Multianalyte Molecular Analysis Using Application-Specific Random Particle Arrays

A method of real time monitoring of a multiplicity of target-oligonucleotide probe binding reactions carried out in the same reaction vessel, where detection of reaction results is performed by imaging signals which indicate binding of said targets to oligonucleotide probes, said oligonucleotide probes being bound to encoded carriers, wherein different types of oligonucleotide probes are bound to differently-encoded carriers and signals associated with differently-encoded carriers can be discriminated, comprising:

• conjugating said carriers with oligonucleotide probes which include two complementary subsequences, separated by a third subsequence, and wherein a first complementary subsequence has a greater number of nucleotides which are complementary to the target subsequence than to the other complementary subsequence;
• providing conditions such that said two complementary subsequences are annealed in the absence of target, but wherein the binding of the target subsequence to the first complementary subsequence causes separation of said two complementary subsequences and generation of a fluorescent signal;
• forming said carriers into a planar array by placing them on a planar surface which is placed inside the reaction vessel;
• adding targets, in solution, to the reaction vessel;
• imaging said planar array to detect said signals at a first time and at least one other time, to thereby monitor difference in signals between the two times and to thus monitor the relative quantity target-ligand binding at said first and other times;
• and
• identifying the types of ligands binding to targets by decoding the carriers associated with signals.