US5134066A
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Improved probes using nucleosides containing 3-dezauracil analogs
Assignee: Monsanto Co
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Filing: 1989-08-29
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Granted: 1992-07-28
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Expires: 2009-08-29
Abstract
Abstract The deazauracil containing 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 E. Rogers
- 👤 Steven H. Gray
- 👤 Balekudru Devadas
- 👤 Steven P. Adams
Bibliographic Details
Application Number
—
Jurisdiction
US
Data Source
google_patents
Last Synchronized
2026-10-30 04:19
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: 31
Claim 1
Independent Claim
97 words
A single-stranded nucleic acid probe which comprises a nucleoside residue of the formula: ##STR76## 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 6-14 aryloxy or C 1 -C 5 alkoxy and in which the nucleoside residue is at least five nucleosides from both ends of the probe and said probe is capable of hybridizing with a target nucleic acid and said hybridizing is mediated by the presence of nondeazauracil nucleotide which are contained within said probe residues.
Claim 2
Dependent Claim
97 words
A single-stranded nucleic acid probe which comprises a nucleoside residue of the formula: ##STR76## 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 6-14 aryloxy or C 1 -C 5 alkoxy and in which the nucleoside residue is at least five nucleosides from both ends of the probe and said probe is capable of hybridizing with a target nucleic acid and said hybridizing is mediated by the presence of nondeazauracil nucleotide which are contained within said probe residues.
Claim 3
Dependent Claim
17 words
The probe of claim 1 in which R 1 , 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
25 words
The probe which is selected from the group consisting of GGCAGCTTYCACATAGTCCA, AGCTTCCAYATGGTCC, AGCTTCCAYATGGTCCA, GCAGCTTYCACATGGTCC, GGCAGCTTYCACATGGTCCA, ATGAATCYGAACAATCG, ATGAATCCGAAYAATCG, TAGCGGCGACGYACGTACAC, CTCTAGGYTGTCGGCCAGCC, TAGGCAGCTTCCAYCTGGTCCAGTAGC, and GGCAGCTTCCACATGGTCYA in which Y=4-hydroxy-1(2'-deoxy-beta-D-erythro-pentofuranosyl)-2(1H)-pyridone.
Claim 16
Dependent Claim
25 words
The probe which is selected from the group consisting of GGCAGCTTYCACATAGTCCA, AGCTTCCAYATGGTCC, AGCTTCCAYATGGTCCA, GCAGCTTYCACATGGTCC, GGCAGCTTYCACATGGTCCA, ATGAATCYGAACAATCG, ATGAATCCGAAYAATCG, TAGCGGCGACGYACGTACAC, CTCTAGGYTGTCGGCCAGCC, TAGGCAGCTTCCAYCTGGTCCAGTAGC, and GGCAGCTTCCACATGGTCYA in which Y=4-hydroxy-1(2'-deoxy-beta-D-erythro-pentofuranosyl)-2(1H)-pyridone.
Claim 17
Dependent Claim
10 words
The probe having the following sequence: GGCAGCTTXCACATGGTCCA, in which X=3-iodo-4-hydroxy-1-(2'-deoxy-beta-D-erythro-pentofuranosyl)-2(1H)-pyridone.
Claim 18
Dependent Claim
10 words
The probe having the following sequence: GGCAGCTTXCACATGGTCCA, in which X=3-iodo-4-hydroxy-1-(2'-deoxy-beta-D-erythro-pentofuranosyl)-2(1H)-pyridone.
Claim 19
Dependent Claim
10 words
The probe having the following sequence: GGCAGCTTXCACATGGTCCA, in which X=5-iodo-4-hydroxy-1-(2'-deoxy-beta-D-erythro-pentofuranosyl)-2(1H)-pyridone.
Claim 20
Dependent Claim
10 words
The probe having the following sequence: GGCAGCTTXCACATGGTCCA, in which X=5-iodo-4-hydroxy-1-(2'-deoxy-beta-D-erythro-pentofuranosyl)-2(1H)-pyridone.
Claim 21
Dependent Claim
10 words
The probe having the following sequence: GGCAGCTTXCACATGGTCCA, in which X=4-0-diphenylcarbamoyl-3-ethenyl-1-(2'-1-deoxy-beta-D-erythropentofuranosyl)-2(1H)-pyridone.
Claim 22
Dependent Claim
10 words
The probe having the following sequence: GGCAGCTTXCACATGGTCCA, in which X=4-0-diphenylcarbamoyl-3-ethenyl-1-(2'-1-deoxy-beta-D-erythropentofuranosyl)-2(1H)-pyridone.
Claim 23
Independent Claim
115 words
A method for preparing hybrid DNA or RNA molecules which comprises hybridizing a target nucleic acid molecule to a single-stranded nucleic acid probe which comprises a nucleoside residue of the formula: ##STR77## 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, and in which the nucleoside residue is at least five nucleosides from both ends of the probe and said probe undergoes hybridization with a target nucleic acid and said hybridization is mediated by the presence of non-deazauracil nucleoside residues which are contained within said probe.
Claim 24
Independent Claim
115 words
A method for preparing hybrid DNA or RNA molecules which comprises hybridizing a target nucleic acid molecule to a single-stranded nucleic acid probe which comprises a nucleoside residue of the formula: ##STR77## 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, and in which the nucleoside residue is at least five nucleosides from both ends of the probe and said probe undergoes hybridization with a target nucleic acid and said hybridization is mediated by the presence of non-deazauracil nucleoside residues which are contained within said probe.
Claim 25
Dependent Claim
29 words
The method of claim 18 in which the hybrid molecule remains as a hybrid between said probe and target nucleic acid molecule when washed at temperatures of 50°-100° C.
Claim 26
Dependent Claim
29 words
The method of claim 18 in which the hybrid molecule remains as a hybrid between said probe and target nucleic acid molecule when washed at temperatures at 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
17 words
The method of claim 18 in which R 1 , R 2 and R 3 are hydrogen.
Claim 29
Dependent Claim
10 words
A nucleic acid duplex comprising a probe of claim 1.
Claim 30
Dependent Claim
19 words
The nucleic acid duplex of claim 23 in which R 1 , R 2 and R 3 are hydrogen.
Claim 31
Dependent Claim
21 words
The nucleic acid duplex of claim 23 in which R 1 and R 2 are hydrogen and R 3 is hydroxy.
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