Provided herein are nanostructure-based sequencing methods and systems. Such methods and systems include contacting an immobilized RNA polymerase with a double-stranded target nucleic acid molecule under sequencing conditions, where the sequencing conditions include the presence of four nucleoside triphosphates, where one of the nucleoside triphosphates is present in a rate-limiting amount; detecting the movement of the target nucleic acid molecule and/or one or more nascent strand(s) through, on or over a nanostructure; repeating the contacting and detecting steps a plurality of times; and determining the sequence of the target nucleic acid molecule based, sequentially, on the presence or absence of a change in the movement in the presence of the at least one nucleoside triphosphate.

Provided herein are nanostructure-based sequencing methods and systems. Such methods and systems include contacting an immobilized RNA polymerase with a double-stranded target nucleic acid molecule under sequencing conditions, where the sequencing conditions include the presence of four nucleoside triphosphates, where one of the nucleoside triphosphates is present in a rate-limiting amount; detecting the movement of the target nucleic acid molecule and/or one or more nascent strand(s) through, on or over a nanostructure; repeating the contacting and detecting steps a plurality of times; and determining the sequence of the target nucleic acid molecule based, sequentially, on the presence or absence of a change in the movement in the presence of the at least one nucleoside triphosphate.

Presented herein are methods and compositions surface-based tagmentation. In particular embodiments, methods of preparing an immobilized library of fragmented and tagged DNA molecules on a solid surface are presented. In particular embodiments, the solid surface comprises immobilized transposomes in a dried format, suitable for reconstitution upon contact with liquid, such as a liquid sample.

Presented herein are methods and compositions surface-based tagmentation. In particular embodiments, methods of preparing an immobilized library of fragmented and tagged DNA molecules on a solid surface are presented. In particular embodiments, the solid surface comprises immobilized transposomes in a dried format, suitable for reconstitution upon contact with liquid, such as a liquid sample.

A bioluminescence energy transfer (BRET) nanosystem having semiconductive quantum rods (QRs) bound by firefly luciferase Photinus pyralis (Ppy) for improved conversion of chemical energy to light, such as in solid-state lighting, near-infrared imaging systems, and in vivo infrared imaging. The nanosystems are formed by synthesizing CdSe/CdS or CdSe/CdS/ZnS quantum rods, rendering the dots hydrophilic and colloidially stable with a facile His-capping, incubating with a Ppy variant (PpyGRTS) at increasing loading ratios, and adding an excess of the luciferin (LH2) substrate to the PpyGRTS-QRs.

The disclosure described herein can be used for very rapid real-time acquisition of short DNA reads that can be used for time-sensitive aneuploidy detection in prenatal and IVF care as well as sequencing of small DNA fragments and amplicons in the field or clinic. This ability can expand the utility of nanopore-based sequencing methods for clinical and research applications.

The disclosure described herein can be used for very rapid real-time acquisition of short DNA reads that can be used for time-sensitive aneuploidy detection in prenatal and IVF care as well as sequencing of small DNA fragments and amplicons in the field or clinic. This ability can expand the utility of nanopore-based sequencing methods for clinical and research applications.

Provided are compositions and methods for detecting a target DNA (double stranded or single stranded) in a sample. In some embodiments, a subject method includes: (a) contacting the sample with: (i) a type V CRISPR/Cas effector protein (e.g., a Cas12 protein such as Cas12a, Cas12b, Cas12c, Cas12d, Cas12e); (ii) a guide RNA (comprising a region that binds to the type V CRISPR/Cas effector protein, and a guide sequence that hybridizes with the target DNA); and (iii) a detector DNA that is single stranded (i.e., a “single stranded detector DNA”) and does not hybridize with the guide sequence of the guide RNA; and (b) measuring a detectable signal produced by cleavage (by the type V CRISPR/Cas effector protein) of the single stranded detector DNA. Also provided are compositions and methods for cleaving single stranded DNAs (e.g., non-target ssDNAs), e.g., inside of a cell.

Provided are compositions and methods for detecting a target DNA (double stranded or single stranded) in a sample. In some embodiments, a subject method includes: (a) contacting the sample with: (i) a type V CRISPR/Cas effector protein (e.g., a Cas12 protein such as Cas12a, Cas12b, Cas12c, Cas12d, Cas12e); (ii) a guide RNA (comprising a region that binds to the type V CRISPR/Cas effector protein, and a guide sequence that hybridizes with the target DNA); and (iii) a detector DNA that is single stranded (i.e., a “single stranded detector DNA”) and does not hybridize with the guide sequence of the guide RNA; and (b) measuring a detectable signal produced by cleavage (by the type V CRISPR/Cas effector protein) of the single stranded detector DNA. Also provided are compositions and methods for cleaving single stranded DNAs (e.g., non-target ssDNAs), e.g., inside of a cell.

The present invention provides a method for isolating Sequencing complexes, said method comprising forming a complex between a nanopore covalently linked to a polymerase and an oligonucleotide that is associated with a purification moiety, separating any unbound/uncomplexed nanopores and oligonucleotides from the complexes by use of a solid support capable of binding the purification moiety, and cleaving bound complexes from the solid support with an enzyme composition.