Methods of Detecting Analytes

A method for determining the location of nucleic acid in a tissue section, the method comprising:

• (a) providing an array comprising a plurality of features on a substrate, wherein a feature of the plurality of features comprises a plurality of capture probes immobilized thereon such that a capture probe of the plurality of capture probes has a free 3′ end, the feature occupying a distinct position on the array, and the capture probe comprising a nucleic acid molecule having the following domains oriented 5′ to 3′:
• (i) a first sequence comprising a positional domain comprising a sequence unique to the feature;
• and
• (ii) a second sequence comprising a capture domain comprising a nucleotide sequence complementary to at least a portion of the nucleic acid to be detected;
• (b) placing the tissue section on the array such that the tissue section covers the feature on the array;
• (c) hybridizing the nucleic acid from the tissue section to the capture domain of the capture probe, such that the nucleic acid is captured by the capture domain;
• (d) generating a complementary DNA molecule by extending the free 3′ end of the capture probe using the captured nucleic acid as a ligation template, such that the generated complementary DNA molecule comprises a nucleotide sequence complementary to the positional domain;
• (e) releasing the generated complementary DNA molecule, or a portion thereof, or generating and releasing a second strand complementary to the generated complementary DNA molecule, or a portion thereof, from the feature on the array, wherein the generated complementary DNA molecule, or the portion thereof, comprises the nucleotide sequence of the positional domain, or the second strand, or the portion thereof, comprises a sequence complementary to the nucleotide sequence of the positional domain;
• and
• (f) identifying the nucleotide sequence of the positional domain present in the generated complementary DNA molecule or a complement thereof, wherein the nucleotide sequence of the positional domain, or the complement thereof, indicates that the generated complementary DNA molecule was obtained from nucleic acid in the tissue section at the distinct position where the tissue section covered the feature, thereby determining the location of the nucleic acid in the tissue section.

The method of claim 1, wherein each capture probe consists of a nucleic acid molecule comprising the following domains oriented 5′ to 3′:

• (i) a cleavage domain;
• (ii) the first sequence comprising the positional domain;
• and
• (iii) the second sequence comprising the capture domain,
• wherein the step of releasing the generated complementary DNA molecule, or the portion thereof, or the second strand, or the portion thereof, from the feature on the array comprises cleaving the cleavage domain.