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dna nanostructure

Xiaofang Zheng, Ruizi Peng, Xi Jiang, Yaya Wang, Shuai Xu, Guoliang Ke, Ting Fu, Qiaoling Liu, Shuang-Yan Huan, Xiaobing Zhang
We have developed a DNA nanoprobe for adenosine triphosphate (ATP) sensing in living cells, based on the split aptamer and the DNA triangular prism (TP). In which nucleic acid aptamer was split into two fragments, the stem of the split aptamer was respectively labeled donor and acceptor fluorophores that underwent an fluorescence resonance energy transfer if two ATP molecules were bound as target molecule to the recognition module. Hence, ATP as a target induced the self-assembly of split aptamer fragments and thereby brought the dual fluorophores into close proximity for high FRET efficiency...
September 21, 2017: Analytical Chemistry
Dandan Wu, Lei Wang, Wei Li, Xiaowen Xu, Wei Jiang
DNA as a novel biomaterial can be used to fabricate different kinds of DNA nanostructures based on its principle of GC/AT complementary base pairing. Studies have shown that DNA nanostructure is a nice drug carrier to overcome big obstacles existing in cancer therapy such as systemic toxicity and unsatisfied drug efficacy. Thus, different types of DNA nanostructure-based drug delivery nanosystems have been designed in cancer therapy. To improve treating efficacy, they are also developed into more functional drug delivery nanosystems...
September 15, 2017: International Journal of Pharmaceutics
Morgan Brittany Johnson, Justin R Halman, Emily Satterwhite, Alexey V Zakharov, My N Bui, Kheiria Benkato, Victoria Goldsworthy, Taejin Kim, Enping Hong, Marina A Dobrovolskaia, Emil F Khisamutdinov, Ian Marriott, Kirill A Afonin
In the past few years, the study of therapeutic RNA nanotechnology has expanded tremendously to encompass a large group of interdisciplinary sciences. It is now evident that rationally designed programmable RNA nanostructures offer unique advantages in addressing contemporary therapeutic challenges such as distinguishing target cell types and ameliorating disease. However, to maximize the therapeutic benefit of these nanostructures, it is essential to understand the immunostimulatory aptitude of such tools and identify potential complications...
September 18, 2017: Small
Wei Diao, Min Tang, Shijia Ding, Xinmin Li, Wenbin Cheng, Fei Mo, Xiaoyu Yan, Hongmin Ma, Yurong Yan
Early detection, diagnosis and treatment of human immune deficiency virus (HIV) infection is the key to reduce acquired immunodeficiency syndrome (AIDS) mortality. In our research, an innovative surface plasmon resonance (SPR) biosensing strategy has been developed for highly sensitive detection of HIV-related DNA based on entropy-driven strand displacement reactions (ESDRs) and double-layer DNA tetrahedrons (DDTs). ESDRs as enzyme-free and label-free signal amplification circuit can be specifically triggered by target DNA, leading to the cyclic utilization of target DNA and the formation of plentiful double-stranded DNA (dsDNA) products...
September 9, 2017: Biosensors & Bioelectronics
Ping Wang, Zhiwei Xia, Juan Yan, Xunwei Liu, Guangbao Yao, Hao Pei, Xiaolei Zuo, Gang Sun, Dannong He
Correction for 'A study of pH-dependence of shrink and stretch of tetrahedral DNA nanostructures' by Ping Wang et al., Nanoscale, 2015, 7, 6467-6470.
September 21, 2017: Nanoscale
Neng Wan, Zhouping Hong, Huading Wang, Xin Fu, Ziyue Zhang, Chao Li, Han Xia, Yan Fang, Maoteng Li, Yi Zhan, Xiangliang Yang
DNA origami makes it feasible to fabricate a tremendous number of DNA nanostructures with various geometries, dimensions, and functionalities. Moreover, an increasing amount of research on DNA nanostructures is focused on biological and biomedical applications. Here, the reversible regulation of microcosmic structural rigidity is accomplished using a DNA origami device in vitro. The designed DNA origami monomer is composed of an internal central axis and an external sliding tube. Due to the external tube sliding, the device transforms between flexible and rigid states...
September 13, 2017: Small
Deepak K Agrawal, Ruoyu Jiang, Seth Reinhart, Abdul M Mohammed, Tyler D Jorgenson, Rebecca Schulman
Precise control over the nucleation, growth, and termination of self-assembly processes is a fundamental tool for controlling product yield and assembly dynamics. Mechanisms for altering these processes programmatically could allow the use of simple components to self-assemble complex final products or to design processes allowing for dynamic assembly or reconfiguration. Here we use DNA tile self-assembly to develop general design principles for building complexes that can bind to a growing biomolecular assembly and terminate its growth by systematically characterizing how different DNA origami nanostructures interact with the growing ends of DNA tile nanotubes...
September 18, 2017: ACS Nano
Takeo Uchida, Keita Abe, Yuma Endo, Shosei Ichiseki, Satoru Akita, Shiyun Liu, Sho Aradachi, Masataka Saito, Akihiko Fukuchi, Taiyo Kikkawa, Theo Dammaretz, Ibuki Kawamata, Yuki Suzuki, Shin-Ichiro M Nomura, Satoshi Murata
A new kind of the Vernier mechanism that is able to control the size of linear assembly of DNA origami nanostructures is proposed. The mechanism is realized by mechanical design of DNA origami, which consists of a hollow cylinder and a rotatable shaft in it connected through the same scaffold. This nanostructure stacks with each other by the shape complementarity at its top and bottom surfaces of the cylinder, while the number of stacking is limited by twisting angle of the shaft. Experiments have shown that the size distribution of multimeric assembly of the origami depends on the twisting angle of the shaft; the average lengths of the multimer are decamer, hexamer, and tetramer for 0°, 10°, and 20° twist, respectively...
September 12, 2017: Small
Weiqi Zhang, Ching-Hsuan Tung
DNA nanostructures largely rely on pairing DNA bases; thus, sequence designing is required. Here, this study demonstrates a sequence-independent strategy to fabricate DNA nanogel (NG) inspired by cisplatin, a chemotherapeutic drug that acts as a DNA crosslinker. A simple heating and cooling of the genomic DNA extracts and cisplatin produces DNA NG with a size controlled by the heating time. Furthermore, the drug-loaded NG is formulated by spontaneously mixing DNA segments, cisplatin, and doxorubicin. The in vitro cell studies demonstrate that the doxorubicin-loaded NG alters the drug distribution in cells while its cytotoxic potential is well-maintained...
September 12, 2017: Macromolecular Rapid Communications
Yue Hu, Zhou Chen, He Zhang, Mingkai Li, Zheng Hou, Xiaoxing Luo, Xiaoyan Xue
Nanocarriers of drugs have attracted significant attention to tackle the problems of drug resistance or nucleic acid drug delivery, which can optimize pharmaceutical parameters and enhance the cellular uptake efficiency. Nowadays, DNA nanostructure presents an opportunity in the field of nanomaterial due to its precise control in shape and size, excellent biocompatibility, as well as multiple sites for targeting decoration. DNA tetrahedron, which is stable and easily synthesized, is used for various applications, including nuclear magnetic resonance imaging, molecular diagnosis, targeting drug delivery, and so on...
November 2017: Drug Delivery
Chiara Novara, Alessandro Chiadò, Niccolò Paccotti, Silvia Catuogno, Carla Lucia Esposito, Gerolama Condorelli, Vittorio De Franciscis, Francesco Geobaldo, Paola Rivolo, Fabrizio Giorgis
In this work, SERS-based microfluidic PDMS chips integrating silver-coated porous silicon membranes were used for the detection and quantitation of microRNAs (miRNAs), which consist of short regulatory non-coding RNA sequences typically over- or under-expressed in connection with several diseases such as oncogenesis. In detail, metal-dielectric nanostructures which provide noticeable Raman enhancements were functionalized according to a biological protocol, adapted and optimized from an enzyme-linked immunosorbent assay (ELISA), for the detection of miR-222...
September 8, 2017: Faraday Discussions
Bibek Uprety, John Jensen, Basu R Aryal, Robert C Davis, Adam T Woolley, John N Harb
This work examines anisotropic electroless plating of DNA-functionalized gold nanorods attached to a DNA origami template to fabricate continuous metal structures of rectangle, square and T shapes. DNA origami, a versatile method for assembling a variety of 2- and 3-D nanostructures, is utilized to construct the DNA breadboard template used for this study. Staple strands on selective sites of the breadboard template are extended with an additional nucleotide sequence for attachment of DNA-functionalized gold nanorods to the template via base pairing...
September 6, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Xiangyuan Ouyang, Mattia De Stefano, Abhichart Krissanaprasit, Anne Louise Bank Kodal, Christian Bech Rosen, Tianqiang Liu, Sarah Helmig, Chunhai Fan, Kurt Vesterager Gothelf
Immobilized antibodies are extensively employed for medical diagnostics such as in enzyme-linked immunosorbent assays. Despite their widespread use the ability to control the orientation on surfaces of immobilized antibodies is very limited. Herein, we report a method for covalent and orientation-selective immobilization of antibodies in designed cavities in 2D and 3D DNA origami structures. Two tris(NTA) modified strands are inserted into the cavity to form NTA-metal complexes with histidine clusters on the Fc domain...
September 5, 2017: Angewandte Chemie
Ke Du, Myeongkee Park, Junjun Ding, Huan Hu, Zheng Zhang
DNA is the hereditary material that contains our unique genetic code. Since the first demonstration of two-dimensional (2D) nanopatterns by using designed DNA origami ~10 years ago, DNA has evolved into a novel technique for 2D and 3D nanopatterning. It is now being used as a template for the creation of sub-10 nm structures via either "top-down" or "bottom-up" approaches for various applications spanning from nanoelectronics, plasmonic sensing, and nanophotonics. The perspective starts with an histroric overview and discusses the current state-of-the-art in DNA nanolithography...
September 4, 2017: Nanotechnology
Sarah Helmig, Kurt Vesterager Gothelf
Signal transfer is central to the controlled exchange of information in biology and advanced technologies. Therefore, the development of reliable, long-ranging signal transfer systems for artificial nanoscale assemblies is of great scientific interest. We have designed such a system for signal transfer between two connected DNA nanostructures, using the hybridization chain reaction (HCR). Two sets of metastable DNA hairpins - of which one is immobilized in specific points along tracks on DNA origami structures - are polymerized to form a continuous DNA duplex, which is visible using atomic force microscopy (AFM)...
September 3, 2017: Angewandte Chemie
Haichao Miao, Elisa De Llano, Johannes Sorger, Yasaman Ahmadi, Tadija Kekic, Tobias Isenberg, M Eduard Groller, Ivan Barisic, Ivan Viola
We present an approach to represent DNA nanostructures in varying forms of semantic abstraction, describe ways to smoothly transition between them, and thus create a continuous multiscale visualization and interaction space for applications in DNA nanotechnology. This new way of observing, interacting with, and creating DNA nanostructures enables domain experts to approach their work in any of the semantic abstraction levels, supporting both low-level manipulations and high-level visualization and modifications...
August 29, 2017: IEEE Transactions on Visualization and Computer Graphics
Sandeepa Kulala Vittala, Sajena Kanangat Saraswathi, Joshy Joseph
Programmable, hierarchical assembly of DNA nanostructures with the precise organization of functional components have been demonstrated previously with tiled assembly and DNA Origami. However, building organized nanostructures with random oligonucleotide strands remains as an elusive problem. Herein, we describe a simple and general strategy in which nanoclusters of a fullerene derivative act as stapler motifs in bringing ordered nanoscale assembly of short oligonucleotide duplexes into micrometer-sized nanowires...
August 31, 2017: Chemistry: a European Journal
Qing Liu, Guocheng Liu, Ting Wang, Jing Fu, Rujiao Li, Linlin Song, Zhen-Gang Wang, Baoquan Ding, Fei Chen
Self-assembled DNA nanostructures hold great promises in the fields of nanofabrication, biosensing and nanomedicine. However, the inherent low stability of the DNA double helices formed by weak interaction largely hinders the assembly and functions of DNA nanostructure. In this study, we redesigned and constructed a 6-helix DNA bundle and a 6-helix DNA nanotube by incorporation of unnatural base pairs, 5-Me-isoC/isoG and A/2-thioT into the double helices. They not only retained the morphologies of the DNA nanostructures, but also showed the enhanced thermal stability and resistance to T7 Exonuclease digestion...
August 30, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Hai-Ling Liu, Jiao Cao, Sumaira Hanif, Chun-Ge Yuan, Jie Pang, Rastislav Levicky, Xing-Hua Xia, Kang Wang
Nanopore structures have been successfully employed in next generation DNA sequencing. For more complicated protein which normally contains 20 different amino acids, identifying the fluctuation of ionic current caused by different amino acids appears inadequate for protein sequencing. Therefore, it is highly desirable to develop size-controllable nanopores with optical activity that can provide additional structural information. Herein, we discovered the novel nanopore properties of the self-assembled ultramicroelectrodes originally developed by Bard and coworkers...
August 30, 2017: Analytical Chemistry
Tao Zhao, Hong-Shuai Zhang, Hao Tang, Jian-Hui Jiang
A label-free nanopore biosensor for detection of DNA target is proposed utilizing hybridization chain reaction (HCR) strategy for signal amplification. The DNA target triggered HCR to form large DNA nanostructure inside the nanopore and out the nanopore membrane, which inducing the ionic current decrease effectively due to the blockage of the nanopore. The developed method achieves a desirable sensitivity of 30fM with a wide linear dynamic range from 0.1 to 10pM and demonstrated good application for real sample analysis...
December 1, 2017: Talanta
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