Blink and you’ll miss it: a new biosensing strategy with nucleic acids

Fluorescent biosensors typically use energy or electron transfer to modulate the emission from a fluorophore. This requirement often makes it difficult to change the biosensor to make it selective to a difference target. In this research highlight we describe a recently reported strategy that relies, for the first time, on fluorescence blinking from nucleic acid-coupled quantum dots to report the presence of a target molecule. This strategy produces a decoupled biosensor, whose fluorescence output is not directly modulated by interaction with the target. The resulting biosensor can be readily modified to sense any target that can be selectively bound to nucleic acids and is therefore much more widely applicable than the vast majority of fluorescent sensors that have been reported.

Activation of Multiple Functionalities Through Interacting Nanoparticles

Nucleic acids are biocompatible, robust, and highly versatile polymers that can be used to design fine-tunable and dynamically responsive nanostructures. In this report, we focus our attention to recently introduced concepts of interdependent, cognate nucleic acid nanoparticles assembly that take advantage of dynamic interactions and consequent shape-switching to trigger the activation of multiple functionalities. Particularly, we discuss re-association of thermodynamically driven complementary nanocubes (“cube” and complementary “anti-cube”) into functional duplexes that do not require toehold interactions or extensive computational design, bringing a new perspective for utility of nucleic acid nanoparticles as a drug carriers, biosensors, and templates for the formation of siRNA duplexes.

Functionalized non-viral cationic vectors for effective siRNA induced cancer therapy

RNA interference (RNAi) has been regarded as a vital asset in the field of therapeutics as it has the capability to silence various disease causing genes including those that cause cancer. Small non-coding RNA molecules such as short interfering RNAs (siRNAs) are one of the extensively studied RNAi inducers for gene modulations. However, the delivery of RNAi inducers including siRNAs is compromised due to the barriers imposed by the biological system such as degradation by nucleases, rapid clearance, high anionic charge, immunogenicity and off-target effects. Viral vectors, in general exhibit high transfection efficiencies but are expensive and likely to confer immunological and safety issues. Therefore, non-viral cationic vectors (NVCVs) have received considerable attention to not only address these issues but also for developing efficacious siRNA delivery vectors. In this review, we will first discuss the historical development of various NVCVs and then will discuss functionalized NVCVs with linkers that provide stability, as well as respond to the cancer cell environment and with cancer cell receptor specific ligands to explicitly target them for improved siRNA efficacy. Multifunctional NVCVs (MNVCVs) that employ multiple synergistically working components to aid siRNA delivery efficacy are also discussed.

Non-viral Vector Mediated RNA Interference Technology for Central Nervous System Injury

Neuronal axons damaged by traumatic injury are unable to spontaneously regenerate in the mammalian adult central nervous system (CNS), causing permanent motor, sensory, and cognitive deficits. Regenerative failure in the adult CNS results from a complex pathology presenting multiple barriers, both the presence of growth inhibitors in the extrinsic microenvironment and intrinsic deficiencies in neuronal biochemistry, to axonal regeneration and functional recovery. There are many strategies for axonal regeneration after CNS injury including antagonism of growth-inhibitory molecules and their receptors, manipulation of cyclic nucleotide levels, and delivery of growth-promoting stimuli through cell transplantation and neurotrophic factor delivery. While all of these approaches have achieved varying degrees of improvement in plasticity, regeneration, and function, there is no clinically effective therapy for CNS injury. RNA interference technology offers strategies for improving regeneration by overcoming the aspects of the injured CNS environment that inhibit neurite growth. This occurs through the knockdown of growth-inhibitory molecules and their receptors. In this review, we discuss the current state of RNAi strategies for the treatment of CNS injury based on non-viral vector mediated delivery.

Aptamer guided delivery of nucleic acid-based nanoparticles

Targeted delivery of bioactive compounds is a key part of successful therapies. In this context, nucleic acid and protein-based aptamers have been shown to bind therapeutically relevant targets including receptors. In the last decade, nucleic acid-based therapeutics coupled to aptamers have emerged as a viable strategy for cell specific delivery. Additionally, recent developments in nucleic acid nanotechnology offer an abundance of possibilities to rationally design aptamer targeted RNA or DNA nanoparticles involving combinatorial use of various intrinsic functionalities. Although a host of issues including stability, safety and intracellular trafficking remain to be addressed, aptamers as simple functional chimeras or as parts of multifunctional self-assembled RNA/DNA nanostructures hold great potential for clinical applications.

Self-assembled DNA/RNA nanoparticles as a new generation of therapeutic nucleic acids: immunological compatibility and other translational considerations

Therapeutic nucleic acids (TNAs) are rapidly being embraced as effective interventions in a variety of genetic disorders, cancers, and viral/microbial infections, as well as for use in improving vaccine efficacy. Many traditional nucleotide-based formulations have been approved for clinical use, while various macromolecular nucleic acids are in different phases of preclinical and clinical development. Various nanotechnology carriers, including but not limited to liposomes, emulsions, dendrimers, and polyplexes, are considered for their improved delivery and reduced toxicity compared to traditional TNAs. Moreover, a new generation of TNAs has recently emerged and is represented by DNA/RNA nanoparticles formed by the self-assembly of DNA, RNA, or hybrid DNA-RNA oligonucleotides into 1D, 2D, and 3D structures of different shapes. In this mini-review, I will discuss immunocompatibility and other translational aspects in the development of this new class of promising nucleic acid therapeutics.

Self-assembly of large RNA structures: learning from DNA nanotechnology

Nucleic acid nanotechnology offers many methods to build self-assembled structures using RNA and DNA. These scaffolds are valuable in multiple applications, such as sensing, drug delivery and nanofabrication. Although RNA and DNA are similar molecules, they also have unique chemical and structural properties. RNA is generally less stable than DNA, but it folds into a variety of tertiary motifs that can be used to produce complex and functional nanostructures. Another advantage of using RNA over DNA is its ability to be encoded into genes and to be expressed in vivo. Here we review existing approaches for the self-assembly of RNA and DNA nanostructures and specifically methods to assemble large RNA structures. We describe de novo design approaches used in DNA nanotechnology that can be ported to RNA. Lastly, we discuss some of the challenges yet to be solved to build micron-scale, multi stranded RNA scaffolds.

Triggering RNAi with multifunctional RNA nanoparticles and their delivery

Proteins are considered to be the key players in structure, function, and metabolic regulation of our bodies. The mechanisms used in conventional therapies often rely on inhibition of proteins with small molecules, but another promising method to treat disease is by targeting the corresponding mRNAs. In 1998, Craig Mellow and Andrew Fire discovered dsRNA-mediated gene silencing via RNA interference or RNAi. This discovery introduced almost unlimited possibilities for new gene silencing methods, thus opening new doors to clinical medicine. RNAi is a biological process that inhibits gene expression by targeting the mRNA. RNAi-based therapeutics have several potential advantages (i) a priori ability to target any gene, (ii) relatively simple design process, (iii) sitespecificity, (iv) potency, and (v) a potentially safe and selective knockdown of the targeted cells. However, the problem lies within the formulation and delivery of RNAi therapeutics including rapid excretion, instability in the bloodstream, poor cellular uptake, and inefficient intracellular release. In an attempt to solve these issues, different types of RNAi therapeutic delivery strategies including multifunctional RNA nanoparticles are being developed. In this mini-review, we will briefly describe some of the current approaches.