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DNA tetrahedron

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...
November 6, 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. After the substrate is recognized by target methyltransferase, the DNA tetrahedron can be methylated to produce methylated DNA sites...
November 13, 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 Pb(2+)...
November 14, 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. Using DNA nanotechnology and inspired 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) signalling mechanism, the "On" to "Off" signal is reversibly responding to "below" and "over" the melting temperature...
October 25, 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
Mala Nath, Mridula, Ranjana Kumari
Diorganotin(IV) and triphenyltin(IV) derivatives of L-proline (HPro) having general formula R2Sn(Pro)2 (R=n-Bu (1), Ph (2)) and Ph3Sn(Pro) (3), respectively, and the mixed ligands di-/triorganotin(IV) derivatives of L-proline and 1,10-phenanthroline (phen) with general formula [R2Sn(Pro)(Phen)Cl] and [R3Sn(Pro)(Phen)] (where R=Me (4 and 7), n-Bu (5 and 8), Ph (6 and 9)), respectively, have been synthesized by microwave-assisted method and characterized by elemental analysis, IR, NMR ((1)H, (13)C and (119)Sn) and DART-mass spectral studies...
September 2017: Journal of Photochemistry and Photobiology. B, Biology
Song Wang, Mengchan Xia, Jie Liu, Sichun Zhang, Xinrong Zhang
We constructed a DNA tetrahedron based multicolor nanoprobe, which could simultaneously imaging of three tumor-related mRNAs in living cells through fluorescence restoration caused by competitive chain replacement reaction. The oligonucleotides used to construct the tetrahedron were extended by adding three 21-base recognition sequences modified with different fluorophores (FAM, Cy3, and Cy5) in the 5' end. Three 11-base complementary sequences modified with quencher (BHQ1 for FAM and BHQ2 for Cy3 and Cy5) were hybridized with the recognition sequences to quench the fluorescence...
June 23, 2017: ACS Sensors
Ji Hee Kang, Kyoung-Ran Kim, Hyukjin Lee, Dae-Ro Ahn, Young Tag Ko
Deoxyribonucleic acid (DNA) is a versatile material with high applicability and inherent biocompatibility. L-DNA, the perfect mirror form of the naturally occurring D-DNA, has been used in DNA nanotechnology. It has thermodynamically identical properties to D-DNA, is capable of self-assembly and bio-orthogonal base-pairing, and is resistant to nuclease activity. We previously constructed an L-DNA tetrahedron (L-Td) and found that this nanostructure has remarkably higher capacity for cell penetration than its natural counterpart (D-Td)...
September 1, 2017: Colloids and Surfaces. B, Biointerfaces
Jinping Wang, May Ching Leong, Eric Zhe Wei Leong, Win Sen Kuan, David Tai Leong
Streptococcus pneumoniae (SP) is a pathogenic bacterium and a major cause of community-acquired pneumonia that could be fatal if left untreated. Therefore, rapid and sensitive detection of SP is crucial to enable targeted treatment during SP infections. In this study, DNA tetrahedron (DNA TH) with a hollow structure is anchored on gold electrodes to construct an electrochemical immunosensor for rapid detection of pneumococcal surface protein A (PspA) peptide and SP lysate from synthetic and actual human samples...
June 8, 2017: Analytical Chemistry
Na Li, Meimei Wang, Xiaonan Gao, Zhengze Yu, Wei Pan, Hongyu Wang, Bo Tang
Multicomponent quantitative detection in living samples is becoming increasingly important; however, the current detection strategy may cause fluorescence self-quenching and reduce the sensitivity of detection. To solve the problem, we develop a DNA tetrahedral nanoprobe to control the dyes distance for simultaneous detection of multiple analytes. Compared to mesoporous silica nanoparticles based nanoprobes, the DNA tetrahedral nanoprobes display enhanced fluorescence intensities due to partially avoiding the fluorescence resonance energy transfer...
June 5, 2017: Analytical Chemistry
Keyao Pan, William P Bricker, Sakul Ratanalert, Mark Bathe
Synthetic DNA is a highly programmable nanoscale material that can be designed to self-assemble into 3D structures that are fully determined by underlying Watson-Crick base pairing. The double crossover (DX) design motif has demonstrated versatility in synthesizing arbitrary DNA nanoparticles on the 5-100 nm scale for diverse applications in biotechnology. Prior computational investigations of these assemblies include all-atom and coarse-grained modeling, but modeling their conformational dynamics remains challenging due to their long relaxation times and associated computational cost...
June 20, 2017: Nucleic Acids Research
Qiu-Mei Feng, Yue-Hua Guo, Jing-Juan Xu, Hong-Yuan Chen
A novel DNA tetrahedron-structured electrochemiluminescence (ECL) platform for bioanalysis with programmable DNA cyclic amplification was developed. In this work, glucose oxidase (GOD) was labeled to a DNA sequence (S) as functional conjugation (GOD-S), which could hybridize with other DNA sequences (L and P) to form GOD-S:L:P probe. In the presence of target DNA and a help DNA (A), the programmable DNA cyclic amplification was activated and released GOD-S via toehold-mediated strand displacement. Then, the obtained GOD-S was further immobilized on the DNA tetrahedral scaffolds with a pendant capture DNA and Ru(bpy)3(2+)-conjugated silica nanoparticles (RuSi NPs) decorated on the electrode surface...
May 11, 2017: ACS Applied Materials & Interfaces
Pengchao Sun, Nan Zhang, Yafang Tang, Yanan Yang, Xiao Chu, Yongxing Zhao
DNA nanostructures prepared by self-assembly possess good stability, high biocompatibility, and low immunogenicity as drug delivery vehicles. In this work, DNA tetrahedron (TD) was constructed and modified with SL2B aptamer (S) and folic acid (F). TD possessed a small diameter (~6 nm) and entered into the nucleus quickly. SL2B aptamer can inhibit cancer cell growth by disturbing vascular endothelial growth factor/Notch signaling pathways. To explore the effect of SL2B number on colorectal cancer inhibition, SL2B multimers (dimer, trimer, and tetramer) were constructed by functionalization of TD with different numbers of SL2B...
2017: International Journal of Nanomedicine
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