EP0415901A2
Expired / Lapsed
EP
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Improved nucleic acid probes
Assignee: Monsanto Co
•
Filing: 1990-08-24
•
Granted: —
•
Expires: 2010-08-24
Abstract
Abstract The probes of the invention are able to withstand higher temperatures, thereby allowing unmatched probes and mismatched probes to be washed off at higher hybridization stringency, thereby eliminating background readings and improving ease and accuracy of probe use.
Inventors
- 👤 Thomas Edward Rogers
- 👤 Balekudru Devadas
- 👤 Steven Haynes Gray
- 👤 Steven Paul Adams
Bibliographic Details
Application Number
—
Jurisdiction
EP
Data Source
google_patents
Last Synchronized
2026-10-29 13:34
CPC Classifications
C; C07; C07H; C07H21/00; C12; C12Q; C12Q1/00; C12Q1/68; C12Q1/6813; C12Q1/6827; C12Q1/6832; C12Q1/6876; C12Q1/6888; C12Q1/689; C12Q1/6895; C12Q1/70; C12Q1/701; C12Q2600/00; C12Q2600/156; Y; Y10; Y10S; Y10S435/00; Y10S435/805
Claims Analysis
Total Claims: 48
Claim 1
Independent Claim
51 words
A single-stranded nucleic acid probe which comprises a nucleoside residue of the formula: in which R 1 and R 2 independently are C 1 -C 5 alkyl, C 2 -C 5 alkenyl, halo or hydrogen, R 3 is hydrogen, hydroxy, C 6 -C 14 aryloxy or C 1 -C 5 alkoxy.
Claim 2
Dependent Claim
51 words
A single-stranded nucleic acid probe which comprises a nucleoside residue of the formula: in which R 1 and R 2 independently are C 1 -C 5 alkyl, C 2 -C 5 alkenyl, halo or hydrogen, R 3 is hydrogen, hydroxy, C 6 -C 14 aryloxy or C 1 -C 5 alkoxy.
Claim 3
Dependent Claim
15 words
The probe of Claim 1 in which Ri, R 2 and R 3 are hydrogen.
Claim 4
Dependent Claim
19 words
The probe of Claim 1 in which R 1 and R 2 are hydrogen and R 3 is hydroxy.
Claim 5
Dependent Claim
19 words
The probe of Claim 1 in which R 1 is iodine and R 2 and R 3 are hydrogen.
Claim 6
Dependent Claim
20 words
The probe of Claim 1 in which R 1 is iodine, R 2 is hydrogen and R 3 is hydroxy.
Claim 7
Dependent Claim
19 words
The probe of Claim 1 in which R 1 is ethenyl and R 2 and R 3 are hydrogen.
Claim 8
Dependent Claim
20 words
The probe of Claim 1 in which R 1 is ethenyl, R 2 is hydrogen and R 3 is hydroxy.
Claim 9
Dependent Claim
19 words
The probe of Claim 1 in which R 1 and R 3 are hydrogen and R 2 is iodine.
Claim 10
Dependent Claim
20 words
The probe of Claim 1 in which R 1 is hydrogen, R 2 is iodine and R 3 is hydroxy.
Claim 11
Dependent Claim
16 words
The probe of Claim 1 in which the probe is 15 to 50 nucleotides in length.
Claim 12
Dependent Claim
16 words
The probe of Claim 1 in which the probe is 15 to 25 nucleotides in length.
Claim 13
Dependent Claim
13 words
The probe of Claim 1 in which the single-stranded nucleic acid is DNA.
Claim 14
Dependent Claim
13 words
The probe of Claim 1 in which the single-stranded nucleic acid is RNA.
Claim 15
Dependent Claim
29 words
The probe which is selected from the group consisting of GGCAGCTTYCACATAGTCCA, AGCTTC-CAYATGGTCC, AGCTTCCAYATGGTCCA, GCAGCTTYCACATGGTCC, GGCAGCTTYCACATGGTCCA, AT-GAATCYGAACAATCG, ATGAATCCGAAYAATCG, TAGCGGCGACGYACGTACAC, CTCTAGGYTGTCGGC-CAGCC, TAGGCAGCTTCCAYCTG GTCCAGTAGC, and GGCAGCTTCCACATGGTCYA in which Y = 4-hydroxy-1 (2-deoxy-beta-D-erythro-pentofuranosyl-2(H)-pyridone.
Claim 16
Dependent Claim
29 words
The probe which is selected from the group consisting of GGCAGCTTYCACATAGTCCA, AGCTTC-CAYATGGTCC, AGCTTCCAYATGGTCCA, GCAGCTTYCACATGGTCC, GGCAGCTTYCACATGGTCCA, AT-GAATCYGAACAATCG, ATGAATCCGAAYAATCG, TAGCGGCGACGYACGTACAC, CTCTAGGYTGTCGGC-CAGCC, TAGGCAGCTTCCAYCTG GTCCAGTAGC, and GGCAGCTTCCACATGGTCYA in which Y = 4-hydroxy-1 (2-deoxy-beta-D-erythro-pentofuranosyl-2(H)-pyridone.
Claim 17
Dependent Claim
13 words
The probe having the following sequence: GGCAGCTTXCACATGGTCCA, in which X = 3-iodo-4-hydroxy-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-2(1 H)-pyridone.
Claim 18
Dependent Claim
13 words
The probe having the following sequence: GGCAGCTTXCACATGGTCCA, in which X = 3-iodo-4-hydroxy-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-2(1 H)-pyridone.
Claim 19
Dependent Claim
13 words
The probe having the following sequence: GGCAGCTTXCACATGGTCCA, in which X = 5-iodo-4-hydroxy-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-2(1 H)-pyridone.
Claim 20
Dependent Claim
13 words
The probe having the following sequence: GGCAGCTTXCACATGGTCCA, in which X = 5-iodo-4-hydroxy-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-2(1 H)-pyridone.
Claim 21
Dependent Claim
13 words
The probe having the following sequence: GGCAGCTTTXCACATGGTCCA, in which X = 4-0-diphenylcarbamoyl-3-ethenyl-1-(2-deoxy-beta-D-erythro-pentofuranosyl))-2(1 H)-pyridone.
Claim 22
Dependent Claim
13 words
The probe having the following sequence: GGCAGCTTTXCACATGGTCCA, in which X = 4-0-diphenylcarbamoyl-3-ethenyl-1-(2-deoxy-beta-D-erythro-pentofuranosyl))-2(1 H)-pyridone.
Claim 23
Independent Claim
98 words
A method for preparing hybrid DNA or RNA molecules which comprises contacting a single-stranded nucleic acid probe which comprises a nucleoside residue of the formula: in which R 1 and R 2 independently are C 1 -C 5 alkyl, C 2 -Cs alkenyl, halo or hydrogen, R 3 is hydrogen, hydroxy, C 6 -C 14 aryloxy or C 1 -C 5 alkoxy, with target nucleic acid sequences under conditions suitable for hybridization, then recovering the hybrid molecule under conditions that remove a hybrid molecule not containing a probe which comprises the nucleoside residue of the above described formula.
Claim 24
Independent Claim
98 words
A method for preparing hybrid DNA or RNA molecules which comprises contacting a single-stranded nucleic acid probe which comprises a nucleoside residue of the formula: in which R 1 and R 2 independently are C 1 -C 5 alkyl, C 2 -Cs alkenyl, halo or hydrogen, R 3 is hydrogen, hydroxy, C 6 -C 14 aryloxy or C 1 -C 5 alkoxy, with target nucleic acid sequences under conditions suitable for hybridization, then recovering the hybrid molecule under conditions that remove a hybrid molecule not containing a probe which comprises the nucleoside residue of the above described formula.
Claim 25
Dependent Claim
18 words
The method of Claim 18 in which the hybrid molecule is recovered at temperatures of 50 -100° C.
Claim 26
Dependent Claim
18 words
The method of Claim 18 in which the hybrid molecule is recovered at temperatures of 65 -85° C.
Claim 27
Dependent Claim
19 words
The method of Claim 18 in which R 1 and R 2 are hydrogen and R 3 is hydroxy.
Claim 28
Dependent Claim
15 words
The method of Claim 18 in which Ri, R 2 and R 3 are hydrogen.
Claim 29
Dependent Claim
9 words
A hybridized molecule comprising a probe of Claim 1.
Claim 30
Dependent Claim
16 words
The hybridized molecule of Claim 23 in which Ri, R 2 and R 3 are hydrogen.
Claim 31
Dependent Claim
20 words
The hybridized molecule of Claim 23 in which R 1 and R 2 are hydrogen and R 3 is hydroxy.
Claim 32
Dependent Claim
20 words
The nucleoside residue of Claim 1 in which R 1 is iodine and R 2 and R 3 are hydrogen.
Claim 33
Dependent Claim
21 words
The nucleoside residue of Claim 1 in which R 1 is iodine, R 2 is hydrogen and R 3 is hydroxy.
Claim 34
Dependent Claim
20 words
The nucleoside residue of Claim 1 in which R 1 and R 3 are hydrogen and R 2 is iodine.
Claim 35
Dependent Claim
21 words
The nucleoside residue of Claim 1 in which R 1 is hydrogen, R 2 is iodine and R 3 is hydroxy.
Claim 36
Dependent Claim
20 words
The nucleoside residue of Claim 1 in which R 1 is ethenyl, and R 2 and R 3 are hydrogen.
Claim 37
Dependent Claim
21 words
The nucleoside residue of Claim 1 in which R 1 is ethenyl, R 2 is hydrogen and R 3 is hydroxy.
Claim 38
Dependent Claim
126 words
A compound of the formula: in which R 1 and R 2 independently are C 1 -C 5 alkyl, C 2 -Cs alkenyl, halo or hydrogen, R 3 is hydrogen, halo, C 1 -C 5 alkoxy or tri(C 1 -C 5 alkyl)substituted silyloxy, R 4 is triphenylmethyl or mono-, di- or tri (C 1 -C 5 alkoxy)-substituted triphenylmethyl, R 5 is hydrogen phosphonate or R'-P'-R" in which R is β-cyanoethyl, C 1 -C 5 alkoxyl or C 1 -C 5 alkyl, and R is morpholino, or mono- or di(C 1 -C 5 alkyl)substituted amino, R 6 is tri(C 1 -C 5 alkyl or C 1 -C 5 alkoxy) substituted silyloxy, benzoyl, methylcarbonyl, carbamoyl, or carbamoyl substituted with C 1 -C 5 alkyl, phenyl, acetyl or isobutyryl.
Claim 39
Dependent Claim
126 words
A compound of the formula: in which R 1 and R 2 independently are C 1 -C 5 alkyl, C 2 -Cs alkenyl, halo or hydrogen, R 3 is hydrogen, halo, C 1 -C 5 alkoxy or tri(C 1 -C 5 alkyl)substituted silyloxy, R 4 is triphenylmethyl or mono-, di- or tri (C 1 -C 5 alkoxy)-substituted triphenylmethyl, R 5 is hydrogen phosphonate or R'-P'-R" in which R is β-cyanoethyl, C 1 -C 5 alkoxyl or C 1 -C 5 alkyl, and R is morpholino, or mono- or di(C 1 -C 5 alkyl)substituted amino, R 6 is tri(C 1 -C 5 alkyl or C 1 -C 5 alkoxy) substituted silyloxy, benzoyl, methylcarbonyl, carbamoyl, or carbamoyl substituted with C 1 -C 5 alkyl, phenyl, acetyl or isobutyryl.
Claim 40
Dependent Claim
31 words
The compound of Claim 32 in which Ri, R 2 and R 3 are hydrogen, R 4 is dimethoxytriphenylmethyl, R is β-cyanoethyl, R is N,N-diisopropyl amino and R 6 is diphenylcarbamoyl.
Claim 41
Dependent Claim
34 words
The compound of Claim 32 in which R 1 and R 2 are hydrogen, R 3 is triisopropylsilyloxy, R 1 is dimethoxytriphenylmethyl, R is β-cyanoethyl, R is N,N-diisopropyl amino and R 6 is diphenylcarbamoyl.
Claim 42
Dependent Claim
34 words
The compound of Claim 32 in which R 1 and R 2 are hydrogen, R 3 is tert-butyl-dimethylsilyloxy, R 4 is dimethoxytriphenylmethyl, R is β-cyanoethyl, R is N,N-diisopropyl amino, and R 6 is diphenylcarbamoyl.
Claim 43
Dependent Claim
34 words
The compound of Claim 32 in which R, is iodine, R 2 is hydrogen, R 3 is hydrogen, R 4 is dimethoxytriphenylmethyl, R is β-cyanoethyl, R is N,N-diisopropyl amino and R 6 is diphenylcarbamoyl.
Claim 44
Dependent Claim
35 words
The compound of Claim 32 in which R 1 is iodine, R 2 is hydrogen, R 3 is triisopropylsilyloxy, R 4 is dimethoxytriphenylmethyl, R is β-cyanoethyl, R" is N,N-diisopropyl amino and R 6 is diphenylcarbamoyl.
Claim 45
Dependent Claim
35 words
The compound of Claim 32 in which R 1 is hydrogen, R 2 is iodine, R 3 is triisopropylsilyloxy, R 4 is dimethoxytrityl, R is β-cyanoethyl, R is N,N-diisopropyl amino and R 6 is diphenylcarbamoyl.
Claim 46
Dependent Claim
36 words
The compound of Claim 32 in which R 1 is hydrogen, R 2 is iodine, R 3 is hydrogen, R 4 is dimeth oxytriphenylmethyl, R is β-cyanoethyl, R" is N,N-diisopropyl amino and R 6 is diphenylcarbamoyl.
Claim 47
Dependent Claim
35 words
The compound of Claim 32 in which R 1 is ethenyl, R 2 is hydrogen, R 3 is triisopropylsilyloxy, R 4 is dimethoxytriphenylmethyl, R' is β-cyanoethyl, R" is N,N-diisopropyl amino and R 6 is diphenylcarbamoyl.
Claim 48
Dependent Claim
35 words
The compound of Claim 32 in which R 1 is ethenyl, R 2 is hydrogen, R 3 is hydrogen, R 4 is dimethoxytriphenylmethyl, R is β-cyanoethyl, R is N,N-diisopropyl amino and R 6 is diphenylcarbamoyl.
References Cited (Backward Citations)
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