US6790945B2
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Fluorescent quenching detection reagents and methods
Assignee: DRUG ROYALTY TRUST 9
•
Filing: 2001-06-06
•
Granted: 2004-09-14
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Expires: 2021-06-06
Abstract
Abstract Oligonucleotide probes containing two labels are provided and are useful in hybridization assays. The probes can also contain a minor groove binding group.
Inventors
- 👤 Eugeny A. Lukhtanov
- 👤 Alexander A. Gall
- 👤 Robert O. Dempcy
- 👤 Nicolaas M. J. Vermeulen
Bibliographic Details
Application Number
—
Jurisdiction
US
Data Source
google_patents
Last Synchronized
2026-10-28 16:41
CPC Classifications
C; C07; C07D; C07D519/00; C07C; C07C245/00; C07C245/02; C07C245/06; C07C245/08; C07F; C07F9/00; C07F9/02; C07F9/06; C07F9/22; C07F9/24; C07F9/2404; C07F9/2408; C07F9/547; C07F9/553; C07F9/572; C07F9/655; C07F9/6552; C07F9/65522; C07F9/6561; C07H; C07H21/00; C09; C09B; C09B29/00; C09B29/06; C09B29/08; C09B29/0805; C09B29/0807; C09B29/0809; C09B29/0811; C09B29/0813; C12; C12Q; C12Q1/00; C12Q1/68; C12Q1/6813; C12Q1/6816; C12Q1/6818; C07B; C07B2200/00; C07B2200/11; C40; C40B; C40B40/00
Claims Analysis
Total Claims: 41
Claim 1
Independent Claim
95 words
A compound having the formula: wherein Ar 1 and Ar 2 are each independently a substituted or unsubstituted aryl group, where at least one of Ar 1 and Ar 2 is a substituted aryl; X 1 is selected from the group consisting of OH, O-dimethoxytrityl, O-methoxytrityl, O-trityl and an oxygen atom having an acid labile blocking group; X 2 is a phosphoramidite; and W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof.
Claim 2
Dependent Claim
95 words
A compound having the formula: wherein Ar 1 and Ar 2 are each independently a substituted or unsubstituted aryl group, where at least one of Ar 1 and Ar 2 is a substituted aryl; X 1 is selected from the group consisting of OH, O-dimethoxytrityl, O-methoxytrityl, O-trityl and an oxygen atom having an acid labile blocking group; X 2 is a phosphoramidite; and W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof.
Claim 3
Dependent Claim
111 words
A compound having the formula: wherein Ar 1 and Ar 2 are each independently a substituted or unsubstituted aryl group, where at least one of Ar 1 and Ar 2 is a substituted aryl; X 1 is selected from the group consisting of H, (C 1 -C 1-C 12 )alkyl, aryl, heteroaryl, and protected or unprotected functional group; X 2 is selected from the group consisting of a phosphorous coupling moiety, a pentafluorophenoxy moiety and a succinimidyl moiety; and W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof.
Claim 4
Dependent Claim
111 words
A compound having the formula: wherein Ar 1 and Ar 2 are each independently a substituted or unsubstituted aryl group, where at least one of Ar 1 and Ar 2 is a substituted aryl; X 1 is selected from the group consisting of H, (C 1 -C 1-C 12 )alkyl, aryl, heteroaryl, and protected or unprotected functional group; X 2 is selected from the group consisting of a phosphorous coupling moiety, a pentafluorophenoxy moiety and a succinimidyl moiety; and W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof.
Claim 5
Dependent Claim
95 words
A compound having the formula: wherein Ar 1 and Ar 2 are each independently a substituted or unsubstituted aryl group,where at least one of Ar 1 and Ar 2 is a substituted aryl; X 1 , is selected from the group consisting of H, (C 1 -C 12 )alkyl, aryl, heteroaryl and protected or unprotected functional group; X 2 is a phosphoramidite; and W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof.
Claim 6
Dependent Claim
95 words
A compound having the formula: wherein Ar 1 and Ar 2 are each independently a substituted or unsubstituted aryl group,where at least one of Ar 1 and Ar 2 is a substituted aryl; X 1 , is selected from the group consisting of H, (C 1 -C 12 )alkyl, aryl, heteroaryl and protected or unprotected functional group; X 2 is a phosphoramidite; and W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof.
Claim 7
Dependent Claim
130 words
A compound having the formula: wherein Ar 1 and Ar 2 are each independently a substituted or unsubstituted aryl group; X 1 is selected from the group consisting of H, (C 1 -C 12 )alkyl, aryl, heteroaryl, and protected or unprotected functional group; X 2 is a moiety reactive towards nucleophiles; W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof; and wherein one of Ar 1 and A 2 is directly or indirectly substituted with a substituted aryl group (A 3 ), where Ar 3 extends the resonance ability of the Ar 1 —N═N—A 2 aromatic system and thereby increases the wavelength absorbance maximum of the compound.
Claim 8
Dependent Claim
130 words
A compound having the formula: wherein Ar 1 and Ar 2 are each independently a substituted or unsubstituted aryl group; X 1 is selected from the group consisting of H, (C 1 -C 12 )alkyl, aryl, heteroaryl, and protected or unprotected functional group; X 2 is a moiety reactive towards nucleophiles; W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof; and wherein one of Ar 1 and A 2 is directly or indirectly substituted with a substituted aryl group (A 3 ), where Ar 3 extends the resonance ability of the Ar 1 —N═N—A 2 aromatic system and thereby increases the wavelength absorbance maximum of the compound.
Claim 9
Dependent Claim
15 words
A compound of claim 4 wherein Ar 1 is directly substituted with Ar 3 .
Claim 10
Dependent Claim
15 words
A compound of claim 4 wherein Ar 1 is indirectly substituted with Ar 3 .
Claim 11
Dependent Claim
15 words
A compound of claim 4 wherein A 2 is directly substituted with Ar 3 .
Claim 12
Dependent Claim
15 words
A compound of claim 4 wherein Ar 2 is indirectly substituted with Ar 3 .
Claim 13
Dependent Claim
145 words
A compound having the formula: wherein Ar 1 and A 2 are each independently a substituted or unsubstituted aryl group; X 1 , is selected from the, group consisting of H, (C 1 -C 12 )alkyl, aryl, heteroaryl, and protected or unprotected functional group; X 2 is a phosphoramidite; W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof; and wherein Ar 1 or Ar 2 is indirectly substituted with an aryl group through a group selected from —(C═C) n — and —(CR′CR′) n — where n is 0 to 5 and R′ is independently selected from hydrogen, (C 1 -C 8 )alkyl and heteroalkyl, unsubstituted aryl and heteroaryl, (unsubstituted aryl)-(C 1 -C 4 )alkyl, and (u nsubstituted aryl)oxy-(C 1 -C 4 )alkyl.
Claim 14
Dependent Claim
145 words
A compound having the formula: wherein Ar 1 and A 2 are each independently a substituted or unsubstituted aryl group; X 1 , is selected from the, group consisting of H, (C 1 -C 12 )alkyl, aryl, heteroaryl, and protected or unprotected functional group; X 2 is a phosphoramidite; W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof; and wherein Ar 1 or Ar 2 is indirectly substituted with an aryl group through a group selected from —(C═C) n — and —(CR′CR′) n — where n is 0 to 5 and R′ is independently selected from hydrogen, (C 1 -C 8 )alkyl and heteroalkyl, unsubstituted aryl and heteroaryl, (unsubstituted aryl)-(C 1 -C 4 )alkyl, and (u nsubstituted aryl)oxy-(C 1 -C 4 )alkyl.
Claim 15
Dependent Claim
107 words
A compound having the formula: wherein Ar 1 and Ar 2 are each independently a substituted or unsubstituted aryl group; X 1 is selected from the group consisting of H, (C 1 -C 12 )alkyl, aryl, heteroaryl, and protected or unprotected functional group; X 2 is a phosphoramidite; W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof; and Ar 1 or Ar 2 is indirectly substituted with an aryl group (Ar 3 ) through a double bond selected from carbon—carbon and nitrogen—nitrogen double bonds.
Claim 16
Dependent Claim
107 words
A compound having the formula: wherein Ar 1 and Ar 2 are each independently a substituted or unsubstituted aryl group; X 1 is selected from the group consisting of H, (C 1 -C 12 )alkyl, aryl, heteroaryl, and protected or unprotected functional group; X 2 is a phosphoramidite; W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof; and Ar 1 or Ar 2 is indirectly substituted with an aryl group (Ar 3 ) through a double bond selected from carbon—carbon and nitrogen—nitrogen double bonds.
Claim 17
Dependent Claim
247 words
A compound having the formula: wherein Ar 1 and A 2 are each independently a substituted or unsubstituted aryl group; X 1 is selected from the group consisting of H, (C 1 -C 12 )alkyl, aryl, heteroaryl, and protected or unprotected functional group; X 2 is a phosphoramidite; W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof; wherein one of Ar 1 and Ar 2 is directly or indirectly substituted with a substituted aryl group (Ar 3 ), where Ar 3 extends the resonance ability of the Ar 1 —N═N—Ar 2 aromatic system and thereby increases the wavelength absorbance maximum of the compound; and at least one of Ar 1 , A 2 and Ar 3 is substituted with -halogen, —OR′, —OC(O)R′, —NR′R″, —SR′, —R′, —CN, —NO 2 , —CO 2 R′, —CONR′R″, —C(O)R′, —OC(O)NR′R″, —NR″C(O)R′, —NRC″C(O) 2 R′, —NR′—C(O)NR″R′″, —NH—C(NH 2 )NH, —NR′C(NH 2 )NH, —NH—C(NH 2 )═NR′, —S(O)R′, —S(O) 2 R′, —S(O) 2 NR′R″, —N3, —CH(Ph) 2 , perfluoro(C 1 -C 4 )alkoxy, and perfluoro(C 1 -C 4 )alkyl, in a number ranging from zero to the total number of open valences on the aromatic ring system; and where R′, R″ and R′″ are independently selected from hydrogen, (C 1 -C 8 )alkyl and heteroalkyl, unsubstituted aryl and heteroaryl, (unsubstituted aryl)-(C 1 -C 4 )alkyl, and (unsubstituted aryl)oxy-(C 1 -C 4 )alkyl.
Claim 18
Dependent Claim
247 words
A compound having the formula: wherein Ar 1 and A 2 are each independently a substituted or unsubstituted aryl group; X 1 is selected from the group consisting of H, (C 1 -C 12 )alkyl, aryl, heteroaryl, and protected or unprotected functional group; X 2 is a phosphoramidite; W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof; wherein one of Ar 1 and Ar 2 is directly or indirectly substituted with a substituted aryl group (Ar 3 ), where Ar 3 extends the resonance ability of the Ar 1 —N═N—Ar 2 aromatic system and thereby increases the wavelength absorbance maximum of the compound; and at least one of Ar 1 , A 2 and Ar 3 is substituted with -halogen, —OR′, —OC(O)R′, —NR′R″, —SR′, —R′, —CN, —NO 2 , —CO 2 R′, —CONR′R″, —C(O)R′, —OC(O)NR′R″, —NR″C(O)R′, —NRC″C(O) 2 R′, —NR′—C(O)NR″R′″, —NH—C(NH 2 )NH, —NR′C(NH 2 )NH, —NH—C(NH 2 )═NR′, —S(O)R′, —S(O) 2 R′, —S(O) 2 NR′R″, —N3, —CH(Ph) 2 , perfluoro(C 1 -C 4 )alkoxy, and perfluoro(C 1 -C 4 )alkyl, in a number ranging from zero to the total number of open valences on the aromatic ring system; and where R′, R″ and R′″ are independently selected from hydrogen, (C 1 -C 8 )alkyl and heteroalkyl, unsubstituted aryl and heteroaryl, (unsubstituted aryl)-(C 1 -C 4 )alkyl, and (unsubstituted aryl)oxy-(C 1 -C 4 )alkyl.
Claim 19
Dependent Claim
9 words
A compound of claim 1 wherein W is acylic.
Claim 20
Dependent Claim
11 words
A compound of claim 1 wherein W comprises a cyclic group.
Claim 21
Dependent Claim
10 words
A compound of claim 2 wherein W is a cyclic.
Claim 22
Dependent Claim
11 words
A compound of claim 2 wherein W comprises a cyclic group.
Claim 23
Dependent Claim
9 words
A compound of claim 3 wherein W is acyclic.
Claim 24
Dependent Claim
11 words
A compound of claim 3 wherein W comprises a cyclic group.
Claim 25
Dependent Claim
9 words
A compound of claim 4 wherein W is acyclic.
Claim 26
Dependent Claim
11 words
A compound of claim 4 wherein W comprises a cyclic group.
Claim 27
Dependent Claim
9 words
A compound of claim 5 wherein W is acyclic.
Claim 28
Dependent Claim
11 words
A compound of claim 5 wherein W comprises a cyclic group.
Claim 29
Dependent Claim
10 words
A compound of claim 6 wherein W is a cyclic.
Claim 30
Dependent Claim
11 words
A compound of claim 6 wherein W comprises a cyclic group.
Claim 31
Dependent Claim
9 words
A compound of claim 7 wherein W is acyclic.
Claim 32
Dependent Claim
11 words
A compound of claim 7 wherein W comprises a cyclic group.
Claim 33
Dependent Claim
9 words
A compound of claim 8 wherein W is acyclic.
Claim 34
Dependent Claim
11 words
A compound of claim 8 wherein W comprises a cyclic group.
Claim 35
Dependent Claim
9 words
A compound of claim 9 wherein W is acyclic.
Claim 36
Dependent Claim
11 words
A compound of claim 9 wherein W comprises a cyclic group.
Claim 37
Dependent Claim
9 words
A compound of claim 10 wherein W is cyclic.
Claim 38
Dependent Claim
11 words
A compound of claim 10 wherein W comprises a cyclic group.
Claim 39
Dependent Claim
9 words
A compound of claim 11 wherein W is acyclic.
Claim 40
Dependent Claim
11 words
A compound of claim 11 wherein W comprises a cyclic group.
Claim 41
Dependent Claim
19 words
A compound of claims 2 , 4 - 8 or 18 - 27 wherein X 2 is a phosphoramidite.
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