Provided herein are compositions and methods involving nucleic acid nanostructures that can encapsulate cargo for use in, for example, therapeutic, diagnostic, and analytical applications. The nanostructures can have a plurality of interconnected subunits configured such that the nanostructures have a continuous torus-like structure with a closed three-dimensional cavity. Preferably, the nanostructure is a nucleic acid mazzocchio. The subunits are connected by linkers having defined lengths to constrain the nanostructure into the continuous torus-like shape. The closed three-dimensional cavity is of defined size to encapsulate any cargo of interest. Cargo can also be positioned in the open hole at the center of the nanostructure. The cargo can be a wide range of compounds including, for example, chemical drugs, small molecules, therapeutics, targeting agents, enzymes, dyes, and fluorescent molecules. As such, the disclosed nanostructures are suitable for delivery of one or more therapeutic, toxic, imaging, diagnostic, or prophylactic agents.

New polynucleotides and new expression vectors for multiplexed microRNA-based shRNAs are provided. The shRNAs generated from these polynucleotides and vectors can knock down the expression of multiple genes with minimum undesirable levels of off-target effects.

Monodisperse structures with precise numbers of polymer arms and oligonucleotide chains conjugated to a backbone are disclosed. The structures, referred to miktoarm conjugates, are resistant to nuclease degradation and are capable of regulating gene expression in the absence of a co-carrier.

The invention provides compositions and methods for reducing expression of a target gene in a cell, involving contacting a cell with an isolated double stranded nucleic acid (dsNA) in an amount effective to reduce expression of a target gene in a cell. The dsNAs of the invention possess a single stranded extension (in most embodiments, the single stranded extension comprises at least one modified nucleotide and/or phosphate back bone modification). Such single stranded extended Dicer-substrate siRNAs (DsiRNAs) were demonstrated to be effective RNA inhibitory agents compared to corresponding double stranded DsiRNAs.

The present invention relates to miRNA interference technology. More specifically the invention relates to circular miRNA sponges that carry a plurality of binding sites directed to at least two types of miRNA and separated by random, non-identical spacers, allowing for the inhibition of functional classes of m1RNAs. Preferably, the binding sites are bulged binding sites wherein each bulge is created by a one base deletion and two base mismatch at positions 9-11 nt from the 3′ end of each binding site. Preferably, each spacer is 6 to 24 nucleotides in length. Preferably, the binding sites are against miR-132 and miR-212, miR-17-5p and miR-18a-5p, or miR-20b-5p and miR-106a-5p. Construction vectors and uses of said miRNA sponges for the treatment of diseases, such as cardiomyopathy and cancer, are also disclosed.

Provided herein are DNAzymes conjugated to an organic moiety and methods of facilitating entry of DNAzymes into bacteria, utilizing same. Also provided are methods of targeting bacterial target genes, methods of treating or inhibiting the progression of bacterial infections, and methods of increasing susceptibility of bacteria to an antibiotic, using the described DNAzymes, which are optionally capable of silencing at least one target gene of bacteria and/or rendering bacteria susceptible to antibiotic treatment.

Bispecific aptamers having a first end that specifically binds to a first tumor specific marker, tumor antigen, or viral protein and a second end that specifically binds to a second tumor specific marker, tumor antigen, or viral protein are provide. The bispecific aptamers can be used to treat cancer or virally infected cells. Generally, the bispecific aptamers bind to two surface proteins, preferably different proteins, on the same cell. In a preferred embodiment the bispecific aptamers bind to two different tumor markers, tumor antigens, tumor specific proteins and combinations thereof.

Provided herein are compositions and methods for CRISPR based RNA-targeting. The compositions include nucleic acid molecules comprising a sequence encoding a Cas13 polypeptide and a sequence encoding a guide RNA comprising one or more spacers and one or more Cas13-specific direct repeats, where the spacers are capable of specifically hybridizing with one or more target RNAs. The disclosure further provides methods of modifying a target RNA in a cell and transgenic organisms.

Nucleic acid products that modulate, interfere with, or inhibit PCSK9 and APOC3 gene expression are provided, together with compositions containing the constructs and methods for their use.

Described are conjugates of nucleic acid nanotubes and cells by linking the nanotubes to a cell surface moiety. Devices, kits, systems, and methods comprising the nanotube cell conjugates are also described.