Method for identifying and characterizing organisms

Claim 1

A method for characterizing an unknown organism species which comprises the steps of: a) hybridizing evolutionarily conserved sequences in the DNA of said organism with conserved DNA sequence information-containing nucleic acid from or derived from a probe organism, said nucleic acid capable of hybridizing to said evolutionarily conserved sequences of said unknown organism DNA; b) determining the position of said conserved sequences in said unknown organism relative to the position of restriction endonuclease cleavage sites in said DNA, thereby to obtain an identifying genetic characterization of said unknown organism; c) comparing said characterization with information from at least two sets of identifying genetic characterizations derived from the same conserved sequences, each of said sets representing the hybridization of evolutionarily conserved sequence-information containing nucleic acid from or derived from said probe organism to the DNA of a known organism, each of said sets defining a known different organism species; and d) establishing the species of said unknown organism.

Claim 2

A method for characterizing an unknown organism species which comprises the steps of: a) hybridizing evolutionarily conserved sequences in the DNA of said organism with conserved DNA sequence information-containing nucleic acid from or derived from a probe organism, said nucleic acid capable of hybridizing to said evolutionarily conserved sequences of said unknown organism DNA; b) determining the position of said conserved sequences in said unknown organism relative to the position of restriction endonuclease cleavage sites in said DNA, thereby to obtain an identifying genetic characterization of said unknown organism; c) comparing said characterization with information from at least two sets of identifying genetic characterizations derived from the same conserved sequences, each of said sets representing the hybridization of evolutionarily conserved sequence-information containing nucleic acid from or derived from said probe organism to the DNA of a known organism, each of said sets defining a known different organism species; and d) establishing the species of said unknown organism.

Claim 6

The method of any of claims 2, 3 or 4 wherein said conserved DNA information-containing nucleic acid probe is an RNA probe.

Claim 7

The method of any of claims 2, 3 or 4 wherein said conserved DNA information-containing nucleic acid probe is DNA complementary to RNA.

Claim 8

The method of claims 2, 3 or 4 wherein said conserved DNA information-containing nucleic acid probe is DNA obtained by nick-translating or cloning DNA complementary to RNA.

Claim 14

The method of any of claims 10 or 12 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 16

The method of any of claims 11 or 14 wherein said prokaryotic organism being characterized is selectively being detected while in the presence of a eukaryotic organism.

Claim 24

The method of any of claims 10 or 12 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 25

A method of identifying an unknown bacterial strain present in a sample which comprises the steps of: a) hybridizing evolutionarily conserved sequences in the DNA of said bacterium with conserved DNA sequence information-containing nucleic acid from or derived from a probe bacterium; b) determining the position of said conserved sequence relative to the position of restriction endonuclease cleavage sites in said DNA, thereby to obtain an identifying genetic characterization of said unknown bacterium; c) comparing said characterization with information from at least two sets of identifying genetic characterizations derived from the same conserved sequences, each of said sets representing the hybridization of evolutionarily conserved sequence information-containing nucleic acid from or derived from said probe bacterium, to the DNA of a known bacterium, each of said sets defining a known different bacterial species; and d) establishing the species of said unkown bacterial strain.

Claim 26

A method of identifying an unknown bacterial strain present in a sample which comprises the steps of: a) hybridizing evolutionarily conserved sequences in the DNA of said bacterium with conserved DNA sequence information-containing nucleic acid from or derived from a probe bacterium; b) determining the position of said conserved sequence relative to the position of restriction endonuclease cleavage sites in said DNA, thereby to obtain an identifying genetic characterization of said unknown bacterium; c) comparing said characterization with information from at least two sets of identifying genetic characterizations derived from the same conserved sequences, each of said sets representing the hybridization of evolutionarily conserved sequence information-containing nucleic acid from or derived from said probe bacterium, to the DNA of a known bacterium, each of said sets defining a known different bacterial species; and d) establishing the species of said unkown bacterial strain.

Claim 32

The method of any of claims 25, 26, 27, or 29 wherein said conserved DNA information-containing nucleic acid from said probe bacterium is detectably labeled.

Claim 36

The method of any of claims 25, 26, 27 or 29 wherein said unknown bacterium is pathogenic towards plants or animals.

Claim 42

The method of any of claims 1 or 24 wherein said evolutionarily conserved sequences code for transfer RNA.

Claim 43

The method of any of claims 1 or 24 wherein said evolutionarily conserved sequences code for a protein differing in its sequence by less than 50% amino acid residues between at least two different organism species.