Methods and compositions are provided to identify oligonucleotides that bind targets of interest. The targets include tissues, cells, circulating biomarkers such as microvesicles, including those derived from various diseases. The oligonucleotides can be used in diagnostic and therapeutic applications.

Methods and compositions are provided to identify oligonucleotides that bind targets of interest. The targets include tissues, cells, circulating biomarkers such as microvesicles, including those derived from various diseases. The oligonucleotides can be used in diagnostic and therapeutic applications.

Methods and compositions are provided to identify oligonucleotides that bind targets of interest. The targets include tissues, cells, circulating biomarkers such as microvesicles, including those derived from various diseases. The oligonucleotides can be used in diagnostic and therapeutic applications.

A method for identification of the most abundant oligonucleotide species in a library of oligonucleotides comprising more than 10.sup.6 oligonucleotide species, wherein the oligonucleotides of the library of oligonucleotides are not inherently capable of exponential amplification by PCR and include a coding sequence, which is characteristic of one oligonucleotide specie of the library of oligonucleotides and only one fixed sequence, which is present in a plurality of oligonucleotide species of the library of oligonucleotides, said fixed sequence being located on a 5′ side of the coding sequence, and wherein the method comprises specifically amplifying the sequence of a hybridised oligonucleotide species using the steps of: incubating the library of oligonucleotides under conditions of hybridization such as to allow complementary coding sequences to hybridize and form hybridized oligonucleotide species; extending a 3′ end of one or more of the hybridised oligonucleotide species, having only one fixed sequence, to provide extended sequences having an extended region, such that the extended region generates a second fixed sequence thereby forming extended sequences having two fixed sequences; amplifying extended sequences comprising two fixed sequences using PCR to provide amplified sequences, and optionally identifying an identity of the amplified sequences thereby revealing an identity of the hybridised oligonucleotide species in the step of incubating. The library of oligonucleotides is selected from the group of a library of encoded molecules, a library of aptamers, a library of reporter sequences derived from a library of encoded molecules, and a library of aptamers.

According to one embodiment of the present invention, a structure includes: a substrate having a patterned surface of one or more binding sites; and a molecular shape made by a polynucleotide platform having a shape corresponding to a shape of a binding site of the one or more binding sites, the molecular shape being bound to one of the one or more binding sites.

A machine-readable medium and methods of reading and writing same are disclosed. The machine-readable medium comprises a substrate having an array of addressable locations thereon, each addressable location adapted to be physically associated with a collection of non-polymeric molecules. The molecules in each collection are selected from a set of unambiguously identifiable molecules, each molecule uniquely associated with a predetermined position in a numerical value, wherein the presence of the molecule in the collection indicates a predetermined digit at the associated position and the absence of said molecule in the collection indicates a zero at said associated position.

Embodiments of the present invention relate to bistable devices constructed using a polynucleotide platform for sensing molecular events including binding or conformational changes of target molecules. Applications include measuring concentration of a target, measuring the effect of environmental conditions on the target, and screening a library for molecules that bind the target or modulate its function. In embodiments, devices include: a top lid, bottom lid, and flexible linker or hinge between them. A device has an open configuration in which the top and bottom lid are separated, and a closed configuration they are bound close together. Binding domains or variations of the target molecule are fixed to a device so that when the molecular event occurs, the device switches from open to closed, or vice versa. Aspects relate to detecting device geometry using, for example, an optical, electronic, magnetic, or DNA signal.

Methods and compositions are provided to identify oligonucleotides that bind targets of interest. The targets include tissues, cells, circulating biomarkers such as microvesicles, including those derived from various diseases. The oligonucleotides can be used in diagnostic and therapeutic applications.

Methods and compositions are provided to identify oligonucleotides that bind targets of interest. The targets include tissues, cells, circulating biomarkers such as microvesicles, including those derived from various diseases. The oligonucleotides can be used in diagnostic and therapeutic applications.

Provided herein, in some embodiments, are devices, systems and methods for high-throughput single-cell polyomics (e.g., genomic, epigenomic, proteomic and/or phenotypic profile) analyses.