Oligonucleotide arrays comprising background probes
First Claim
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1. A method for making a chemical array comprising:
- arraying a plurality of biopolymers on a substrate, thereby forming a plurality of features comprising biopolymers at known locations on the substrate, wherein at least one feature comprises specific hybridization probes designed or selected to specifically bind to target sequences and background probes for evaluating non-specific binding of target.
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Abstract
The invention relates to chemical arrays comprising a plurality of features comprising biopolymers at known locations on the substrate, wherein at least one feature comprises specific hybridization probes designed or selected to bind to specific target sequences and background probes for evaluating non-specific binding of target. Methods, systems, and kits for making and using the arrays are also described.
7 Citations
35 Claims
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1. A method for making a chemical array comprising:
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arraying a plurality of biopolymers on a substrate, thereby forming a plurality of features comprising biopolymers at known locations on the substrate, wherein at least one feature comprises specific hybridization probes designed or selected to specifically bind to target sequences and background probes for evaluating non-specific binding of target. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 33, 34, 35)
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- 18. A chemical array comprising a plurality of features, wherein each feature comprises a plurality of specific hybridization probes and background probes, and wherein the background probe sequences comprise a subsequence of the specific hybridization probes and background probes within at least two features are identical.
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21. A method for detecting specific binding of a target molecule in a sample to a probe comprising:
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providing an array comprising a plurality of biopolymer features arrayed at known locations on a substrate, wherein at least one feature comprises a plurality of specific hybridization probes and a plurality of background probes;
detecting binding of target to a feature and determining an amount of binding at the feature;
determining an amount of binding of target to background probes in the feature to determine an amount of non-specific binding.
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31. A method for evaluating non-specific background signal at a feature on a chemical array which comprises background probes and specific hybridization probes, comprising:
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positioning a template within an area of an array or an image of an array that is predicted to have a feature deposited or written thereon, wherein the template conforms in dimensions to an area of a feature comprising background probes, and excludes an area of the feature comprising specific hybridization probes; and
extracting feature information within the template area.
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32. A method comprising:
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receiving data for a feature on a chemical array comprising both specific hybridization probes designed or selected to specifically bind to target sequences and background probes for evaluating non-specific binding of target; and
detecting an amount of specific hybridization to the target sequences.
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Specification