Method for detecting polynucleotides with immobilized polynucleotide probes identified based on T.sub.m
First Claim
1. A method of identifying probes and thereafter detecting the presence of a particular organism, infectious agent, or biological component of a cell or organism in a sample derived from biological material that contains polynucleotides, by detecting an analyte polynucleotide in said sample that is indicative of the presence of said organism, infectious agent, or biological component, said method comprising the step of:
- (a) identifying a first polynucleotide probe having a nucleotide sequence complementary to a first nucleotide sequence contained in an analyte polynucleotide specific to a particular organism, infectious agent, or biological component, said first polynucleotide probe having a melting temperature (Tm) within a preselected range with said analyte polynucleotide at a selected sodium and formamide concentration, by a method comprising;
(i) retrieving from a database a plurality of user-selected gene sequences including a gene sequence from said organism, infectious agent, or biological component, and inputting said sequences into a computer system for calculating Tm ;
(ii) calculating the Tm '"'"'s of a plurality of candidate probes having nucleotide sequences derived from the gene sequence from said organism, infectious agent, or biological component, at the selected sodium and formamide concentration with said gene sequence from said organism, infectious agent, or biological component, using said computer system;
(iii) calculating the Tm '"'"'s of said plurality of candidate probes having nucleotide sequences at the selected sodium and formamide concentration with each of said user-selected gene sequences other than that of said gene sequence from said organism, infectious agent, or biological component; and
(iv) identifying said first polynucleotide probe as the candidate probe which has a Tm with said analyte polynucleotide within the preselected range at the selected sodium and formamide concentration, and that has the lowest Tm overall with the other user-selected gene sequences;
(b) immobilizing said first polynucleotide probe to a solid support;
(c) hybridizing said analyte polynucleotide in said sample to said first nucleotide sequence of said first polynucleotide probe, if said analyte polynucleotide is present in said sample;
(d) identifying a second polynucleotide probe having a nucleotide sequence complementary to a second nucleotide sequence contained in said analyte polynucleotide, said second polynucleotide probe being different from said first nucleotide sequence, said second polynucleotide probe having a Tm with said analyte polynucleotide at a selected sodium and formamide concentration, said Tm being approximately the same or lower than the Tm of said first polynucleotide probe;
(e) hybridizing said second polynucleotide probe to said second sequence of said analyte polynucleotide hybridized to said first polynucleotide probe; and
(f) determining the presence of said particular organism, infectious agent, or biological component in said sample by detecting the presence of said second polynucleotide probe on said solid support.
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Abstract
A method for detecting the presence of a particular organism, infectious agent, or biological component of a cell or organism in a sample, based on sandwich hybridization in which first and second probes are used, and the specificity of the first probe is determined based on its melting temperature (Tm) with the target polynucleotide at a selected sodium and formamide concentration.
76 Citations
37 Claims
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1. A method of identifying probes and thereafter detecting the presence of a particular organism, infectious agent, or biological component of a cell or organism in a sample derived from biological material that contains polynucleotides, by detecting an analyte polynucleotide in said sample that is indicative of the presence of said organism, infectious agent, or biological component, said method comprising the step of:
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(a) identifying a first polynucleotide probe having a nucleotide sequence complementary to a first nucleotide sequence contained in an analyte polynucleotide specific to a particular organism, infectious agent, or biological component, said first polynucleotide probe having a melting temperature (Tm) within a preselected range with said analyte polynucleotide at a selected sodium and formamide concentration, by a method comprising; (i) retrieving from a database a plurality of user-selected gene sequences including a gene sequence from said organism, infectious agent, or biological component, and inputting said sequences into a computer system for calculating Tm ; (ii) calculating the Tm '"'"'s of a plurality of candidate probes having nucleotide sequences derived from the gene sequence from said organism, infectious agent, or biological component, at the selected sodium and formamide concentration with said gene sequence from said organism, infectious agent, or biological component, using said computer system; (iii) calculating the Tm '"'"'s of said plurality of candidate probes having nucleotide sequences at the selected sodium and formamide concentration with each of said user-selected gene sequences other than that of said gene sequence from said organism, infectious agent, or biological component; and (iv) identifying said first polynucleotide probe as the candidate probe which has a Tm with said analyte polynucleotide within the preselected range at the selected sodium and formamide concentration, and that has the lowest Tm overall with the other user-selected gene sequences; (b) immobilizing said first polynucleotide probe to a solid support; (c) hybridizing said analyte polynucleotide in said sample to said first nucleotide sequence of said first polynucleotide probe, if said analyte polynucleotide is present in said sample; (d) identifying a second polynucleotide probe having a nucleotide sequence complementary to a second nucleotide sequence contained in said analyte polynucleotide, said second polynucleotide probe being different from said first nucleotide sequence, said second polynucleotide probe having a Tm with said analyte polynucleotide at a selected sodium and formamide concentration, said Tm being approximately the same or lower than the Tm of said first polynucleotide probe; (e) hybridizing said second polynucleotide probe to said second sequence of said analyte polynucleotide hybridized to said first polynucleotide probe; and (f) determining the presence of said particular organism, infectious agent, or biological component in said sample by detecting the presence of said second polynucleotide probe on said solid support. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36)
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17. A kit for identifying the presence of an organism, infectious agent, or biological component of a cell or organism in a biological sample, comprising:
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a microtiter plate having a plurality of wells, to which at least two different polynucleotide probes are immobilized, each polynucleotide probe being immobilized to a different well, each polynucleotide probe being complementary to or homologous to a first nucleotide sequence in an analyte polynucleotide specific to a different organism, infectious agent, or biological component to be detected, each polynucleotide probe having approximately the same Tm within the range of from approximately 48°
C. to approximately 60°
C., each polynucleotide probe being identified by a method comprising;(i) retrieving from a database a plurality of user-selected gene sequences including a gene sequence from said organism, infectious agent, or biological component, and inputting said sequences into a computer system for calculating Tm ; (ii) calculating the Tm '"'"'s of a plurality of candidate probes having nucleotide sequences derived from the gene sequence from said organism, infectious agent, or biological component, at the selected sodium and formamide concentration with said gene sequence from said organism, infectious agent, or biological component, using said computer system; (iii) calculating the Tm '"'"'s of said plurality of candidate probes having nucleotide sequences at the selected sodium and formamide concentration with each of said user-selected gene sequences other than that of said gene sequence from said organism, infectious agent, or biological component; and (iv) identifying each of said polynucleotide probes as the candidate probe which has a Tm with said analyte polynucleotide within the preselected range at the selected sodium and formamide concentration, and that has the lowest Tm overall with the other user-selected gene sequences; and a common polynucleotide probe complementary to or homologous to a second nucleotide sequence in said analyte polynucleotide of said organism, infectious agent, or biological component, said common polynucleotide probe being complementary to polynucleotide contained in a plurality of different organisms, infectious agents, or biological components, said common polynucleotide probe having about the same or lower Tm than each specific polynucleotide probe. - View Dependent Claims (18, 19, 20, 21, 22, 23)
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25. A method of identifying probes and thereafter detecting the presence of an organism, infectious agent, or biological component of a cell or organism in a sample derived from biological material that contains polynucleotides, by detecting an analyte polynucleotide in said sample that is indicative of the presence of said organism, infectious agent, or biological component, said method comprising the steps of:
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(a) immobilizing a first polynucleotide probe to a solid support, said first polynucleotide probe having a nucleotide sequence complementary to a first nucleotide sequence contained in an analyte polynucleotide, common to a plurality of different organisms, infectious agents, or biological components, said first polynucleotide probe having a Tm within a preselected range between approximately 48°
C. and approximately 60°
C. with said analyte polynucleotide at a selected sodium and formamide concentration;(b) identifying a second polynucleotide probe having a label thereon, wherein the nucleotide sequence of said second polynucleotide probe is complementary to a second nucleotide sequence contained in said analyte polynucleotide, specific to an organism, infectious agent, or biological component, and has approximately the same Tm as said first polynucleotide probe so that said first and second polynucleotide probes can hybridize to said analyte polynucleotide under the same conditions, said identification being conducted, by a method comprising; (i) retrieving from a database a plurality of user-selected gene sequences including the gene sequence of said organism, infectious agent, or biological component, and inputting said sequences into a computer system for calculating Tm ; (ii) calculating the Tm '"'"'s of a plurality of candidate probes having nucleotide sequences derived from the gene sequence from said organism, infectious agent, or biological component, at the selected sodium and formamide concentration with said gene sequence from said organism, infectious agent, or biological component, using said computer system; (iii) calculating the Tm '"'"'s of said plurality of candidate probes having nucleotide sequences at the selected sodium and formamide concentration with each of said user-selected gene sequences other than that of said gene sequence from said organism, infectious agent, or biological component; and (iv) identifying said second polynucleotide probe as the candidate probe which has a Tm within the preselected range with said analyte polynucleotide and has the lowest Tm overall with the other user-selected gene sequences; (c) contacting the polynucleotides present in said sample with said first polynucleotide probe and said second polynucleotide probe having a label thereon with said polynucleotides present in said sample, whereby said first nucleotide sequence contained in said analyte polynucleotide hybridizes to said first polynucleotide probe, and said second polynucleotide probe hybridizes to said second nucleotide sequence contained in said analyte polynucleotide, if said analyte polynucleotide is present in said sample; and (d) determining the presence of said organism, infectious agent, or biological component in said sample by detecting the presence of said label on said second polynucleotide probe if hybridized to said analyte polynucleotide. - View Dependent Claims (26, 27)
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37. A method of identifying probes and thereafter detecting the presence of a particular polynucleotide in a sample, said method comprising the step of:
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(a) identifying a first polynucleotide probe having a nucleotide sequence complementary to a first nucleotide sequence contained in said particular polynucleotide, said first polynucleotide probe having a melting temperature (Tm) within a preselected range with said particular polynucleotide at a selected sodium and formamide concentration, by a method comprising; (i) retrieving from a database a plurality of user-selected gene sequences including the gene sequence of said organism, infectious agent, or biological component, and inputting said sequences into a computer system for calculating Tm ; (ii) calculating the Tm '"'"'s of a plurality of candidate probes having nucleotide sequences derived from the gene sequence from said organism, infectious agent, or biological component, at the selected sodium and formamide concentration with said gene sequence form said organism, infectious agent, or biological component, using said computer system; (iii) calculating the Tm '"'"'s of said plurality of candidate probes having nucleotide sequences at the selected sodium and formamide concentration with each of said user-selected gene sequence other than that of said gene sequence from said organism, infectious agent, or biological component; and (iv) identifying said first polynucleotide probe as the candidate probe which has a Tm within the preselected range with said particular polynucleotide indicative of the presence of said organism, infectious agent, or biological component, and that has the lowest Tm overall with the other user-selected gene sequences; (b) immobilizing said first polynucleotide probe to a solid support; (c) hybridizing said particular polynucleotide in said sample to said first nucleotide sequence of said first polynucleotide probe, if said particular polynucleotide is present in said sample; (d) identifying a second polynucleotide probe having a nucleotide sequence complementary to a second nucleotide sequence contained in said particular polynucleotide, different from said first nucleotide sequence, and having a Tm with said particular polynucleotide at a selected sodium and formamide concentration, said Tm being approximately the same or lower than the Tm of said first polynucleotide probe; (e) hybridizing said second polynucleotide probe to said second sequence of said particular polynucleotide hybridized to said first polynucleotide probe; and (f) determining the presence of said particular polynucleotide in said sample by detecting the presence of said second polynucleotide probe on said solid support.
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Specification