Advances in DNA Nanotechnology.

Abstract

In the 1980s, Seeman first proposed the concept of utilizing nucleic acids to construct self-assembled nanomaterials,1 which has led to a fast-growing area of DNA nanotechnology that far exceeds the original function of DNA as genetic materials. Nowadays, numerous static and dynamic DNA/RNA nanostructures have been designed and synthesized following the highly specific Watson–Crick base-pairing rule. More recently, with the development of various new techniques, the field of DNA nanotechnology has been experiencing a rapid expansion and enrichment, facilitating the construction of various patterns with different components, which hold great potential for applications including optical/plasmonic sensors, nanophotonic devices, and nanorobotics. To highlight the state-of-the-art in this field, we have organized this special issue of “Advances in DNA Nanotechnology,” by inviting active international researchers who presented invited talks at the Sixth and Seventh International Workshop on DNA Nanotechnology. The former workshop was organized by Dongsheng Liu (Tsinghua University, China), Jwa-Min Nam (Seoul National University, Korea), Chunhai Fan (Shanghai Institute of Applied Physics, CAS, China), and Shu Wang (Institute of Chemistry, CAS, China), held on August 26–28, 2017, in Beijing, China; the latter was organized by Chunhai Fan (Shanghai Institute of Applied Physics, CAS), Dongsheng Liu (Tsinghua University), Chengde Mao (Purdue University/Southwest University), and Shu Wang (Institute of Chemistry, CAS), held on June 1–3, 2018, in Chongqing, China. This Special Issue contains 21 articles, including 3 Research Articles, 6 Concepts and 12 Reviews. It covers a broad range of subjects, providing readers the most up-to-date progress in DNA nanotechnology. To expand the application of DNA nanostructures, it is highly desirable to lower the cost of synthesis of DNA strands. Mao and colleagues (https://doi.org/10.1002/smll.201805552) report a strategy to assemble a series of DNA microparticles from one component DNA strand. These DNA microparticles can be modified to carry additional single-stranded tails on their surfaces, allowing for the capture of other nucleic acids or attachment of CpG motifs to stimulate immune responses. RNA aptamers are useful building blocks for constructing functional nucleic acid-based nanoarchitectures. Sugimoto and co-workers (https://doi.org/10.1002/smll.201805062) report an efficient method for efficient aptamer optimization. This technique enables re-selection of aptamers from a partially randomized library, using RNA-capturing microsphere particles displaying different clones of identical DNA and RNA sequences. Different from static nanostructures, dynamic nanostructures can undergo an on-demand transformation in the structure, properties, and motion in response to various external stimuli. The Review by Park and co-workers (https://doi.org/10.1002/smll.201900504) introduces recent advances in dynamic DNA nanostructures, focusing on hybrid structures fabricated from DNA-conjugated molecules, polymers, and nanoparticles, and discusses their potential applications and future perspectives. In the Review by Zhang et al. (https://doi.org/10.1002/smll.201900228), reconfigurable elements, assembly strategies and readout signals for constructing dynamic DNA structures are briefly introduced, followed by the introduction of applications of dynamic DNA structures in biological sensing and imaging, molecular cargo transportation and DNA walkers and circuits. The Review from Lo and colleagues (https://doi.org/10.1002/smll.201805481) covers the recent progress in the development of photoresponsive DNA-based systems and emphasizes their advantages over other stimuli-responsive systems with discussion on the design and mechanisms to trigger the photoresponses. The potential application, challenges faced and further development of photocontrolled DNA-based systems are also presented. The Concept by Wang et al. (https://doi.org/10.1002/smll.201900013) summarizes and classifies power supply, machine actuation, and motion behavior of DNA machines on origami platforms, and discusses strategies utilized for programming motion behavior of DNA machines on DNA origami with representative examples. Nam and co-workers (https://doi.org/10.1002/smll.201900998) briefly review the recent advances in nano-bio computing, and highlight the concept of nano-bio computing on lipid bilayers where nanoscale computing units are dynamically tethered to a lipid bilayer to process complex molecular information as a network. DNA nanotechnology has dramatically expanded nanoscale molecule engineering and contributed to the spatial arrangement of various components, such as fluorophores, biomolecules, metallic and semiconductor nanoparticles (NPs). The static structural and functional patterns assembled on DNA origami are reviewed by Song and co-workers (https://doi.org/10.1002/smll.201805554), as well as the reconfigurable assembled architectures regulated through dynamic DNA nanotechnology, focusing on the strategies for creating different nanoscale patterns with DNA origami for various applications. Pilo-Pais and colleagues (https://doi.org/10.1002/smll.201804418) report a facile approach to assemble plasmonic antennas consisting of two 40 nm metallic nanoparticles with a single colloidal quantum dot (QD) positioned at the hot spot. Depending on the antenna configuration, the fluorescence emission can be enhanced up to 30-fold compared to single QDs without antenna. Lu and colleagues (https://doi.org/10.1002/smll.201900975) overview the recent advances in the use of DNA as engineered codes for controlling the morphology in the growth of mono- and bimetallic nanoparticles. They summarize the fundamental insights into rules governing DNA controlled growth mechanisms and provide a perspective into the future directions of DNA-mediated nanoparticle synthesis. Tian and his co-workers (https://doi.org/10.1002/smll.201805401) review recent developments in the fabrication of three-dimensional lattices with DNA shell coated nanoparticles, emphasizing the design and DNA-driven assembly of superlattices. The Review authored by Macfarlane and co-workers (https://doi.org/10.1002/smll.201805424) highlights the characteristics of DNA grafted nanoparticles as “programmable atom equivalent” (PAE) building blocks for synthesizing NP superlattices, drawing a correlation between PAE assembly and atomic crystallization. The Concept by Cecconello and Simmel (https://doi.org/10.1002/smll.201805419) covers several key advances in the field of chiral DNA nanoarchitectures, presenting different strategies to construct chiral nanoshapes with DNA, which allow programming chirality at increasingly larger length scales. Wang and co-workers (https://doi.org/10.1002/smll.201804044) provide a Concept on the precise manipulation of DNA-protein nanoarchitectures, which highlights site-specific DNA-protein conjugation, regulation of protein orientation using DNA scaffolds, and co-assembly principles upon unique structural motifs. The Concept by Fu et al. (https://doi.org/10.1002/smll.201900256) discusses the recent progress in DNA-scaffolded compartmentalization, focusing on their applications in enzyme encapsulation, liposome assembly, artificial transmembrane nanopores, and smart drug delivery. Hui et al. (https://doi.org/10.1002/smll.201805428) provides a brief overview of recent developments of DNA-based nanofabrication in their Concept article, emphasizing recent results that can be potentially translated to large-scale patterning for surface engineering applications. The Review authored by Zhang and Liu (https://doi.org/10.1002/smll.201805246) covers recent developments in molecular imprinting with functional DNA, a field that just emerged in the last five years. They further discuss future research directions in this new area. As DNA nanostructures are biocompatible and can enter mammalian cells without the aid of transfection agents, DNA-based platforms have shown the potential in numerous biological or biomedical applications. Choi and co-workers (https://doi.org/10.1002/smll.201805416) review and discuss the recent progress in elucidating the “cell-nano” interactions of DNA nanostructures, with an emphasis on tile-based structures, origami-based structures, and nanoparticle-templated structures. The Review by Ma and Salaita (https://doi.org/10.1002/smll.201900961) focuses on force sensing DNA probes employed in studies of mechanotransduction in living systems. It describes fundamental aspects of force-induced melting of DNA hairpins and duplexes, and highlights the achievements in using these DNA-based molecular probes to study forces that are important to cellular functions such as immune cell response, platelet activation and cell adhesion. The Review from Kizer et. al. (https://doi.org/10.1002/smll.201805386) highlights some of the main criteria that DNA nanostructures satisfy as drug delivery vehicles, focusing on advances in drug delivery and tracking, enhancing internalization, and prolonging stability. The Review by Yuan et. al. (https://doi.org/10.1002/smll.201900172) addresses the recent progress in nucleic acid-based functional nanomaterials as advanced cancer therapeutics in three main cancer therapies (chemotherapy, gene therapy and immunotherapy), and discusses the challenges and future development for true clinical translation. We are greatly indebted to all contributing authors, reviewers, and editorial assistants of this special issue for their effort and support. We wish that the collection of articles covering a broad range brings readers a timely overview and helps newcomers to be familiar with the major developments in the booming field of DNA Nanotechnology. Chunhai Fan is a K. C. Wong Chair Professor at Shanghai Jiao Tong University (SJTU). Before joining SJTU, he was a CAS Distinguished Professor at the Shanghai Institute of Applied Physics, Chinese Academy of Sciences. He is a fellow of Royal Society of Chemistry (FRSC), an elected fellow of the International Society of Electrochemistry (ISE) and American Association for the Advancement of Science (AAAS). His research interests include DNA nanotechnology, biosensing and bioimaging. Qian Li obtained her Ph.D. degree from the Stratingh Institute for Chemistry at the University of Groningen in 2011. She conducted postdoctoral research in the Division of Physical Biology at Shanghai Institute of Applied Physics (SINAP), Chinese Academy of Sciences (CAS), and joined the faculty in 2014. She was promoted to associate professor in 2015 and moved to the School of Chemistry and Chemical Engineering at Shanghai Jiao Tong University (SJTU) in 2018. Her current research interests are focused on assembly and imaging of functional nucleic acids nanostructures.