Composition of matter comprising library of first nucleic acid analyte copies

• US 20050009077A1
• Filed: 07/27/2004
• Published: 01/13/2005
• Est. Priority Date: 06/30/2001
• Status: Active Grant

• Current Assignee: Enzo Life Sciences Incorporated (Enzo Biochem Incorporated)
• Original Assignee: Enzo Life Sciences Incorporated (Enzo Biochem Incorporated)
• Inventors: Stavrianopoulos, Jannis G., Donegan, James J., Rabbani, Flazar, Coleman, Jack
• Granted Patent: US 9,790,621 B2
• Time in Patent Office: Days
• US Class Current: 506/16
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00599 Solution-phase processes
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12N 15/1006 by means of a solid support carrier, e.g. particles, polymers
• CPC Class Codes: C12N 15/1058 Directional evolution of libraries, e.g. evolution of libraries is achieved by mutagenesis and screening or selection of mixed population of organisms
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2545/114 involving a quantitation step
• CPC Class Codes: C12Q 2563/179 the label being a nucleic acid
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/514 characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array
• CPC Class Codes: C12Q 2565/537 : characterised by the capture oligonucleotide acting as a primer
• CPC Class Codes: C40B 40/00 : Libraries per se, e.g. arrays, mixtures
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: G01N 33/68 : involving proteins, peptides or amino acids involving lipoproteins G01N33/92

Abstract

This invention provides novel compositions and processes for analyte detection, quantification and amplification. Nucleic acid arrays and libraries of analytes are usefully incorporated into such compositions and processes. Universal detection elements, signaling entities and the like are employed to detect and if necessary or desirable, to quantify analytes. Amplification of target analytes are also provided by the compositions and processes of this invention.

Claims

1-211. -211. (CANCELED).

212. A composition of matter comprising a library of first nucleic acid copies, said first nucleic acid copies being hybridized to an array of nucleic acids, said nucleic acids being fixed or immobilized to a solid support, wherein said first nucleic acid copies comprise an inherent universal detection target (UDT) and a universal detection element (UDE) attached to said UDT, wherein said UDE generates a signal directly or indirectly to detect the presence or quantity of said analytes.

213. The composition of claim 212, wherein said library of analytes is derived from a biological source selected from the group consisting of organs, tissues and cells.

214. The composition of claim 212, wherein said analytes are selected from the group consisting of genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA and a combination of any of the foregoing.

215. The composition of claim 212, wherein said nucleic acid array is selected from the group consisting of DNA, RNA and analogs thereof.

216. The composition of claim 215, wherein said analogs comprise PNA.

217. The composition of claims 215 or 216, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

218. The composition of claim 212, wherein said solid support is porous or non-porous.

219. The composition of claim 218, wherein said porous solid support is selected from the group consisting of polyacrylamide and agarose.

220. The composition of claim 218, wherein said non-porous solid support comprises glass or plastic.

221. The composition of claim 212, wherein said solid support is transparent, translucent, opaque or reflective.

222. The composition of claim 212, wherein said nucleic acids are directly or indirectly fixed or immobilized to said solid support.

223. The composition of claim 222, wherein said nucleic acids are indirectly fixed or immobilized to said solid support by means of a chemical linker or linkage arm.

224. The composition of claim 212, wherein said inherent UDT is selected from the group consisting of poly T segments, secondary structures, consensus sequences, and a combination of any of the foregoing.

225. The composition of claim 224, wherein said consensus sequences is selected from the group consisting of signal sequences for polyA addition, splicing elements, multicopy repeats, and a combination of any of the foregoing.

226. The composition of claim 212, wherein said UDE is selected from the group consisting of nucleic acids, nucleic acid analogs, polypeptides, polysaccharides, synthetic polymers and a combination of any of the foregoing.

227. The composition of claim 226, wherein said analogs comprise PNA.

228. The composition of claim 212, wherein said UDE generates a signal directly or indirectly.

229. The composition of claim 228, wherein said direct signal generation is selected from the group consisting of a fluorescent compound, a phosphorescent compound, a chemiluminescent compound, a chelating compound, an electron dense compound, a magnetic compound, an intercalating compound, an energy transfer compound and a combination of any of the foregoing.

230. The composition of claim 228, wherein said indirect signal generation is selected from the group consisting of an antibody, an antigen, a hapten, a receptor, a hormone, a ligand, an enzyme and a combination of any of the foregoing.

231. The composition of claim 230, wherein said enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.

232. A composition of matter comprising a library of first nucleic acid copies, said first nucleic acid copies being hybridized to an array of nucleic acids, said nucleic acids being fixed or immobilized to a solid support, wherein said first nucleic acid copies comprise one or more non-inherent universal detection targets (UDTs) and one or more universal detection elements (UDEs) attached to said UDTs, wherein said UDEs generate a signal directly or indirectly to detect the presence or quantity of said analytes, and wherein said UDTs are either:

(i) at the 5′

ends of said first nucleic acid copies and not adjacent to an oligoT segment or sequence, or (ii) at the 3′

ends of said first nucleic acid copies, or (iii) both (i) and (ii).

233. The composition of claim 232, wherein said library of analytes is derived from a biological source selected from the group consisting of organs, tissues and cells.

234. The composition of claim 232, wherein said analytes are selected from the group consisting of genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA and a combination of any of the foregoing.

235. The composition of claim 232, wherein said nucleic acid array is selected from the group consisting of DNA, RNA and analogs thereof.

236. The composition of claim 235, wherein said analogs comprise PNA.

237. The composition of claims 235 or 236, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

238. The composition of claim 232, wherein said solid support is porous or non-porous.

239. The composition of claim 238, wherein said porous solid support is selected from the group consisting of polyacrylamide and agarose.

240. The composition of claim 238, wherein said non-porous solid support comprises glass or plastic.

241. The composition of claim 232, wherein said solid support is transparent, translucent, opaque or reflective.

242. The composition of claim 232, wherein said nucleic acids are directly or indirectly fixed or immobilized to said solid support.

243. The composition of claim 242, wherein said nucleic acids are indirectly fixed or immobilized to said solid support by means of a chemical linker or linkage arm.

244. The composition of claim 232, wherein said non-inherent universal detection target (UDT) comprises homopolymeric sequences.

245. The composition of claim of 232, wherein said non-inherent universal detection target (UDT) comprises heteropolymeric sequences.

246. The composition of claim 232, wherein said UDE is selected from the group consisting of nucleic acids, nucleic acid analogs, polypeptides, polysaccharides, synthetic polymers and a combination of any of the foregoing.

247. The composition of claim 246, wherein said analogs comprise PNA.

248. The composition of claim 232, wherein said UDE generates a signal directly or indirectly.

249. The composition of claim 248, wherein said direct signal generation is selected from the group consisting of a fluorescent compound, a phosphorescent compound, a chemiluminescent compound, a chelating compound, an electron dense compound, a magnetic compound, an intercalating compound, an energy transfer compound and a combination of any of the foregoing.

250. The composition of claim 248, wherein said indirect signal generation is selected from the group consisting of an antibody, an antigen, a hapten, a receptor, a hormone, a ligand, an enzyme and a combination of any of the foregoing.

251. The composition of claim 250, wherein said enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.

252-952. -952. (CANCELED)