Multidentate arrays
First Claim
1. A method for producing an addressable array of features comprising:
- receiving a target polynucleotide;
determining an evaluated probe set for said target polynucleotide, wherein said set comprises probes that simultaneously bind to said target when said probes are present in the same feature of an addressable array; and
fabricating an addressable array comprising said evaluated probe set present in the same feature of said addressable array as a mixed probe feature.
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Abstract
A method of evaluating for the presence of a target polynucleotide in a sample, using an addressable array of multiple polynucleotide probes linked to a substrate. The sample is exposed to the array and a set of polynucleotide target probes, such that target polynucleotide which may be present will bind to a predetermined feature of the array through multiple target probes of the set by forming at respective target regions on a target molecule, simultaneous hybrids with anti-target regions of the multiple target probes. A binding pattern on the array is observed and the presence of the target polynucleotide evaluated based on the observed binding pattern. Kits using such arrays, and methods for selecting target probes are further provided.
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Citations
14 Claims
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1. A method for producing an addressable array of features comprising:
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receiving a target polynucleotide; determining an evaluated probe set for said target polynucleotide, wherein said set comprises probes that simultaneously bind to said target when said probes are present in the same feature of an addressable array; and fabricating an addressable array comprising said evaluated probe set present in the same feature of said addressable array as a mixed probe feature. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8)
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9. A method for providing custom addressable arrays of features, comprising the acts of:
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receiving a user selection of one or more probe set identifiers that each identify a plurality of potential probes; determining verified probe sets of verified probes corresponding to the probe set identifiers, wherein said sets comprise probes that simultaneously bind to a target when said probes are present in the same feature of an addressable array; generating a custom addressable array design based, at least in part, upon the verified probe sets; and providing to the user one or more addressable arrays based on the addressable array design, wherein said probes that simultaneously bind to a target are present in the same feature of said addressable array as a mixed probe feature.
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10. A method for providing custom addressable arrays of features, comprising the acts of:
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receiving a user selection of one or more probe set identifiers that identify one or more potential probes; determining verified probe sets of verified probes corresponding to the probe set identifiers, wherein said sets comprise probes that simultaneously bind to a target when said probes are present in the same feature of said addressable array; generating a custom addressable array design based, at least in part, upon the verified probe sets wherein said probes that simultaneously bind to a target are present in the same feature of said addressable array as a mixed probe feature; and enabling for display to the user a representation of one or more aspects of the custom probe array design via one or more graphical user interfaces enabled to receive a user selection specifying acceptance, modification, or rejection of the custom probe array design; and
providing to the user one or more probe arrays based on the probe array design and responsive to the user specification of acceptance or modification. - View Dependent Claims (11, 12, 13, 14)
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Specification