Methods and apparatus for detecting polynucleotide hybridization

A method of detecting a polynucleotide, the method comprising:

• contacting a sample polynucleotide with a reference polynucleotide at an assay site, wherein at least one of the reference and sample polynucleotides is labeled with a luminophore;
• illuminating the assay site with light capable of stimulating luminescence from the luminophore;
• detecting light transmitted from the assay site;
• converting the detected light to a signal;
• discriminating between a first portion of the signal that is attributable to light emitted by the luminophore and a second portion of the signal that is attributable to a background;
• and
• deriving information relating to the extent of hybridization between the sample polynucleotide and the reference polynucleotide based on the extent of polarization of the light emitted from the hybrid.

A method of detecting hybridization between first and second polynucleotides, the method comprising:

• providing a substrate containing at least two assay sites, each assay site being located in a well having a shape;
• contacting a first polynucleotide with a second polynucleotide at each assay site, wherein at least one of the two polynucleotides is bound to a luminophore;
• directing a light beam to each assay site, wherein the light beam has a shape that substantially matches the shape of the well;
• and
• determining the extent of hybridization between the first polynucleotide and the second polynucleotide based on detecting polarized light emitted from the luminophore at each assay site.

A kit for determining sequence information relating to a sample polynucleotide, the kit comprising:

• a substrate having plural assay sites;
• a plurality of reference polynucleotides, each reference polynucleotide having a different sequence;
• and
• a luminophore capable of labeling a polynucleotide.