Nucleic acid concatemers and methods for stabilizing and/or compacting the same

A method comprising:

• (a) contacting the biological sample with a padlock probe comprising a sequence that hybridizes to a target nucleic acid in the biological sample,
• wherein the padlock probe comprises:
• (i) a first hybridizing region and a second hybridizing region capable of hybridizing to each other, wherein the first and second hybridizing regions are linked by a loop region and
• (ii) one or more barcode sequences;
• (b) generating a rolling circle amplification product (RCP) at a location in the biological sample using a circularized padlock probe as a template, wherein the padlock probe is circularized to generate the circularized padlock probe using the target nucleic acid and/or a splint as template,
• wherein the RCP comprises multiple copies of complementary sequences of the first and second hybridizing regions, and
• wherein the complementary sequences of the first and second hybridizing regions from different copies hybridize to one another, thereby compacting and/or stabilizing the RCP at the location in the biological sample;
• and
• (c) detecting the RCP at the location in the biological sample.

A method comprising:

• (a) contacting the biological sample with a padlock probe comprising a sequence that hybridizes to a target nucleic acid in the biological sample,
• wherein the padlock probe comprises:
• (i) a first hybridizing region and a second hybridizing region capable of hybridizing to each other, wherein the first and second hybridizing regions are linked by a first loop region;
• (ii) a third hybridizing region and a fourth hybridizing region capable of hybridizing to each other, wherein the third and fourth hybridizing regions are linked by a second loop region;
• and
• (iii) one or more barcode sequences in the first and/or second loop regions;
• (b) generating a rolling circle amplification product (RCP) at a location in the biological sample using a circularized padlock probe as a template, wherein the padlock probe is circularized to generate the circularized padlock probe using the target nucleic acid and/or a splint as template,
• wherein the RCP comprises multiple copies of complementary sequences of the first, second, third, and fourth hybridizing regions, and
• wherein the complementary sequences of the first and second hybridizing regions from two or more different copies hybridize to one another and the complementary sequences of the third and fourth hybridizing regions from two or more different copies hybridize to one another, thereby compacting and/or stabilizing the RCP at the location in the biological sample;
• and
• (c) detecting the RCP at the location in the biological sample.