辐射，温度变化及其组合。

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