Geometry of a DNA Nanostructure Influences Its Endocytosis: Cellular Study on 2D, 3D, and in Vivo Systems

Fabrication of nanoscale DNA devices to generate 3D nano-objects with precise control of shape, size, and presentation of ligands has shown tremendous potential for therapeutic applications. The interactions between the cell membrane and different topologies of 3D DNA nanostructures are crucial for designing efficient tools for interfacing DNA devices with biological systems. The practical applications of these DNA nanocages are still limited in cellular and biological systems owing to the limited understanding of their interaction with the cell membrane and endocytic pathway. The correlation between the geometry of DNA nanostructures and their internalization efficiency remains elusive. We investigated the influence of the shape and size of 3D DNA nanostructures on their cellular internalization efficiency. We found that one particular geometry, i.e., the tetrahedral shape, is more favored over other designed geometries for their cellular uptake in 2D and 3D cell models. This is also replicable for cellular processes like cell invasion assays in a 3D spheroid model, and passing the epithelial barriers in in vivo zebrafish model systems. Our work provides detailed information for the rational design of DNA nanodevices for their upcoming biological and biomedical applications.

Rolling Circle Replication for Biosensing, Bioimaging, and Biomedicine

Rolling circle replication (RCR), including rolling circle amplification (RCA) and rolling circle transcription (RCT), is an isothermal enzymatic reaction. Because of its high amplification efficiency, RCR is a powerful biosensing tool for detecting biomolecules. In recent years, RCR has also been extended to the field of bioimaging to better understand biological pathways. Furthermore, RCR provides a simple technique to design and generate DNA/RNA structures with unique advantages in delivering drugs and enhanced targeting ability. In this review, we introduce the fundamentals of RCR and describe the most recent advances in RCR-based detection methods and delivery vehicles for biosensing, bioimaging, and biomedicine. Finally, some challenges and further opportunities of RCR-based biotechnology are discussed.

Chemotherapeutic drug-DNA hybrid nanostructures for anti-tumor therapy

Compared to traditional drug delivery systems, DNA nanostructure-based drug delivery systems have several advantages including programmable sequences, precise size and shape, high drug payloads, excellent biocompatibility and biodegradability. To date, a wide range of chemotherapeutic drug-DNA hybrid nanostructures have been developed for anti-tumor therapy. In this review, the constructions of various DNA nanostructures for anticancer drug delivery are firstly summarized. Next, the anticancer drug loading methods for DNA nanostructures are presented. Then, the recent applications of chemotherapeutic drug-DNA hybrid nanostructures for drug delivery are highlighted. In the end, the challenges and opportunities of the chemotherapeutic drug-DNA hybrid nanostructure-based delivery system are discussed. The designs of drug-DNA hybrid systems, including the constructions of nanostructures and the strategies for drug loading, largely influence the efficiency of drug delivery. Recent studies have focused on the development of novel drug-DNA hybrid systems to acquire more precise and efficient therapy for various diseases. A systematic review of the design strategies of chemotherapeutic drug-DNA hybrid nanostructures will benefit the innovation and development of the chemotherapeutic drug-based chemotherapy in clinics.

A Tubular DNA Nanodevice as a siRNA/Chemo-Drug Co-delivery Vehicle for Combined Cancer Therapy

Using the DNA origami technique, we constructed a DNA nanodevice functionalized with small interfering RNA (siRNA) within its inner cavity and the chemotherapeutic drug doxorubicin (DOX), intercalated in the DNA duplexes. The incorporation of disulfide bonds allows the triggered mechanical opening and release of siRNA in response to intracellular glutathione (GSH) in tumors to knockdown genes key to cancer progression. Combining RNA interference and chemotherapy, the nanodevice induced potent cytotoxicity and tumor growth inhibition, without observable systematic toxicity. Given its autonomous behavior, exceptional designability, potent antitumor activity and marked biocompatibility, this DNA nanodevice represents a promising strategy for precise drug design for cancer therapy.

The applications of functionalized DNA nanostructures in bioimaging and cancer therapy

Deoxyribonucleic acid (DNA) is a molecular carrier of genetic information that can be fabricated into functional nanomaterials in biochemistry and engineering fields. Those DNA nanostructures, synthesized via Watson-Crick base pairing, show a wide range of attributes along with excellent applicability, precise programmability, and extremely low cytotoxicity in vitro and in vivo. In this review, the applications of functionalized DNA nanostructures in bioimaging and tumor therapy are summarized. We focused on approaches involving DNA origami nanostructures due to their widespread use in previous and current reports. Non-DNA origami nanostructures such as DNA tetrahedrons are also covered. Finally, the remaining challenges and perspectives regarding DNA nanostructures in the biomedical arena are discussed.

Designer, Programmable 3D DNA Nanodevices to Probe Biological Systems

DNA nanotechnology is a unique field that provides simple yet robust design techniques for self-assembling nanoarchitectures with extremely high potential for biomedical applications. Though the field began to exploit DNA to build various nanoscale structures, it has now taken a different path, diverging from the creation of complex structures to functional DNA nanodevices that explore various biological systems and mechanisms. Here, we present a brief overview of DNA nanotechnology, summarizing the key strategies for construction of various DNA nanodevices, with special focus on three-dimensional (3D) nanocages or polyhedras. We then discuss biological applications of 3D DNA nanocages, particularly tetrahedral DNA cages, in their ability to program and modulate cellular systems, in biosensing, and as tools for targeted therapeutics. We conclude with a final discussion on challenges and perspectives of 3D DNA nanodevices in biomedical applications.

A sensitive electrochemical strategy via multiple amplification reactions for the detection of E. coli O157: H7

The sensitive and efficient strategy remains a central challenge for early diagnosis of pathogenic bacteria. Herein, an ultrasensitive electrochemical biosensor was proposed based on the multiple amplification strategy via the 3D DNA walker, rolling circle amplification (RCA) and hybridization chain reaction (HCR) for the accurate detection of Escherichiacoli O157:H7 (E. coli O157:H7). Firstly, the target sequence extracted from E. coli O157:H7 was transformed and amplified by the DNA walker firstly. Subsequently, a large number of transformed nucleic acid sequences were amplified by the RCA reaction. And then, the progress of HCR was triggered by every fragment in RCA products to form a long double-stranded DNA sequence to immobilize electrochemical indicators, generating a significantly enhanced electrochemical signal. As expected, a high sensitivity with a detection limit of 7 CFU/mL was achieved based on the proposed multiple amplification strategy, which is superior to most current methods for E. coli O157: H7 assay. The multiple amplification strategy could be readily expanded for the detection of various pathogenic bacteria, providing a new approach for early diagnosis of pathogenic microorganisms or other diseases.

DNA Nanostructure-Based Systems for Intelligent Delivery of Therapeutic Oligonucleotides

In the beginning of the 21st century, therapeutic oligonucleotides have shown great potential for the treatment of many life-threatening diseases. However, effective delivery of therapeutic oligonucleotides to the targeted location in vivo remains a major issue. As an emerging field, DNA nanotechnology is applied in many aspects including bioimaging, biosensing, and drug delivery. With sequence programming and optimization, a series of DNA nanostructures can be precisely engineered with defined size, shape, surface chemistry, and function. Simply with hybridization, therapeutic oligonucleotides including unmethylated cytosine-phosphate-guanine dinucleotide oligos, small interfering RNA (siRNA) or antisense RNA, single guide RNA of the regularly interspaced short palindromic repeat-Cas9 system, and aptamers, are successfully loaded on DNA nanostructures for delivery. In this progress report, the development history of DNA nanotechnology is first introduced, and then the mechanisms and means for cellular uptake of DNA nanostructures are discussed. Next, current approaches to deliver therapeutic oligonucleotides with DNA nanovehicles are summarized. In the end, the challenges and opportunities for DNA nanostructure-based systems for the delivery of therapeutic oligonucleotides are discussed.

A DNA Nanotube-Peptide Biocomplex for mRNA Detection and Its Application in Cancer Diagnosis and Targeted Therapy

A biocomplex of DNA nanotube-peptide, consisting of six concatenated DNA strands, three locked DNA strands, and a cell-penetrating peptide, is reported. The barrel-structured DNA nanotube-peptide was successfully applied as a codrug-delivery system for targeting cancer therapy. The mucin 1 protein (MUC-1) aptamer is part of a DNA nanotube that can specifically recognize MUC-1 protein on the surface of MCF-7 cells. Cyclo (Arg-Gly-Asp-d-Phe-Lys; cRGD), as a cell-penetrating peptide, facilitates recruitment and uptake of targeting drugs by binding to integrin receptors (α_v β₃ ) of the cytomembrane surface. Anticancer drugs doxorubicin (DOX) and paclitaxel (PTX) were loaded into the capsulated DNA nanotube-peptide (CDNP), which was used as codrug cargo models. The as-prepared biocomplex can be utilized not only to deliver drugs, but also to achieve anticancer effects in vivo. Experimental results suggested that the treatment efficacy of the codrug delivery platform (CDNP/DOX/PTX) was better than that of a single-drug delivery platform (CDNP/DOX or CDNP/PTX). This system, which is composed of DNA strands and peptide, has good biocompatibility and biodegradability. Furthermore, the system can readily detect target mRNA in MCF-7 cells in vitro. The detection limits of mRNA are 9.7×10^-8 and 1.8×10^-8  m with CDNP/DOX and CDNP/PTX-FITC (FITC=fluorescein isothiocyanate), respectively, as probes.

Facilitation of DNA self-assembly by relieving the torsional strains between building blocks

Paranemic crossover (PX) DNA motifs were designed and used for self-assembly of two dimensional lattices. The PX motifs tested include overwound and underwound ones, and different forms of self-assembled two-dimensional (2D) lattices were generated, demonstrating the correlation between the helical torsional strain within the system and the quality of the lattice formed. Relief of the torsional strain by adjusting the number of base pairs in the JX region adjacent to the PX motifs, facilitates and optimizes DNA self-assembly, which leads to 2D lattices of greater uniformity and higher yield. This study demonstrated that the helical relationship among DNA building blocks is a critical factor for the tile-based self-assembly of large nanostructures.

Facile Chemical Strategy to Hydrophobically Modify Solid Nanoparticles Using Inverted Micelle-Based Multicapsule for Efficient Intracellular Delivery

Theranostic nanoparticles have incredible potential for biomedical applications by enabling visual confirmation of therapeutic efficacy. Numerous issues challenge their clinical translation and are primarily related to the complex chemistry and scalability of synthesizing Nanoparticles. We report a 2-step chemical strategy for high-throughput intracellular delivery of organic and inorganic solid nanoparticles. This process takes an additional step beyond hydrophobic surface modification facilitated by inverted micelle transfer, toward the packing of multiple solid nanoparticles into a soft-shelled lipid capsule, termed the Nano-multicapsule (NMC). This technique is high yielding and does not require the complex purification steps in anaerobic/hydrophobic reactions for hydrophobic modification. To demonstrate the efficacy across different material compositions, we separately entrapped ∼10 nm gold and carbon nanoparticles (AuNP and CNP) within inverted micelles, and subsequently NMCs, then quantified their internalization in a human breast cancer cell line. For encapsulated AuNPs (NMC-AuNP), we confirmed greater cellular internalization of gold through ICP-OES and TEM analyses. Raman spectroscopic analysis of cells treated with encapsulated CNPs (NMC-CNP) also exhibited high degrees of uptake with apparent intracellular localization as opposed to free CNP treatment.

Systemic Delivery of Bc12-Targeting siRNA by DNA Nanoparticles Suppresses Cancer Cell Growth

Short interfering RNA (siRNA) is a promising molecular tool for cancer therapy, but its clinical success is limited by the lack of robust in vivo delivery systems. Rationally designed DNA nanoparticles (DNPs) have emerged as facile delivery vehicles because their physicochemical properties can be precisely controlled. Nonetheless, few studies have used DNPs to deliver siRNAs in vivo, and none has demonstrated therapeutic efficacy. Herein, we constructed a number of DNPs of rectangular and tubular shapes with varied dimensions using the modular DNA brick method for the systemic delivery of siRNA that targets anti-apoptotic protein Bcl2. The siRNA delivered by the DNPs inhibited cell growth both in vitro and in vivo, which suppressed tumor growth in a xenograft model that specifically correlated with Bcl2 depletion. This study suggests that DNPs are effective tools for the systemic delivery of therapeutic siRNA and have great potential for further clinical translation.

Engineering the Surface of Smart Nanocarriers Using a pH-/Thermal-/GSH-Responsive Polymer Zipper for Precise Tumor Targeting Therapy In Vivo

Nanocarrier surface chemistry plays a vital role in mediating cell internalization and enhancing delivery efficiency during in vivo chemotherapy. Inspired by the ability of proteins to alter their conformation to mediate functions, a pH-/thermal-/glutathione-responsive polymer zipper consisting of cell-penetrating poly(disulfide)s and thermosensitive polymers bearing guanidinium/phosphate (Gu⁺ /pY^- ) motifs to spatiotemporally tune the surface composition of nanocarriers for precise tumor targeting and efficient drug delivery is developed. Surface engineering allows the nanocarriers to remain undetected during blood circulation and favors passive accumulation at tumor sites, where the acidic microenvironment and photothermal heating break the pY^- /Gu⁺ binding and rupture the zipper, thereby exposing the penetrating shell and causing enhanced cellular uptake via counterion-/thiol-/receptor-mediated endocytosis. The in vivo study demonstrates that by manipulating the surface states on command, the nanocarriers show longer blood circulation time, minimized uptake and drug leakage in normal organs, and enhanced accumulation and efficient drug release at tumor sites, greatly inhibiting tumor growth with only slight damage to normal tissues. If integrated with a photothermal dye approved by the U.S. Food and Drug Administration (FDA), polymer zipper would provide a versatile protocol for engineering nanomedicines with high selectivity and efficiency for clinical cancer treatment.

Beyond the Fold: Emerging Biological Applications of DNA Origami

The use of DNA as a material for nanoscale construction has blossomed in the past decade. This is largely attributable to the DNA origami technique, which has enabled construction of nanostructures ranging from simple two-dimensional sheets to complex three-dimensional objects with defined curves and edges. These structures are amenable to site-specific functionalization with nanometer precision, and have been shown to exhibit cellular biocompatibility and permeability. The DNA origami technique has already found widespread use in a variety of emerging biological applications such as biosensing, enzyme cascades, biomolecular analysis, biomimetics, and drug delivery. We highlight a few of these applications and comments on the prospects for this rapidly expanding field of research.

DNA Nanotechnology for Precise Control over Drug Delivery and Gene Therapy

Nanomedicine has been growing exponentially due to its enhanced drug targeting and reduced drug toxicity. It uses the interactions where nanotechnological components and biological systems communicate with each other to facilitate the delivery performance. At this scale, the physiochemical properties of delivery systems strongly affect their capacities. Among current delivery systems, DNA nanotechnology shows many advantages because of its unprecedented engineering abilities. Through molecular recognition, DNA nanotechnology can be used to construct a variety of nanostructures with precisely controllable size, shape, and surface chemistry, which can be appreciated in the delivery process. In this review, different approaches that are currently used for the construction of DNA nanostructures are reported. Further, the utilization of these DNA nanostructures with the well-defined parameters for the precise control in drug delivery and gene therapy is discussed.

Hybrid, multiplexed, functional DNA nanotechnology for bioanalysis

DNA nanotechnology allows for the realization of novel multiplexed assays in bioanalytical sciences.