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DNA tetrahedron

Kyoung-Ran Kim, Dohyeon Hwang, Juhyeon Kim, Chang-Yong Lee, Wonseok Lee, Dae Sung Yoon, Dongyun Shin, Sun-Joon Min, Ick Chan Kwon, Hak Suk Chung, Dae-Ro Ahn
Despite the extremely high substrate specificity and catalytically amplified activity of enzymes, the lack of efficient cellular internalization limits their application as therapeutics. To overcome this limitation and to harness enzymes as practical biologics for targeting intracellular functions, we developed the streptavidin-mirror DNA tetrahedron hybrid as a platform for intracellular delivery of various enzymes. The hybrid consists of streptavidin, which provides a stoichiometrically controlled loading site for the enzyme cargo and an L-DNA (mirror DNA) tetrahedron, which provides the intracellular delivery potential...
April 30, 2018: Journal of Controlled Release: Official Journal of the Controlled Release Society
Sai Wang, Yiyang Dong, Xingguo Liang
Although surface plasmon resonance (SPR) technique and aptamer technology shows great potential in analytical and biological chemistry, direct capture and analysis of small molecules using SPR remains tough. Detection sensitivity of aptasensor and recognition ability of aptamer is limited, because direct immobilization of aptamer causes large steric hindrance and strand entanglement. Herein, we chose a typical small molecule-tetracycline (Mw. 444.4 g/mol) as a model, and combined aptamer technology, DNA nanostructure, and commercial Biacore T200 SPR instrument to develop a straightforward format SPR aptasensor...
June 30, 2018: Biosensors & Bioelectronics
Ying Zhang, Zhenhua Shuai, Hao Zhou, Zhimin Luo, Bing Liu, Yinan Zhang, Lei Zhang, Shufen Chen, Jie Chao, Lixing Weng, Quli Fan, Chunhai Fan, Wei Huang, Lianhui Wang
Analysis of biomolecules at the single-molecule level is a great challenge in molecular diagnostics, gene profiling, and environmental monitoring. In this work, we design a smart plasmonic nanobiosensor based on individual Au@Ag core-shell nanocube (Au@Ag NC) modified with tetrahedron-structured DNA (tsDNA) for detecting microRNA 21 (miR-21) at the single-molecule level. An average localized surface plasmon resonance (LSPR) scattering spectral wavelength shift of approximately 0.4 nm can be obtained for a single miR-21 hybridization event on the nanobiosensor...
March 21, 2018: Journal of the American Chemical Society
Fabio Lapenta, Jana Aupič, Žiga Strmšek, Roman Jerala
The design of new protein folds represents a grand challenge for synthetic, chemical and structural biology. Due to the good understanding of the principles governing its pairing specificity, coiled coil (CC) peptide secondary structure elements can be exploited for the construction of modular protein assemblies acting as a proxy for the straightforward complementarity of DNA modules. The prerequisite for the successful translation of the modular assembly strategy pioneered by DNA nanotechnology to protein design is the availability of orthogonal building modules: a collection of peptides that assemble into CCs only with their predetermined partners...
February 5, 2018: Chemical Society Reviews
Yuezhou Zhang, Jing Tu, Dongqing Wang, Haitao Zhu, Sajal Kumar Maity, Xiangmeng Qu, Bram Bogaert, Hao Pei, Hongbo Zhang
DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg2+ ) to produce a variety of DNA nanostructures...
February 1, 2018: Advanced Materials
Mingxuan Gao, Douglas Daniel, Hongyan Zou, Shuoxing Jiang, Su Lin, Chengzhi Huang, Sidney M Hecht, Shengxi Chen
A DNA tetrahedron having a single-strand DNA edge was used to detect a dengue virus RNA sequence. Novel tandem toehold-mediated displacement reactions (tTMDR) were developed to amplify the fluorescence signal from the DNA tetrahedron. Using an excess of the DNA tetrahedron each target RNA was recycled about 103 times during the tTMDR process. This amplification process was used for the sensitive detection of dengue virus RNA in this study. As few as 6 copies of RNA per sample could be detected using a photon count technique with single molecule sensitivity...
January 23, 2018: Chemical Communications: Chem Comm
Xiaoting Liu, Lina Wu, Lei Wang, Wei Jiang
To enhance efficacy of chemotherapy and achieve real-time imaging of cancer cells, it is crucial to develop nanocarriers with targeted drug delivery capacity and fluorescence property for cancer theranostics. Herein, a dual-targeting DNA tetrahedron nanocarrier (MUC1-Td-AS1411) was constructed for breast cancer cell imaging and targeted drug delivery. This nanocarrier consisted of three components: (i) DNA tetrahedron core for multivalent conjugation of function ligands and loading doxorubicin (Dox); (ii) activatable MUC1 aptamer probe (MUC1-probe), formed by the hybridization of MUC1 aptamer sequence with fluorophore extended from one vertex and complementary sequence with quencher, for targeting and imaging MUC1 protein on cytomembrane; (iii) AS1411 aptamer, which was hybridized to the overhang on three vertexes via prolonged sequence, for binding to nucleolin...
March 1, 2018: Talanta
Mei-Xing Li, Qiu-Mei Feng, Zhen Zhou, Wei Zhao, Jing-Juan Xu, Hong-Yuan Chen
Gold nanodendrites (Au NDs) exhibit extremely strong electromagnetic field located around multiple tip branches due to a plasmon coupling effect. In this work, a novel LSPR-enhanced ECL emission from CdTe nanocrystals (NCs) by Au NDs for the detection of nucleic acid is reported. This system is composed of a thin film of CdTe NCs on glassy carbon electrode (GCE) as anodic ECL emitter and Au NDs as plasmon enhancer. DNA tetrahedron embedded with a stem-loop hairpin structure on one edge was applied as a switch to regulate the distance between CdTe NCs and Au NDs...
January 16, 2018: Analytical Chemistry
Liying Wang, Zhenyu Meng, Felicia Martina, Huilin Shao, Fangwei Shao
DNA tetrahedron as the simplest 3D DNA nanostructure has been applied widely in biomedicine and biosensing. Herein, we design and fabricate a series of circular assemblies of DNA tetrahedron with high purity and decent yields. These circular nanostructures are confirmed by endonuclease digestion, gel electrophoresis and atomic force microscopy. Inspired by rotary protein motor, we demonstrate these circular architectures can serve as a stator for a rotary DNA motor to achieve the circular rotation. The DNA motor can rotate on the stators for several cycles, and the locomotion of the motor is monitored by the real-time fluorescent measurements...
December 1, 2017: Nucleic Acids Research
Xiaoyan Zhou, Min Zhao, Xiaolei Duan, Bin Guo, Wei Cheng, Shijia Ding, Huangxian Ju
As a potential detection technique, highly rigid and versatile functionality of DNA tetrahedron nanostructures is often used in biosensing systems. In this work, a novel multifunctional nanostructure has been developed as an "off-on" fluorescent probe for detection of target methyltransferase by integrating the elements of DNA tetrahedron, target recognition, and dual-labeled reporter. This sensing system is initially in an "OFF" state owing to the close proximity of fluorophores and quenchers...
November 22, 2017: ACS Applied Materials & Interfaces
Shuang Wang, Shasha Lu, Jiahui Zhao, Jianshe Huang, Xiurong Yang
G-quadruplex plays roles in numerous physiological and pathological processes of organisms. Due to the unique properties of G-quadruplex (e.g., forming G4/hemin complexes with catalytic activity and electron acceptability, binding with metal ions, proteins, fluorescent ligands, and so on), it has been widely applied in biosensing. But the formation process of G-quadruplex is not yet fully understood. Here, a DNA tetrahedron platform with higher reproducibility, regenerative ability, and time-saving building process was coupled with dual polarization interferometry technique for the real-time and label-free investigation of the specific interaction process of guanine-rich singled-stranded DNA (G-rich ssDNA) and Pb2+ ...
November 29, 2017: ACS Applied Materials & Interfaces
Nuli Xie, Jin Huang, Xiaohai Yang, Xiaoxiao He, Jianbo Liu, Jiaqi Huang, Hongmei Fang, Kemin Wang
Accurate measurement of intracellular temperature is of great significance in biology and medicine. With use of DNA nanotechnology and inspiration by nature's examples of "protective and reversible responses" exoskeletons, a scallop-inspired DNA nanomachine (SDN) is desgined as a ratiometric nanothermometer for intracellular temperature sensing. The SDN is composed of a rigid DNA tetrahedron, where a thermal-sensitive molecular beacon (MB) is embedded in one edge of the DNA tetrahedron. Relying on the thermal-sensitive MB and fluorescence resonance energy transfer (FRET) signaling mechanism, the "On" to "Off" signal is reversibly responding to "below" and "over" the melting temperature...
November 3, 2017: Analytical Chemistry
Jue Wang, Wenbo Cheng, Fanyu Meng, Mo Yang, Yue Pan, Peng Miao
Theophylline is a popular drug for many respiratory diseases. However, certain toxic side effects may be developed and the narrow safety range raises the demand for sensitive methods to constantly monitor theophylline levels. This study presents an electrochemical approach towards theophylline detection based on the recognition by split RNA aptamers. Target induced construction of hand-in-hand RNA nanowire on the electrode surface could further absorb silver nanoparticles (Ag NPs) as electrochemical species...
October 13, 2017: Biosensors & Bioelectronics
Ajasja Ljubetič, Fabio Lapenta, Helena Gradišar, Igor Drobnak, Jana Aupič, Žiga Strmšek, Duško Lainšček, Iva Hafner-Bratkovič, Andreja Majerle, Nuša Krivec, Mojca Benčina, Tomaž Pisanski, Tanja Ćirković Veličković, Adam Round, José María Carazo, Roberto Melero, Roman Jerala
Polypeptides and polynucleotides are natural programmable biopolymers that can self-assemble into complex tertiary structures. We describe a system analogous to designed DNA nanostructures in which protein coiled-coil (CC) dimers serve as building blocks for modular de novo design of polyhedral protein cages that efficiently self-assemble in vitro and in vivo. We produced and characterized >20 single-chain protein cages in three shapes-tetrahedron, four-sided pyramid, and triangular prism-with the largest containing >700 amino-acid residues and measuring 11 nm in diameter...
November 2017: Nature Biotechnology
Xue Yang, Yanli Wen, Lele Wang, Chaoqun Zhou, Qian Li, Li Xu, Lanying Li, Jiye Shi, Ratnesh Lal, Shuzhen Ren, Jiang Li, Nengqin Jia, Gang Liu
A "sandwich-like" biosensor was developed on the basis of the magnetic bead platform for sensitive detection of breast cancer 1 (BRCA1) DNA. In the present study, a tetrahedron-structured reporter probe (TSRP) was designed, in which 3 vertices of the tetrahedron were labeled with digoxin (Dig), and the other one was labeled with a detection probe. TSRP here provided accurate enzyme loading and well-organized spatial arrangement for optimized signal amplification. The detection limit of this biosensor was as low as 10 fM, which is at least 4 orders of magnitude lower than that of the single DNA probe (100 pM), and the signal gain was 2 times higher than the analysis using three one-dimensional (1D) reporter probes...
November 8, 2017: ACS Applied Materials & Interfaces
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
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
Nuli Xie, Shiyuan Liu, Xiaohai Yang, Xiaoxiao He, Jin Huang, Kemin Wang
With the rapid development of DNA nanotechnology, various DNA nanostructures with different shapes and sizes have been self-assembled using "bottom-up" fabrication strategies and applied to a wide range of fields such as biosensors, drug delivery and tools for molecular biology. As a classical and simple polyhedron, DNA tetrahedron can be easily synthesised by a one-step assembly. Due to the excellent biocompatibility and cellular permeability, it provides a universal and promising platform to construct a series of biosensors and drug delivery systems for living cells studies...
August 24, 2017: Analyst
Guiyu Zhang, Zhiyong Zhang, Junen Yang
As a nano-sized drug carrier with the advantage of modifiability and proper biocompatibility, DNA tetrahedron (DNA tetra) delivery is hopeful to enhance the inhibitory efficiency of nontargeted anticancer drugs. In this investigation, doxorubicin (Dox) was assembled to a folic acid-modified DNA tetra via click chemistry to prepare a targeted antitumor agent. Cellular uptake efficiency was measured via fluorescent imaging. Cytotoxicity, inhibition efficiency, and corresponding mechanism on colon cancer cell line HT-29 were evaluated by MTT assay, cell proliferation curve, western blot, and flow cytometry...
August 15, 2017: Nanoscale Research Letters
Li Xu, Wen Liang, Yanli Wen, Lele Wang, Xue Yang, Shuzhen Ren, Nengqin Jia, Xiaolei Zuo, Gang Liu
Electrochemical DNA biosensor has unique advantages for on-site pathogenic microorganism detection, yet the detection of long DNA towards genome DNA (gDNA) analysis remains challenge. In this work, we report a novel electrochemical biosensor for the ultrasensitive analysis of mecA DNA on methicillin-resistant Staphylococcus aureus (MRSA) genome, using a multi-signal probes (MSP) system. The MSP consists of 7 biotin-labelled signal probes that will combine to the target DNA in a prehybridization step, and then the complex will be captured by a DNA tetrahedron structure probe (TSP) on the electrode surface...
August 8, 2017: Biosensors & Bioelectronics
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