Patent ID: 7122303

Claim:
A hybridization assay comprising: (a) contacting a sample of target nucleic acids with a collection of substrate bound probe nucleic acid features that includes at least one hybridization nucleic acid feature and at least one background nucleic acid feature that is an empirically observed inactive probe that does not hybridize to a fully complementary fluorescently labeled target nucleic acid as determined in an assay wherein said probe is provided in an array that is contacted with said fluorescently labeled fully complementary target under said hybridization conditions, wherein said contacting occurs between 10-25° C. below the average temperature (T m ) at which nucleotide hybrids of the contacted collection are 50% melted; (b) separating unbound target nucleic acids/label from said collection of probe nucleic acid features; (c) detecting a signal, if present, from said at least one background feature and said at least one hybridization nucleic acid feature; and (d) subtracting a detected signal from said at least one background nucleic acid feature from signal detected from said at least one hybridization nucleic acid feature; wherein said method is further characterized by including a target nucleic acid labeling step prior to said detecting step(c).