Nucleic acid labeling compounds

• US 20050287563A1
• Filed: 05/10/2005
• Published: 12/29/2005
• Est. Priority Date: 01/23/1996
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: McGall, Glenn H., Barone, Anthony D.
• Granted Patent: US 7,423,143 B2
• Time in Patent Office: Days
• US Class Current: 435/6.11
• CPC Class Codes: A61K 49/0032 Methine dyes, e.g. cyanine dyes
• CPC Class Codes: A61K 49/0043 Fluorescein, used in vivo
• CPC Class Codes: A61K 49/0052 Small organic molecules oligomers, polymers, dendrimers A61K49/0054
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical

Abstract

Nucleic acid labeling compounds containing heterocyclic derivatives are disclosed. The heterocyclic derivative containing compounds are synthesized by condensing a heterocyclic derivative with a cyclic group (e.g. a ribofuranose derivative). The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.

Claims

1-171. -171. (canceled)

172. A nucleic acid labeling compound of the following structure:

173. The nucleic acid labeling compound of claim 172, wherein A is H or H₄O₉P₃⁻

with an appropriate counterion.

174. The nucleic acid labeling compound of claim 172, wherein X is O.

175. The nucleic acid labeling compound of claim 172, wherein Y is OR₉, wherein R₉ is H, alkyl or aryl.

176. The nucleic acid labeling compound of claim 172, wherein Z is OR₁₀, wherein R₁₀ is H, alkyl or aryl.

177. The nucleic acid labeling compound of claim 172, wherein L is —

C(O)NH(CH₂),NH—

, wherein n is an integer ranging from about 2 to about 10.

178. The nucleic acid labeling compound of claim 172, wherein M is —

NH(CH₂),NH—

or —

C(O)(CH₂),NH—

wherein n is and integer from about 0 to about 5.

179. The nucleic acid labeling compound of claim 172, wherein Q is biotin.

180. The nucleic acid labeling compound of claim 172, wherein

A is H₄O₉P₃⁻

with an appropriate counterion;

X is O;

Y is H or OH;

Z is H or OH;

L is —

C(O)NH(CH₂)₂NH—

,

M is —

C(O)(CH₂)₅NH—

; and

Q is biotin.

181. The nucleic acid labeling compound of claim 172, wherein the compound is a stereoisomer.

182. The nucleic acid labeling compound of claim 181, wherein the compound has the following structure:

183. The nucleic acid labeling compound of claim 180, wherein the compound has the following structure:

184. The nucleic acid labeling compound of claim 182, wherein A is H or H₄O₉P₃⁻

with an appropriate counterion.

185. The nucleic acid labeling compound of claim 182, wherein X is O.

186. The nucleic acid labeling compound of claim 182, wherein Y is OR₉, wherein R₉ is H, alkyl or aryl.

187. The nucleic acid labeling compound of claim 182, wherein Z is OR₁₀, wherein R₁₀ is H, alkyl or aryl.

188. The nucleic acid labeling compound of claim 182, wherein L is —

C(O)NH(CH₂)_nNH—

, wherein n is an integer ranging from about 2 to about 10.

189. The nucleic acid labeling compound of claim 182, wherein M is —

NH(CH₂),NH—

or —

C(O)(CH₂)_nNH—

wherein n is and integer from about 0 to about 5.

190. The nucleic acid labeling compound of claim 182, wherein Q is biotin.

191. The nucleic acid labeling compound of claim 183, wherein A is H or H₄O₉P₃⁻

with an appropriate counterion.

192. The nucleic acid labeling compound of claim 183, wherein X is O.

193. The nucleic acid labeling compound of claim 183, wherein Y is OR₉, wherein R₉ is H, alkyl or aryl.

194. The nucleic acid labeling compound of claim 183, wherein Z is OR₁₀, wherein R₁₀ is H, alkyl or aryl.

195. The nucleic acid labeling compound of claim 183, wherein L is —

C(O)NH(CH₂)_nNH—

, wherein n is an integer ranging from about 2 to about 10.

196. The nucleic acid labeling compound of claim 183, wherein M is —

NH(CH₂)_nNH—

or —

C(O)(CH₂),NH—

wherein n is and integer from about 0 to about 5.

197. The nucleic acid labeling compound of claim 183, wherein Q is biotin.

198. A nucleic acid derivative produced by coupling a nucleic acid labeling compound according to claim 182 with a nucleic acid.

199. The nucleic acid derivative of claim 198, wherein the coupling comprises incubating with a terminal transferase.

200. A hybridization product comprising the nucleic acid derivative according to claim 198 bound to a complementary probe.

201. The hybridization product of claim 200, wherein the probe is attached to a solid support.

202. The hybridization product of claim 201, wherein the solid support is glass.

203. A nucleic acid derivative produced by coupling a nucleic acid labeling compound according to claim 183 with a nucleic acid.

204. The nucleic acid derivative of claim 203, wherein the coupling comprises incubating with a terminal transferase.

205. A hybridization product comprising the nucleic acid derivative according to claim 203 bound to a complementary probe.

206. The hybridization product of claim 205, wherein the probe is attached to a solid support.

207. The hybridization product of claim 206, wherein the solid support is glass.

208. A method of synthesizing a nucleic acid derivative comprising coupling a nucleic acid labeling compound according to claim 182 to a nucleic acid.

209. The method of claim 208, wherein the coupling is achieved using a terminal transferase.

210. A method of detecting a nucleic acid comprising hybridizing a nucleic acid derivative according to claim 208 with a complementary probe.

211. The method according to claim 210, wherein the probe is attached to a solid support.

212. The method according to claim 211, wherein said solid support is glass.

213. A method of synthesizing a nucleic acid derivative comprising coupling a nucleic acid labeling compound according to claim 183 to a nucleic acid.

214. The method of claim 213, wherein the coupling is achieved using a terminal transferase.

215. A method of detecting a nucleic acid comprising hybridizing a nucleic acid derivative according to claim 213 with a complementary probe.

216. The method according to claim 215, wherein the probe is attached to a solid support.

217. The method according to claim 216, wherein said solid support is glass.