Detection of target nucleic acid sequences using different detection temperatures
The present invention relates to detection of target nucleic acid sequences using different detection temperatures. The present invention employing different detection temperatures enables to detect a plurality of target nucleic acid sequences in conventional real-time manners even with a single type of label in a single reaction vessel. The conventional technologies detect a plurality of target nucleic acid sequences by a melting analysis after target amplification. Unlikely, the present invention does not require a melting analysis after target amplification, such that the time for analysis is greatly reduced.
1. A method for detecting two target nucleic acid sequences in a sample using different detection temperatures, comprising:
(a) incubating the sample with two signal-generating means for detection of the two target nucleic acid sequences in a single first reaction vessel and detecting a generated signal by using a single type of detector; wherein the two target nucleic acid sequences are known; wherein each of the target nucleic acid sequences is detected by a corresponding signal-generating means; wherein each of the two signal-generating means comprises an oligonucleotide with a fluorescent label and when each of the two signal-generating means comprises primers and probes, the nucleotide sequences of the primers and probes are designed not to bind to each other; wherein one of the two target nucleic acid sequences has a high detection temperature and the other has a low detection temperature determined by the corresponding signal-generating means; wherein the signal-generating means for the target nucleic acid sequence having the high detection temperature generates a signal at the high detection temperature and at the low detection temperature, dependently on the presence of the target nucleic acid sequence having the high detection temperature, and the signal-generating means for the target nucleic acid sequence having the low detection temperature generates a signal at the low detection temperature, dependently on the presence of the target nucleic acid sequence having the low detection temperature; wherein the high detection temperature is a temperature at which a signal is generated from the signal-generating means for the target nucleic acid sequence having the high detection temperature, and the low detection temperature is a temperature at which a signal is generated from the two signal-generating means; wherein the wavelengths of signals to be generated by the two signal-generating means are not differentiated by the single type of detector; wherein the detection is performed only at both the high detection temperature and the low detection temperature at each cycle, selected several cycles or end-point of real-time PCR (polymerase chain reaction) and wherein the two target nucleic acid sequences are amplified; and
(b) determining the presence of the two target nucleic acid sequences by the signals detected in the step (a); wherein (i) the presence of the target nucleic acid sequence having the high detection temperature is determined by the signal detected at the high detection temperature and (ii) the presence of the target nucleic acid sequence having the low detection temperature is determined by comparing a difference between the signal intensity detected at the high detection temperature and the signal intensity detected at the low detection temperature with a threshold, wherein the difference is calculated by multiplying the signal detected at the high detection temperature by a reference value and then subtracting the multiplication result from the signal detected at the low detection temperature, wherein the reference value is obtained by (i) subjecting the target nucleic acid sequence having the high detection temperature to real-time PCR using the signal-generating means for the target nucleic acid sequence having the high detection temperature in a second reaction vessel other than the first reaction vessel in the step (a), (ii) detecting signals only at the high detection temperature and the low detection temperature in each cycle, selected several cycles or end-point of real-time PCR, and (iii) then obtaining a ratio of the signal detected at the low detection temperature to the signal detected at the high detection temperature;
wherein the method does not comprise a melting curve analysis.
2. The method according to claim 1 , wherein the signal-generating means for each of the target nucleic acid sequences are a signal-generating means to generate a signal in a dependent manner on the formation of a duplex.
3. The method according to claim 1 , wherein the signal-generating means for each of the target nucleic acid sequences are a signal-generating means by formation of a duplex in a dependent manner on cleavage of a mediation oligonucleotide having 15-150 nucleotides specifically hybridized with the target nucleic acid sequence.
4. The method according to claim 1 , wherein the signal-generating means for the target nucleic acid sequence having the high detection temperature is a signal-generating means by cleavage of a detection oligonucleotide having 5-100 nucleotides by an enzyme having 5′-nuclease activity, and the signal-generating means for the target nucleic acid sequence having the low detection temperature is a signal-generating means by the formation of a duplex.
5. The method according to claim 1 , wherein the signal-generating means for the target nucleic acid sequence having the high detection temperature is a signal-generating means by cleavage of a detection oligonucleotide having 5-100 nucleotides by an enzyme having 5′ nuclease activity, and the signal-generating means for the target nucleic acid sequence having the low detection temperature is a signal-generating means by formation of a duplex in a dependent manner on cleavage of a mediation oligonucleotide having 15-150 nucleotides specifically hybridized with the target nucleic acid sequence.
6. The method according to claim 1 , wherein the two signal-generating means comprise an identical label and the wavelengths of signals from the label are not differentiated by the single type of detector.
7. The method according to claim 1 , wherein when the signal is not detected at the high detection temperature, the determination of the presence of the target nucleic acid sequence having the low detection temperature is made by the signal detected at the low detection temperature.
8. The method according to claim 1 , wherein when the target nucleic acid sequence having the high detection temperature is present, the presence of the target nucleic acid sequence having the low detection temperature is determined by calculating the difference with a reference value.
9. The method according to claim 8 , wherein the reference value, is obtained by (i) incubating the target nucleic acid sequence having the high detection temperature with a signal-generating means for detection of the target nucleic acid sequence having the high detection temperature in a second reaction vessel other than the first reaction vessel in the step (a), (ii) detecting signals at both the high detection temperature and the low detection temperature, and (iii) then obtaining a difference between the signal detected at the high detection temperature and the signal detected at the low detection temperature.
10. The method according to claim 1 , wherein the two target nucleic acid sequences comprise a nucleotide variation and one of the two target nucleic acid sequences comprises one type of the nucleotide variation and the other comprises the other type of the nucleotide variation.