Nucleic Acid-Based Structures Research Articles

Targeted siRNA delivery using aptamer‐siRNA chimeras and aptamer‐conjugated nanoparticles

The sequence-specific gene-silencing ability of small interfering RNA (siRNA) has been exploited as a new therapeutic approach for the treatment of a variety of diseases. However, efficient and safe delivery of siRNA into target cells is still a challenge in the clinical development of siRNA-based therapeutics. Recently, nucleic acid-based aptamers that target cell surface proteins have emerged as a new class of targeting moieties due to their high specificity and avidity. To date, various aptamer-mediated siRNA delivery systems have been developed to enhance the RNA interference (RNAi) efficacy of siRNA via targeted delivery. In this review, we summarize recent advances in developing aptamer-mediated siRNA delivery systems for RNAi therapeutics, mainly aptamer-siRNA chimeras and aptamer-functionalized nanocarriers incorporating siRNA, with a focus on their molecular designs and formulations. In addition, the challenges and engineering strategies of aptamer-mediated siRNA delivery systems for clinical translation are discussed. This article is categorized under: Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease.

Nanoscale platforms for messenger RNA delivery.

Messenger RNA (mRNA) has become a promising class of drugs for diverse therapeutic applications in the past few years. A series of clinical trials are ongoing or will be initiated in the near future for the treatment of a variety of diseases. Currently, mRNA-based therapeutics mainly focuses on ex vivo transfection and local administration in clinical studies. Efficient and safe delivery of therapeutically relevant mRNAs remains one of the major challenges for their broad applications in humans. Thus, effective delivery systems are urgently needed to overcome this limitation. In recent years, numerous nanoscale biomaterials have been constructed for mRNA delivery in order to protect mRNA from extracellular degradation and facilitate endosomal escape after cellular uptake. Nanoscale platforms have expanded the feasibility of mRNA-based therapeutics, and enabled its potential applications to protein replacement therapy, cancer immunotherapy, therapeutic vaccines, regenerative medicine, and genome editing. This review focuses on recent advances, challenges, and future directions in nanoscale platforms designed for mRNA delivery, including lipid and lipid-derived nanoparticles, polymer-based nanoparticles, protein derivatives mRNA complexes, and other types of nanomaterials. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Lipid-Based Structures Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.

Mix‐and‐match nanobiosensor design: Logical and spatial programming of biosensors using self‐assembled DNA nanostructures

The evergrowing need to understand and engineer biological and biochemical mechanisms has led to the emergence of the field of nanobiosensing. Structural DNA nanotechnology, encompassing methods such as DNA origami and single-stranded tiles, involves the base pairing-driven knitting of DNA into discrete one-, two-, and three-dimensional shapes at nanoscale. Such nanostructures enable a versatile design and fabrication of nanobiosensors. These systems benefit from DNA's programmability, inherent biocompatibility, and the ability to incorporate and organize functional materials such as proteins and metallic nanoparticles. In this review, we present a mix-and-match taxonomy and approach to designing nanobiosensors in which the choices of bioanalyte and transduction mechanism are fully independent of each other. We also highlight opportunities for greater complexity and programmability of these systems that are built using structural DNA nanotechnology. This article is categorized under: Implantable Materials and Surgical Technologies > Nanomaterials and Implants Diagnostic Tools > Biosensing Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

Bacteriophage lambda: The path from biology to theranostic agent.

Viral particles provide an attractive platform for the engineering of semisynthetic therapeutic nanoparticles. They can be modified both genetically and chemically in a defined manner to alter their surface characteristics, for targeting specific cell types, to improve their pharmacokinetic features and to attenuate (or enhance) their antigenicity. These advantages derive from a detailed understanding of virus biology, gleaned from decades of fundamental genetic, biochemical, and structural studies that have provided mechanistic insight into virus assembly pathways. In particular, bacteriophages offer significant advantages as nanoparticle platforms and several have been adapted toward the design and engineering of "designer" nanoparticles for therapeutic and diagnostic (theranostic) applications. The present review focuses on one such virus, bacteriophage lambda; I discuss the biology of lambda, the tools developed to faithfully recapitulate the lambda assembly reactions in vitro and the observations that have led to cooptation of the lambda system for nanoparticle design. This discussion illustrates how a fundamental understanding of virus assembly has allowed the rational design and construction of semisynthetic nanoparticles as potential theranostic agents and illustrates the concept of benchtop to bedside translational research. This article is categorized under: Biology-Inspired Nanomaterials> Protein and Virus-Based Structures Biology-Inspired Nanomaterials> Nucleic Acid-Based Structures.

Implication of multivalent aptamers in DNA and DNA–RNA hybrid structures for efficient drug delivery in vitro and in vivo

To examine proper multivalency and type of aptamers in linear nucleic acid-based structures for efficient intracellular uptakes, we designed linear DNA structures with single and dual aptamers targeting guanosine-rich oligonucleotide 100 (AS1411) and mucin 1 (MUC-1). Multivalent linear DNA structures containing dual types of aptamers showed significantly superior cellular internalization. In addition, multivalent aptamer-immobilized DNA–RNA hybrid structures showed excellent tumor accumulation in vivo without liver toxicity and very low nonspecific cytokine induction. Thus, these multivalent nucleic acid based structures with dual types of aptamers can be specifically applied as carriers of therapeutic nucleic acids without inducing noticeable systemic toxicity.

Oral nucleic acid therapy using multicompartmental delivery systems.

Nucleic acid-based therapeutics has the potential for treating numerous diseases by correcting abnormal expression of specific genes. Lack of safe and efficacious delivery strategies poses a major obstacle limiting clinical advancement of nucleic acid therapeutics. Oral route of drug administration has greater delivery challenges, because the administered genes or oligonucleotides have to bypass degrading environment of the gastrointestinal (GI) tract in addition to overcoming other cellular barriers preventing nucleic acid delivery. For efficient oral nucleic acid delivery, vector should be such that it can protect encapsulated material during transit through the GI tract, facilitate efficient uptake and intracellular trafficking at desired target sites, along with being safe and well tolerated. In this review, we have discussed multicompartmental systems for overcoming extracellular and intracellular barriers to oral delivery of nucleic acids. A nanoparticles-in-microsphere oral system-based multicompartmental system was developed and tested for in vivo gene and small interfering RNA delivery for treating colitis in mice. This system has shown efficient transgene expression or gene silencing when delivered orally along with favorable downstream anti-inflammatory effects, when tested in a mouse model of intestinal bowel disease. WIREs Nanomed Nanobiotechnol 2018, 10:e1478. doi: 10.1002/wnan.1478 This article is categorized under: Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Emerging Technologies.

Collective helicity switching of a DNA-coat assembly.

Hierarchical assemblies of biomolecular subunits can carry out versatile tasks at the cellular level with remarkable spatial and temporal precision. As an example, the collective motion and mutual cooperation between complex protein machines mediate essential functions for life, such as replication, synthesis, degradation, repair and transport. Nucleic acid molecules are far less dynamic than proteins and need to bind to specific proteins to form hierarchical structures. The simplest example of these nucleic acid-based structures is provided by a rod-shaped tobacco mosaic virus, which consists of genetic material surrounded by coat proteins. Inspired by the complexity and hierarchical assembly of viruses, a great deal of effort has been devoted to design similarly constructed artificial viruses. However, such a wrapping approach makes nucleic acid dynamics insensitive to environmental changes. This limitation generally restricts, for example, the amplification of the conformational dynamics between the right-handed B form to the left-handed Z form of double-stranded deoxyribonucleic acid (DNA). Here we report a virus-like hierarchical assembly in which the native DNA and a synthetic coat undergo repeated collective helicity switching triggered by pH change under physiological conditions. We also show that this collective helicity inversion occurs during translocation of the DNA-coat assembly into intracellular compartments. Translating DNA conformational dynamics into a higher level of hierarchical dynamics may provide an approach to create DNA-based nanomachines.

Nucleic Acid Engineering: RNA Following the Trail of DNA.

The self-assembly feature of the naturally occurring biopolymer, DNA, has fascinated researchers in the fields of materials science and bioengineering. With the improved understanding of the chemical and structural nature of DNA, DNA-based constructs have been designed and fabricated from two-dimensional arbitrary shapes to reconfigurable three-dimensional nanodevices. Although DNA has been used successfully as a building block in a finely organized and controlled manner, its applications need to be explored. Hence, with the myriad of biological functions, RNA has recently attracted considerable attention to further the application of nucleic acid-based structures. This Review categorizes different approaches of engineering nucleic acid-based structures and introduces the concepts, principles, and applications of each technique, focusing on how DNA engineering is applied as a guide to RNA engineering.

DNA nanotechnology: a curiosity or a promising technology?

DNA nanotechnology, the design and self-assembly of artificial nucleic acid-based structures or systems, has developed with breathtaking pace in recent years. The technology offers an unparalleled ability to control structure and function at the molecular level and the sizes of the structures are expanding towards the micrometer domain. The question is whether the technology offers solutions to any real-life problems, or if it will remain an academic discipline. Here, we discuss this question by extrapolating from recent developments in the field.

Aptamers for allosteric regulation

Aptamers are useful for allosteric regulation because they are nucleic acid-based structures in which ligand binding induces conformational changes that may alter the function of a connected oligonucleotide at a distant site. Through this approach, a specific input is efficiently converted into an altered output. This property makes these biomolecules ideally suited to function as sensors or switches in biochemical assays or inside living cells. The ability to select oligonucleotide-based recognition elements in vitro in combination with the availability of nucleic acids with enzymatic activity has led to the development of a wide range of engineered allosteric aptasensors and aptazymes. Here, we discuss recent progress in the screening, design and diversity of these conformational switching oligonucleotides. We cover their application in vitro and for regulating gene expression in both prokaryotes and eukaryotes.

Double Elimination Voltammetry of Short Oligonucleotides

AbstractIn connection with adsorptive stripping (AdS) technique, elimination voltammetry with linear scan (EVLS) in double mode was successfully employed in the analysis of homo‐ODNs: 5′‐AAA AAA AAA‐3′ (dA9) and 5′‐CCC CCC CCC‐3′ (dC9), and hetero‐ODNs: 5′‐CCC AAA CCC‐3′ (H3), 5′‐CAC CAC CAC‐3′ (H4), and 5′‐ACC CAC CCA‐3′ (H9) on hanging mercury drop electrode (HMDE). Analogously to single EVLS function E4 (conserving the diffusion current Id and eliminating kinetic and charging currents Ik, Ic) for the electroactive substance adsorbed, the double EVLS function E4 yields well readable peak‐counterpeaks of reducible nucleic acid bases (adenine A and cytosine C). In comparison with single EVLS these peak‐counterpeaks are higher by more than one order of magnitude (twenty times for dA9, fourteen times for dC9, from eight to sixteen times for hetero‐ODNs). The increase of reduction signals with higher resolution was also observed using other two EVLS functions in double mode, the functions E5 eliminating Ic and Id, but conserving Ik and E6 eliminating Id and Ik, but conserving Ic. The amplifications of double /single EVLS signals of A and C range from 3.4 to 8.4, and from 3.1 to 8.3 for E5 and E6, respectively. It was proved that AdS double EVLS offers a new, fast, simple and inexpensive electroanalytical tool, which can be considered as a device not only for very good resolution of A and C in ODNs, but also for sensitive detection of changes in the primary structure of nucleic acid bases in ODN chains, depending on experimental conditions, such as pH, temperature, and time and potential of accumulation.

Stoichiometric analysis of protein- and nucleic acid-based structures in the cell nucleus

We describe a method to image selectively the protein-based architecture in the eukaryotic cell nucleus using nitrogen and phosphorus mapping. In addition, we describe a method to determine total mass as well as stoichiometric relationships between protein and RNA. This method is illustrated using particulate structures in the nucleus called interchromatin granules. In so doing, we demonstrate that these granules contain heterogeneous nuclear RNA, and have an average protein and RNA content of 3.094 and 1.672 MDa, respectively. We also tested the sensitivity of phosphorus detection by exogenously applying purified duplex DNA to the surfaces of thin sections, and have shown that structures as small as single molecules of duplex DNA can be detected in situ using these electron spectroscopic imaging techniques.

Vibrational spectra and molecular structure of nucleic acid bases and their complexes in low temperature matrices

New results of investigations on the molecular structure of canonic bases of uracil and thymine are given. Using theoretical calculations it is shown that increase of band numbers in the range of CO stretching vibrations of the high-resolution IR spectra and uracil and thymine may be due to the existence of the different conformations of these compounds. IR spectra and the structure of hydrates and selfassociates of cytosine isolated in Ar matrices are also studied. Keto-enolic equilibrium is shown to shift to the keto-form on the intermolecular interactions in the matrix.

Structure of nucleic acid bases in calf thymus DNA modified by the potent mutagen, 10-azabenzo[a]pyrene-4,5-oxide.

Modified nucleic acid bases were isolated from the hydrolysates of calf thymus DNA bound with 10-azabenzo[a]pyrene-4, 5-oxide. The structures of two modified cytosines were proposed.

Nitrous acid effect on cleavage and development in fertilized frog eggs.

NITROUS acid causes deamination of primary amino groups attached to the ring structure of nucleic acid bases; the products have been demonstrated to cause mutations in viruses1,2, bacteria3, moulds4,5 and yeasts6. Apart from a study demonstrating chromosomal fragmentation in monocotyledon root tips treated with nitrous acid7, no report of HNO2 having an effect on higher organisms has been found.