公开(公告)号：US20060024681A1

公开(公告)日：2006-02-02

申请号：US10978224

申请日：2004-10-29

申请人： Douglas Smith ,  Joel Malek ,  Kevin McKernan

发明人： Douglas Smith ,  Joel Malek ,  Kevin McKernan

IPC分类号： C12Q1/68 ,  C12P19/34

CPC分类号： C12Q1/6806 ,  C12P19/34 ,  C12Q1/6816 ,  C12Q2525/191 ,  C12Q2521/313 ,  C12Q2525/131 ,  C12Q2521/501

摘要： Methods for producing a paired tag from a nucleic acid sequence are provided in which the paired tag comprises the 5′ end tag and 3′ end tag of the nucleic acid sequence. In one embodiment, the nucleic acid sequence comprises two restriction endonuclease recognition sites specific for a restriction endonuclease that cleaves the nucleic acid sequence distally to the restriction endonuclease recognition sites. In another embodiment, the nucleic acid sequence further comprises restriction endonuclease recognition sites specific for a rare cutting restriction endonuclease. Methods of using paired tags are also provided. In one embodiment, paired tags are used to characterize a nucleic acid sequence. In a particular embodiment, the nucleic acid sequence is a genome. In one embodiment, the characterization of a nucleic acid sequence is karyotyping. Alternatively, in another embodiment, the characterization of a nucleic acid sequence is mapping of the sequence. In a further embodiment, a method is provided for identifying nucleic acid sequences that encode at least two interacting proteins.

摘要翻译： 提供了从核酸序列产生配对标签的方法，其中配对标签包含核酸序列的5'末端标签和3'末端标签。 在一个实施方案中，核酸序列包含限制性内切核酸酶特异性的两个限制性内切核酸酶识别位点，其将核酸序列向远端切割至限制性内切核酸酶识别位点。 在另一个实施方案中，核酸序列还包含限制性内切核酸酶识别位点，其特异于稀有切割限制性内切核酸酶。 还提供了使用配对标签的方法。 在一个实施方案中，配对标签用于表征核酸序列。 在一个具体实施方案中，核酸序列是基因组。 在一个实施方案中，核酸序列的表征是核型分析。 或者，在另一个实施方案中，核酸序列的表征是序列的映射。 在另一个实施方案中，提供了用于鉴定编码至少两种相互作用蛋白质的核酸序列的方法。

公开(公告)号：US20050026218A1

公开(公告)日：2005-02-03

申请号：US10858837

申请日：2004-06-01

申请人： Joel Malek

发明人： Joel Malek

IPC分类号： C07H21/04 ,  C07K14/29 ,  C12N1/21 ,  G01N33/569 ,  G01N33/53 ,  C07K14/195

CPC分类号： C07H21/04 ,  C07K14/29 ,  G01N33/56911 ,  G01N2333/29 ,  G01N2500/02 ,  Y02A50/59

摘要： The present invention relates to isolated nucleic acids that encode polypeptides that interact with T4SS (referred to herein as “T4SS interactor nucleic acids” and “T4SS interactor polypeptides”) and complements, orthologs, portions and variants thereof. The present invention also relates to isolated T4SS interactor polypeptides, orthologs and portions thereof, and antibodies or antigen binding fragments thereof that specifically bind a T4SS interactor polypeptide. The present invention also relates to constructs and host cells comprising the nucleic acid molecules described herein. In addition, the present invention relates to uses of the nucleic acid and polypeptide molecules provided herein.

摘要翻译： 本发明涉及编码与T4SS（本文中称为“T4SS相互作用核酸”和“T4SS相互作用多肽”）以及其互补序列，直向同源物，其部分和变体相互作用的多肽的分离的核酸。 本发明还涉及分离的T4SS相互作用多肽，直向同源物及其部分，以及特异性结合T4SS相互作用多肽的抗体或其抗原结合片段。 本发明还涉及包含本文所述的核酸分子的构建体和宿主细胞。 此外，本发明涉及本文提供的核酸和多肽分子的用途。

公开(公告)号：US20070172839A1

公开(公告)日：2007-07-26

申请号：US11338620

申请日：2006-01-24

申请人： Douglas Smith ,  Joel Malek

发明人： Douglas Smith ,  Joel Malek

IPC分类号： C12Q1/68 ,  C12P19/34 ,  C07H21/04

CPC分类号： C12Q1/6855 ,  C12N15/1093

摘要： A pair of asymmetrical, partially double-stranded oligonucleotide adapters are provided wherein the pair of adapters comprise a first asymmetrical oligonucleotide adapter comprising a single-stranded 3′ overhang and a second asymmetrical double-stranded oligonucleotide adapter comprising a single-stranded 5′ overhang and at least one blocking group on the strand of said second asymmetrical oligonucleotide adapter that does not comprise the 5′ overhang. Also provided are a pair of double-stranded Y oligonucleotide adapters and a pair of double-stranded bubble oligonucleotide adapters and methods of using said asymmetrical adapters for amplification of at least one double stranded nucleic acid molecule, wherein the amplification produces a plurality of amplified nucleic acid molecules having a different nucleic acid sequence at each end are also described. Also provided is a method for exponentially amplifying one strand in a double-stranded nucleic acid molecule. Also provided are methods for preparing libraries of paired tags using COS-linkers. Also provided are cleavable adapters comprising an affinity tag and a cleavable linkage, wherein cleaving the cleavable linkage produces two complementary ends. Methods of using the cleavable adapters to produce a paired tag library are also described.

摘要翻译： 提供了一对不对称的部分双链寡核苷酸衔接子，其中该对衔接子包含第一不对称寡核苷酸衔接子，其包含单链3'突出端和包含单链5'突出端的第二不对称双链寡核苷酸衔接子， 所述第二不对称寡核苷酸适配器的链上至少有一个不包含5'突出端的封闭基团。 还提供了一对双链Y寡核苷酸衔接子和一对双链泡沫寡核苷酸衔接子以及使用所述不对称衔接子扩增至少一个双链核酸分子的方法，其中扩增产生多个扩增核酸 还描述了在每一端具有不同核酸序列的酸分子。 还提供了用于指数增加双链核酸分子中的一条链的方法。 还提供了使用COS-接头来制备配对标签库的方法。 还提供了包含亲和标签和可切割键的可切割衔接子，其中切割可切割连接键产生两个互补末端。 还描述了使用可切割适配器产生配对标签库的方法。