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Abstract

The invention provides a system and reagents for carrying out multiplexed analytical measurements using the hybridization of oligonucleotide tags to addressable solid phase supports to obtain simultaneous readouts from hundreds to tens of thousands of reactions. In one aspect of the invention, analyte interaction moieties, such as oligonucleotide probes, are produced that are each labeled with a unique synthesis tag constructed from a set of two-nucleotide 'words.' During or after an assay, the synthesis tags are converted to hybridization tags that are used in the readout step. Hybridization tags are constructed to maximize discrimination in the readout. Hybridization tags of the invention are preferably constructed from oligonucleotide 'words' selected from a minimally cross-hybridizing set using combinatorial synthesis techniques. In a further aspect, discrimination in the readout is enhanced by employing hybridization tags that are constructed with words having the 'comma-less' property and by minimizing or eliminating extraneous nucleic acids associated with the hybridization tag during a readout step.

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First Claim