Reactions on a solid surface

A method for characterizing a nucleic acid comprising:

• a) providing:
• i. a sample suspected of containing a target nucleic acid;
• ii. oligonucleotides capable of hybridizing to said target nucleic acid to form an invasive cleavage structure, wherein said oligonucleotides comprise first and second oligonucleotides, said first oligonucleotide comprising a portion complementary to a first region of said target nucleic acid and said second oligonucleotide comprising a 3′ portion and a 5′ portion, said 5′ portion complementary to a second region of said target nucleic acid downstream of and contiguous to said first portion of said target nucleic acid;
• iii. a solid support, wherein one or more of said oligonucleotides is attached to said solid support;
• and
• iv. an agent capable of detecting the presence of an invasive cleavage structure;
• b) exposing said sample to said oligonucleotides and said agent, wherein said exposing said sample to said oligonucleotides and said agent comprises exposing said sample to said oligonucleotides and said agent under conditions wherein an invasive cleavage structure is formed between a target nucleic acid and said oligonucleotides if said target nucleic acid is present in said sample;
• and
• c) detecting said invasive cleavage structure.

A method for cleaving multiple oligonucleotides comprising:

• a) providing:
• i. a plurality of first oligonucleotides attached to a solid support;
• ii. a second oligonucleotide attached to said solid support;
• and
• iii. a cleavage agent;
• wherein said first oligonucleotides comprise a portion complementary to a first region of a target nucleic acid;
• and wherein said second oligonucleotide comprises a 3′ portion and a 5′ portion, said 5′ portion complementary to a second region of said target nucleic acid downstream of and contiguous to said first portion of said target nucleic acid;
• b) exposing said solid support to said cleavage agent under conditions such that:
• i. a first cleavage structure is formed, said first cleavage structure comprising one of said first oligonucleotides and said second oligonucleotide;
• ii. said cleavage agent cleaves said first oligonucleotide in said first cleavage structure to produce a first cleavage fragment;
• iii. after cleavage of said first first oligonucleotide, a second cleavage structure is formed, said second cleavage structure comprising a second of said first oligonucleotides and said second oligonucleotide;
• iv. said cleavage agent cleaves said first oligonucleotide in said second cleavage structure to produce a second cleavage fragment;
• wherein said conditions comprise exposing a target nucleic acid to said solid support;
• and
• c) detecting the presence of said first or said second cleavage fragments.