Systems, tools and methods of assaying biological materials using spatially-addressable arrays

An assay system comprising:

• an array apparatus that comprises a plurality of first probes on a substrate in an array of features, at least some first probes being different from others in the plurality of first probes, a different first probe being located at a different feature and being a different address on the array, wherein each of said at least some first probes comprises a first nucleotide with a reversed polarity relative to other nucleotides of said first probe;
• and
• a plurality of second probes, each second probe comprising a first region and a second region, one or both of the first region and the second region being different from respective other first regions and other second regions of at least some of the second probes, such that some of the second probes in the plurality of second probes are different, the first region of the second probe binding with a respective first probe,
• wherein the first region of at least some second probes comprises a second nucleotide with the same polarity as said reversed polarity of said first nucleotide;
• wherein said second nucleotide preferentially binds to the first nucleotide of the first probes instead of to a complementary nucleotide whose polarity has not been reversed, and
• wherein the second region of the second probes binds with a specific target of a biological material to be assayed to address the specific target to a feature address on the array corresponding to the respective first probe.