EP0120658A2
Expired / Lapsed
EP
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Method for identifying and characterizing organisms
Assignee: WEBSTER, JOHN A., JR.
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Filing: 1984-03-16
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Granted: —
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Expires: 2004-03-16
Abstract
Abstract A method of characterizing an unknown organism species comprises determining the position of part or whole of evolutionarily conserved sequences in genetic material of said organism, relative to a known position of restriction endonuclease cleavage sites in said genetic material (other than by determining the chromatographic pattern of retriction endonuclease digested DNA from said unknown organism, which digested DNA has been hybridized or reassociated with ribosomal RNA information containing nucleic acid from or derived from a known probe organism), thereby to obtain an identifying genetic characterization of said unknown organism, and comparing said characterization with information from at least two sets of identifying genetic characterizations derived from the same conserved sequences, each of said sets defining a known organism species.
Inventors
- 👤 John A. Webster, Jr.
Bibliographic Details
Application Number
—
Jurisdiction
EP
Data Source
google_patents
Last Synchronized
2026-11-02 02:42
CPC Classifications
C; C12; C12Q; C12Q1/00; C12Q1/68; C12Q1/6876; C12Q1/6888; C12Q1/6813; C12Q1/6827; C12Q1/683
Claims Analysis
Total Claims: 64
Claim 1
Independent Claim
115 words
A method of characterizing an unknown organism species which comprises: determining the position of part or whole of evolutionarily conserved sequences in genetic material of said organism relative to a known position in said genetic material (other than by determining the chromatographic pattern of restriction endonuclease digested DNA from said known organism, which digested DNA has been hybridized or reassociated with ribosomal RNA information-containing nucleic acid from or derived from a known probe organism), thereby to obtain an identifying genetic characterization of said unknown organism, and comparing said characterization with information from at least two sets of identifying genetic characterizations derived from the same conserved sequences, each of said sets defining a known organism species.
Claim 2
Independent Claim
115 words
A method of characterizing an unknown organism species which comprises: determining the position of part or whole of evolutionarily conserved sequences in genetic material of said organism relative to a known position in said genetic material (other than by determining the chromatographic pattern of restriction endonuclease digested DNA from said known organism, which digested DNA has been hybridized or reassociated with ribosomal RNA information-containing nucleic acid from or derived from a known probe organism), thereby to obtain an identifying genetic characterization of said unknown organism, and comparing said characterization with information from at least two sets of identifying genetic characterizations derived from the same conserved sequences, each of said sets defining a known organism species.
Claim 3
Dependent Claim
22 words
A method as claimed in Claim 1, wherein the I known position is defined by one or more restriction endonuclease cleavage sites.
Claim 4
Dependent Claim
13 words
A method as claimed in Claim 1, wherein the genetic material is DNA.
Claim 5
Dependent Claim
61 words
A method as claimed in Claim 1, which comprises comparing the chromatographic pattern of restriction endonuclease digested DNA from said unknown organism, which digested DNA has been hybridized or reassociated with conserved DNA sequence information-containing nucleic acid from or derived from a probe organism or from a consensus sequence, with equivalent chromatographic patterns of at least two known different organism species.
Claim 6
Dependent Claim
17 words
A method as claimed in Claim 4, wherein said conserved DNA information-containing nucleic acid is detectably labelled.
Claim 7
Dependent Claim
19 words
A method as claimed in Claim 5, wherein said conserved DNA information-containing nucleic acid is radiolabelled or metal labelled.
Claim 8
Dependent Claim
21 words
A method as claimed in Claim 4,.5 or 6, wherein said conserved DNA information-containing nucleic acid probe is an RNA probe.
Claim 9
Dependent Claim
23 words
A method as claimed in Claim 4, 5 or 6, wherein said conserved DNA information-containing nucleic acid probe is DNA complementary to RNA.
Claim 10
Dependent Claim
29 words
A method as claimed in Claim 4, 5 or 6, wherein said conserved DNA information-containing nucleic acid probe is DNA obtained by nick-translating or cloning DNA complementary to RNA.
Claim 11
Independent Claim
31 words
A method as claimed in any one of Claims 1 to 4, wherein said unknown organism being characterized is a cell or cells of a strain in an in vitro culture.
Claim 12
Independent Claim
40 words
A method as claimed in any one of claims 1 to 4, wherein said unknown organism being characterized and said probe organism are both from the same kingdom, subkingdom, division, subdivision, phylum, subphylum, class, subclass, order, family, tribe or genus.
Claim 13
Dependent Claim
20 words
A method as claimed in Claim 4, wherein said unknown organism being characterized and said probe organism are both eukaryotic.
Claim 14
Dependent Claim
20 words
A method as claimed in Claim 4, wherein said unknown organism being characterized and said probe organism are both prokaryotic.
Claim 15
Dependent Claim
21 words
A method as claimed in Claim 4, wherein said unknown organism being characterized is eukaryotic and said probe organism is prokaryotic.
Claim 16
Dependent Claim
35 words
A method as claimed in Claim 12 or 14, which further comprises detecting for the presence of a nucleic acid sequence or sequences creating a taxon below the rank of species or an infrasubspecific subdivision.
Claim 17
Dependent Claim
21 words
A method as claimed in Claim 4, wherein said unknown organism being characterized is prokaryotic and said probe organism is eukaryotic.
Claim 18
Dependent Claim
27 words
A method as claimed in Claim 13 or 16, wherein said prokaryotic organism being characterized is selectively being detected while in the presence of a eukaryotic organism.
Claim 19
Dependent Claim
14 words
A method as claimed in Claim 17, wherein said prokaryotic organism is a bacterium.
Claim 20
Dependent Claim
38 words
A method as claimed in Claim 12, wherein the DNA from said eukaryotic organism being characterized is nuclear DNA, and the conserved DNA information-containing nucleic acid from said eukaryotic probe organism is not derived from mitochondria or chloroplasts.
Claim 21
Dependent Claim
38 words
A method as claimed in Claim 12, wherein the DNA from said eukaryotic organism being characterized is mitochondrial DNA and the conserved DNA information-containing nucleic acid from said eukaryotic probe organism is derived - from mitochondria or chloroplasts.
Claim 22
Dependent Claim
35 words
A method as claimed in Claim 12, wherein DNA from said eukaryotic organism being characterized is chloroplast DNA and.the conserved DNA information-containing nucleic acid from said eukaryotic probe organism is derived from mitochondria or chloroplasts.
Claim 23
Dependent Claim
22 words
A method as claimed in Claim 14, wherein said = DNA from said eukaryotic organism being characterized is derived from mitochondrial DNA.
Claim 24
Dependent Claim
20 words
A method as claimed in.Claim 14, wherein said DNA from said eukaryotic organism being characterized is derived from chloroplast DNA.
Claim 25
Dependent Claim
21 words
A.method as claimed in Claim 16, wherein said conserved DNA information-containing nucleic acid probe. is derived from mitochondria or from chloroplasts.
Claim 26
Dependent Claim
34 words
A method as claimed in Claim 12 or 14, which further comprises identifying in said unknown eukaryotic organism being characterized a virus, or a virus-derived DNA creating a taxon below the rank of species.
Claim 27
Independent Claim
120 words
A method of identifying a bacterium of an unknown bacterial strain present in a sample which comprises: determining the position of part or whole of evolutionarily conserved sequences in DNA of said bacterium, relative to a known position in said DNA (other than by determining the chromatographic pattern of restriction endonuclease digested DNA from said unknown organism, which digested DNA has been hybridized or reassociated with ribosomal RNA information-containing nucleic acid from or derived from a known probe organism), thereby to obtain an identifying genetic characterization of said unknown bacterium, and comparing said characterization with information from at least two sets of identifying genetic characterizations derived from the same conserved sequences, each of said sets defining a known bacterial species.
Claim 28
Independent Claim
120 words
A method of identifying a bacterium of an unknown bacterial strain present in a sample which comprises: determining the position of part or whole of evolutionarily conserved sequences in DNA of said bacterium, relative to a known position in said DNA (other than by determining the chromatographic pattern of restriction endonuclease digested DNA from said unknown organism, which digested DNA has been hybridized or reassociated with ribosomal RNA information-containing nucleic acid from or derived from a known probe organism), thereby to obtain an identifying genetic characterization of said unknown bacterium, and comparing said characterization with information from at least two sets of identifying genetic characterizations derived from the same conserved sequences, each of said sets defining a known bacterial species.
Claim 29
Dependent Claim
21 words
A method as claimed in Claim 26, wherein the known position is defined by one or more restriction endonuclease cleavage sites.
Claim 30
Dependent Claim
54 words
A method as claimed in Claim 26, which comprises comparing the chromatographic pattern of restriction-endonuclease digested DNA from said unknown bacterium, which digested DNA has been hybridized or reassociated with conserved.DNA sequence information-containing nucleic acid from or derived from a probe bacterium or from a consensus sequence, with equivalent chromatographic patterns of known bacteria.
Claim 31
Dependent Claim
24 words
A method as claimed in Claim 26, wherein said unknown bacterium is present in a fermentation medium or in a secretion or excretion product.
Claim 32
Dependent Claim
19 words
A method as claimed in Claim 26, wherein said unknown bacterium is present in or associated with eukaryotic tissue.
Claim 33
Dependent Claim
21 words
A method as claimed in Claim 30, wherein said _ bacterium is present in or associated with animal or plant cells.
Claim 34
Dependent Claim
23 words
A method as claimed in Claim 30, wherein said bacterium is present in or associated with human cells,.or associated with plant root cells.
Claim 35
Independent Claim
26 words
A method as claimed in any one of Claims 28 to 32, wherein said conserved DNA information-containing nucleic acid from said probe bacterium is detectably labelled.
Claim 36
Dependent Claim
17 words
A method as claimed in Claim 33, wherein said label is a radiolabel or a metal label.
Claim 37
Dependent Claim
17 words
A method as claimed in Claim 33, wherein said nucleic acid from said probe bacterium is RNA.
Claim 38
Dependent Claim
21 words
A method as claimed in Claim 33, wherein said. nucleic acid from said probe bacterium is complementary DNA to RNA. -
Claim 39
Independent Claim
22 words
A method as claimed in any one of Claims 28 to 32, wherein said unknown bacterium is pathogenic towards plants or animals.
Claim 40
Independent Claim
38 words
A method as claimed in any one of Claims 28 to 32, which further comprises detecting for the presence of a nucleic acid sequence or sequences creating a taxon below the rank of species, or an infrasubspecific subdivision.
Claim 41
Dependent Claim
21 words
A method as claimed in Claim 38, wherein said nucleic-acid sequence or sequences are all or part of a bacteriophage genome.
Claim 42
Dependent Claim
28 words
A method as claimed in Claim 38, wherein said nucleic acid sequence or sequences are all or part of an extrachromosomal genetic element, a plasmid, or an episome.
Claim 43
Dependent Claim
21 words
A method as claimed in Claim 38,.wherein said sequence or sequences code for an R-factor or for an antibiotic resistance factor.
Claim 44
Dependent Claim
27 words
A method as claimed in Claim 28, wherein said chromatographic patterns of known bacteria are present in a catalog containing patterns for at least two different bacteria.
Claim 45
Dependent Claim
89 words
A kit comprising a carrier being compartmentalized to receive in close confinement therein one or more container means, wherein a first container means contains conserved genetic material sequence information-containing nucleic acid (other than ribosomal RNA information-containing nucleic acid) from or derived from a probe organism or from a consensus sequence; and wherein said kit also contains a catalog having hybridized or r eassociated chromatographic band patterns for at least two known different organism species, or said kit contains at least two known organism species, or genetic material derived therefrom.
Claim 46
Dependent Claim
89 words
A kit comprising a carrier being compartmentalized to receive in close confinement therein one or more container means, wherein a first container means contains conserved genetic material sequence information-containing nucleic acid (other than ribosomal RNA information-containing nucleic acid) from or derived from a probe organism or from a consensus sequence; and wherein said kit also contains a catalog having hybridized or r eassociated chromatographic band patterns for at least two known different organism species, or said kit contains at least two known organism species, or genetic material derived therefrom.
Claim 47
Dependent Claim
13 words
A kit as claimed in Claim 43, wherein the genetic material is DNA.
Claim 48
Dependent Claim
24 words
-45. A kit as claimed in Claim 43 or 44, which also comprises a second container means containing one or more restriction endonuclease enzymes.
Claim 49
Dependent Claim
19 words
A kit as claimed in Claim 44, wherein the conserved DNA sequence information-containing nucleic acid probe is detectably labelled.
Claim 50
Dependent Claim
74 words
A kit comprising a carrier being compartmentalized to receive in close confinement therein one or more container means, wherein a first container means contains conserved DNA sequence information-containing nucleic acid (other than ribosomal RNA information-containing nucleic acid) from or derived from a probe organism or from a consensus sequence, said nucleic acid being in detectably labelled form; and wherein said kit also comprises a second container means containing one or more restriction endonuclease enzymes.
Claim 51
Dependent Claim
74 words
A kit comprising a carrier being compartmentalized to receive in close confinement therein one or more container means, wherein a first container means contains conserved DNA sequence information-containing nucleic acid (other than ribosomal RNA information-containing nucleic acid) from or derived from a probe organism or from a consensus sequence, said nucleic acid being in detectably labelled form; and wherein said kit also comprises a second container means containing one or more restriction endonuclease enzymes.
Claim 52
Dependent Claim
20 words
A kit as.claimed in Claim 43, 45 or 47, wherein said conserved DNA sequence information-containing nucleic acid probe is RNA.
Claim 53
Dependent Claim
24 words
A kit as claimed in Claim 43, 45 or 47, wherein said conserved DNA sequence information-containing nucleic acid probe is DNA complementary to RNA.
Claim 54
Dependent Claim
21 words
A kit as claimed in Claim 48, which also comprises a container means containing one or more detectably labelled deoxynucleoside triphosphates.
Claim 55
Dependent Claim
17 words
A kit as claimed in Claim 43, 45 or 47, wherein said probe organism is a prokaryote.
Claim 56
Dependent Claim
17 words
A kit as claimed in Claim 43, 45 or 47, wherein said probe organism is a eukaryote.
Claim 57
Dependent Claim
13 words
A kit as claimed in Claim 51, wherein said prokaryote is a bacterium.
Claim 58
Dependent Claim
21 words
A kit as claimed in Claim 52, wherein said nucleic acid probe of said eukaryote is derived from an organelle thereof.
Claim 59
Dependent Claim
20 words
A kit as claimed in Claim 49, wherein said cDNA is labelled with 32 P, 14 C or 3 H.
Claim 60
Dependent Claim
21 words
A kit as claimed in Claim 49, wherein said cDNA is a faithful copy of the RNA it is derived from.
Claim 61
Dependent Claim
23 words
A kit as claimed in Claim 43, 45 or 47, which also comprises one or more container means containing viral nucleic acid probes.
Claim 62
Dependent Claim
26 words
A kit as claimed in Claim 43, 45 or 47 wherein said catalog is a book, a computer tape, a computer disk, or a computer memory.
Claim 63
Dependent Claim
18 words
A kit as claimed in Claim 43, 45 or 47, wherein said catalogue also includes viral chromatographic patterns.
Claim 64
Dependent Claim
19 words
A kit as claimed in Claim 43, 45 or 47 wherein said catalogue also includes patterns for infrasubspecific taxons.
References Cited (Backward Citations)
No citation records indexed.
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