Detection and quantification process for more than one nucleic acid in library

• US 20060172310A1
• Filed: 07/27/2004
• Published: 08/03/2006
• 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, Elazar, Coleman, Jack
• Granted Patent: US 9,234,234 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• 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. (canceled)

2-146. -146. (canceled)

147. A process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of:

a) providing;

(i) an array of fixed or immobilized nucleic acids complementary to said nucleic acids of interest;

(ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified;

(iii) means for attaching one or more universal detection targets (UDT) to a nucleic acid;

(iv) universal detection elements (UDE) which generates a signal directly or indirectly;

b) attaching said UDTs (iii) to said library of nucleic acid analytes (ii);

c) hybridizing said library (ii) with said array of nucleic acids (i) to form hybrids if said nucleic acids of interest are present;

d) contacting said UDEs with said UDTs to form a complex bound to said array;

e) detecting or quantifying said more than one nucleic acid of interest by detecting or measuring the amount of signal generated from UDEs bound to said array.

148. The process of claim 147, wherein said nucleic acid array is selected from the group consisting of DNA, RNA and analogs thereof.

149. The process of claim 148, wherein said analogs comprise PNA.

150. The process of claims 148 or 149, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

151. The process of claim 147, wherein said solid support is porous or non-porous.

152. The process of claim 151, wherein said porous solid support is selected from the group consisting of polyacrylamide and agarose.

153. The process of claim 151, wherein said non-porous solid support comprises glass or plastic.

154. The process of claim 147, wherein said solid support is transparent, translucent, opaque or reflective.

155. The process of claim 147, wherein said nucleic acids are directly or indirectly fixed or immobilized to said solid support.

156. The process of claim 155, wherein said nucleic acids are indirectly fixed or immobilized to said solid support by means of a chemical linker or linkage arm.

157. The process of claim 147, wherein said library of analytes is derived from a biological source selected from the group consisting of organs, tissues and cells.

158. The process of claim 147, 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.

159. The process of claim 147, wherein said attaching means add homopolymeric sequences through an enzyme selected from the group consisting of poly A polymerase and terminal transferase.

160. The process of claim 147, wherein said attaching means add homopolymeric or heteropolymeric sequences through an enzyme selected from the group consisting of DNA ligase and RNA ligase.

161. The process of claim 147, wherein said UDE is selected from the group consisting of nucleic acids, nucleic acid analogs and modified forms thereof.

162. The process of claim 161, wherein said analogs comprise PNA.

163. The process of claim 147, wherein said UDE generates a signal directly or indirectly.

164. The process of claim 163, 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.

165. The process of claim 163, 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.

166. The process of claim 165, wherein said enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.

167. The process of claim 147, comprising one or more washing steps.

168. A process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of:

a) providing;

(i) an array of fixed or immobilized nucleic acids complementary to said nucleic acids of interest;

(ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified;

(iii) means for attaching one or more universal detection targets (UDT) to a nucleic acid;

(iv) universal detection elements (UDE) which generates a signal directly or indirectly;

b) attaching said UDTs (iii) to said library of nucleic acid analytes (ii);

c) contacting said UDEs with said UDTs in said library of nucleic acid analytes to form one or more complexes;

d) hybridizing said library (ii) with said array of nucleic acids (i) to form hybrids if said nucleic acids of interest are present;

e) detecting or quantifying said more than one nucleic acid of interest by detecting or measuring the amount of signal generated from UDEs bound to said array.

169. The process of claim 168, wherein said nucleic acid array is selected from the group consisting of DNA, RNA and analogs thereof.

170. The process of claim 169, wherein said analogs comprise PNA.

171. The process of claims 169 or 170, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

172. The process of claim 168, wherein said solid support is porous or non-porous.

173. The process of claim 172, wherein said porous solid support is selected from the group consisting of polyacrylamide and agarose.

174. The process of claim 172, wherein said non-porous solid support comprises glass or plastic.

175. The process of claim 168, wherein said solid support is transparent, translucent, opaque or reflective.

176. The process of claim 168, wherein said nucleic acids are directly or indirectly fixed or immobilized to said solid support.

177. The process of claim 176, wherein said nucleic acids are indirectly fixed or immobilized to said solid support by means of a chemical linker or linkage arm.

178. The process of claim 168, wherein said library of analytes is derived from a biological source selected from the group consisting of organs, tissues and cells.

179. The process of claim 168, 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.

180. The process of claim 168, wherein said attaching means add homopolymeric sequences through an enzyme selected from the group consisting of poly A polymerase and terminal transferase.

181. The process of claim 168, wherein said attaching means add homopolymeric or heteropolymeric sequences through an enzyme selected from the group consisting of DNA ligase and RNA ligase.

182. The process of claim 168, wherein said UDE is selected from the group consisting of nucleic acids, nucleic acid analogs and modified forms thereof.

183. The process of claim 182, wherein said analogs comprise PNA.

184. The process of claim 168, wherein said UDE generates a signal directly or indirectly.

185. The process of claim 184, 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.

186. The process of claim 184, 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.

187. The process of claim 186, wherein said enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.

188. The process of claim 168, comprising one or more washing steps.

189. A process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of:

a) providing;

(i) an array of fixed or immobilized nucleic acids complementary to said nucleic acids of interest;

(ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; and

(iii) universal detection elements (UDEs) which bind to a domain formed by nucleic acid hybrids for complex formation and generate a signal directly or indirectly;

b) hybridizing said library (ii) with said array of nucleic acids (i) to form hybrids if said nucleic acids of interest are present, wherein said formed hybrids generate a domain for complex formation;

c) contacting said UDEs with said hybrids to form a complex bound to said array;

d) detecting or quantifying said more than one nucleic acid of interest by detecting or measuring the amount of signal generated from UDEs bound to said array.

190. The process of claim 189, wherein said nucleic acid array is selected from the group consisting of DNA, RNA and analogs thereof.

191. The process of claim 190, wherein said analogs comprise PNA.

192. The process of claims 190 or 191, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

193. The process of claim 189, wherein said solid support is porous or non-porous.

194. The process of claim 193, wherein said porous solid support is selected from the group consisting of polyacrylamide and agarose.

195. The process of claim 193, wherein said non-porous solid support comprises glass or plastic.

196. The process of claim 189, wherein said solid support is transparent, translucent, opaque or reflective.

197. The process of claim 189, wherein said nucleic acids are directly or indirectly fixed or immobilized to said solid support.

198. The process of claim 197, wherein said nucleic acids are indirectly fixed or immobilized to said solid support by means of a chemical linker or linkage arm.

199. The process of claim 189, wherein said library of analytes is derived from a biological source selected from the group consisting of organs, tissues and cells.

200. The process of claim 189, 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.

201. The process of claim 189, wherein said domain for complex formation is selected from the group consisting of DNA-DNA hybrids, DNA-RNA hybrids, RNA-RNA hybrids, DNA-PNA hybrids and RNA-PNA hybrids.

202. The process of claim 189, wherein said signaling entity complexed to said domain is selected from the group consisting of proteins and intercalators.

203. The process of claim 202, wherein said proteins comprise nucleic acid binding proteins which bind preferentially to double-stranded nucleic acid.

204. The process of claim 203, wherein said nucleic acid binding proteins comprise antibodies.

205. The process of claim 204, wherein said antibodies are specific for nucleic acid hybrids selected from the group consisting of DNA-DNA hybrids, DNA-RNA hybrids, RNA-RNA hybrids, DNA-PNA hybrids and RNA-PNA hybrids

206. The process of claim 202, wherein said intercalators are selected from the group consisting of ethidium bromide, diethidium bromide, acridine orange and SYBR Green.

207. The process of claim 189, wherein said proteins generate a signal directly or indirectly.

208. The process of claim 207, 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.

209. The process of claim 207, 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.

210. The process of claim 209, wherein said enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.

211. The process of claim 189, further comprising one or more washing steps.

212-952. -952. (canceled)