Systems and methods for predicting oligonucleotide melting temperature (TmS)
First Claim
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1. A method of predicting the melting temperature (Tm) of an oligonucleotide sequence, comprising:
- inputting into a computer system data representing a sequence of N bases of an identified oligonucleotide having N-1 neighboring base pairs;
calculating in the computer system a (Tm) of the identified oligonucleotide sequence using the nearest neighbor thermodynamic parameters for each of the N-1 neighboring base pairs in the identified sequence, wherein said identified sequence includes at least one modified base selected from the group consisting of unsubstituted and 3-substituted pyrazolo[3,4-d]pyrimidines and 5-substituted pyrimidines, each nearest neighbor thermodynamic parameter defining a thermodynamic contribution of two corresponding neighboring bases; and
providing an output to a display or a user using the processing module, wherein said output represents a Tm of the identified oligonucleotide sequence.
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Abstract
Software systems and methods for predicting the melting temperature (Tm) and other characteristics of oligonucleotides, including modified oligonucleotides. Modified oligonucleotides are provided containing bases selected from unsubstituted and 3-substituted pyrazolo[3,4-d]pyrimidines and 5-substituted pyrimidines, and optionally have attached minor groove binders and reporter groups.
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Citations
24 Claims
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1. A method of predicting the melting temperature (Tm) of an oligonucleotide sequence, comprising:
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inputting into a computer system data representing a sequence of N bases of an identified oligonucleotide having N-1 neighboring base pairs; calculating in the computer system a (Tm) of the identified oligonucleotide sequence using the nearest neighbor thermodynamic parameters for each of the N-1 neighboring base pairs in the identified sequence, wherein said identified sequence includes at least one modified base selected from the group consisting of unsubstituted and 3-substituted pyrazolo[3,4-d]pyrimidines and 5-substituted pyrimidines, each nearest neighbor thermodynamic parameter defining a thermodynamic contribution of two corresponding neighboring bases; and providing an output to a display or a user using the processing module, wherein said output represents a Tm of the identified oligonucleotide sequence. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23)
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9. A computer readable storage medium including computer code for controlling a processor to calculate the melting temperature (Tm) of an oligonucleotide, the computer code including instructions that cause the processor to perform the following steps:
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input into a processing module data representing a sequence of N bases of an identified oligonucleotide having N-1 neighboring base pairs; retrieve nearest neighbor thermodynamic parameters for each of the N-1 neighboring base pairs in the identified sequence from a memory, wherein said identified sequence includes at least one modified base selected from the group consisting of unsubstituted and 3-substituted pyrazolo[3,4-d]pyrimidines and 5-substituted pyrimidines, each nearest neighbor thermodynamic parameter defining a thermodynamic contribution of two corresponding neighboring bases; calculate a melting temperature (Tm) of the identified oligonucleotide sequence using the retrieved nearest neighbor thermodynamic parameters; and provide an output to a display or a user using the processing module, wherein said output represents a Tm of the identified oligonucleotide sequence. - View Dependent Claims (10, 11, 12, 13, 14, 15, 16, 24)
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17. A computer system for predicting the melting temperature (Tm) of an oligonucleotide sequence, comprising:
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a memory unit for storing nearest neighbor thermodynamic parameters; user interface means for identifying a nucleotide sequence having N bases and N-1 neighboring base pairs, wherein at least one of said N bases includes a modified base, wherein the means for identifying includes means for receiving a user entered nucleotide sequence and; processing means, coupled to the memory unit, for retrieving nearest neighbor parameters for each of the N-1 neighboring base pairs in the identified sequence from the memory unit, for calculating a melting temperature (Tm) of the identified oligonucleotide sequence using the nearest neighbor thermodynamic parameters, and for providing an output to a display or a user, wherein said output represents a Tm of the identified oligonucleotide sequence, and wherein said identified sequence includes at least one modified base selected from the group consisting of unsubstituted and 3-substituted pyrazolo[3,4-d]pyrimidines and 5-substituted pyrimidines, each nearest neighbor thermodynamic parameter defining a thermodynamic contribution of two corresponding neighboring bases. - View Dependent Claims (18, 19)
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Specification