Methods for searching polynucleotide probe targets in databases
AssigneeApplera Corporation
InventorsCharles R. Scafe, Nicolas Peyret, Francisco M. De La Vega, Ryan T. Koehler, Eugene G. Spier
Life of this patent
Estimating the term…
Abstract
Methods for determining the binding affinity of a probe to a target or targets in a polynucleotide composite using an automated system. Such methods determine relative binding sites based on thermodynamic principles, using a thermodynamic alphabet and a thermodynamic scoring matrix, with appropriate computer software, such as BLASTP. The invention also provides methods for designing polynucleotide probes to be used in hybridization assays, and minimizing the occurrence of cross-hybridization.
Claims27
A method for identifying polynucleotides to which a probe may bind in a composite of individual polynucleotides, using an automated system, comprising the steps of:
- a) converting the nucleic acid sequence of said probe to a thermodynamic alphabet sequence using a thermodynamic alphabet;
- b) comparing said thermodynamic alphabet sequence of said probe to the thermodynamic alphabet sequences of individual polynucleotides in said composite, using said automated system.
A method according to claim 11 wherein said BLAST program is BLASTP.
A method for determining the specificity of binding of a polynucleotide probe to a polynucleotide target in a polynucleotide composite comprising said target and a plurality of other individual polynucleotides, using an automated system, said method comprising the steps of:
- a) converting the nucleic acid sequence of said probe to a thermodynamic alphabet sequence using a thermodynamic alphabet;
- b) comparing said thermodynamic alphabet sequence of said probe to the thermodynamic alphabet sequence of said target and said other individual polynucleotides in said composite, using said automated system, so as to find one or more other potential alternative targets to which said probe may bind;
- c) calculating the binding affinities of said probe to said target and to said potential alternative targets;
- d) comparing the binding affinities of said target and said potential alternative targets.
A method for designing a polynucleotide probe for a polynucleotide target, said probe having reduced cross-hybridization potential to other polynucleotides in a polynucleotide composite comprising said target and other polynucleotides, comprising the steps of:
- a) selecting an initial probe;
- b) converting the nucleic acid sequence of said initial probe to a thermodynamic alphabet sequence using a thermodynamic alphabet;
- c) comparing said thermodynamic alphabet sequence of said initial probe to the thermodynamic alphabet sequence of said target and said other polynucleotides in said composite, using an automated system, so as to identify one or more of potential alternative targets with which said probe may bind;
- d) calculating the binding affinities of said probe to said target and to said potential alternative targets;
- e) comparing the binding affinities of said target and said potential alternative targets;
- and
- f) altering said initial probe design to a create a second probe design having a reduced binding affinity to other polynucleotides by repeating steps a) through e) with respect to said second probe design.
Dependencies are inferred from the claim text.