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DNA tetrahedron

John Benedict Readman, George Dickson, Nick G Coldham
The bacterial cell wall presents a barrier to the uptake of unmodified synthetic antisense oligonucleotides, such as peptide nucleic acids, and so is one of the greatest obstacles to the development of their use as therapeutic anti-bacterial agents. Cell-penetrating peptides have been covalently attached to antisense agents, to facilitate penetration of the bacterial cell wall and deliver their cargo into the cytoplasm. Although they are an effective vector for antisense oligonucleotides, they are not specific for bacterial cells and can exhibit growth inhibitory properties at higher doses...
January 12, 2017: Nucleic Acid Therapeutics
Fang Xu, Haifeng Dong, Yu Cao, Huiting Lu, Xiangdan Meng, Wenhao Dai, Xueji Zhang, Khalid Abdullah Al-Ghanim, Shahid Mahboob
A highly sensitive and multiple microRNA (miRNA) detection method by combining three-dimensional (3D) DNA tetrahedron-structured probes (TSPs) to increase the probe reactivity and accessibility with duplex-specific nuclease (DSN) for signal amplification for sensitive miRNA detection was proposed. Briefly, 3D DNA TSPs labeled with different fluorescent dyes for specific target miRNA recognition were modified on a gold nanoparticle (GNP) surface to increase the reactivity and accessibility. Upon hybridization with a specific target, the TSPs immobilized on the GNP surface hybridized with the corresponding target miRNA to form DNA-RNA heteroduplexes, and the DSN can recognize the formed DNA-RNA heteroduplexes to hydrolyze the DNA in the heteroduplexes to produce a specific fluorescent signal corresponding to a specific miRNA, while the released target miRNA strands can initiate another cycle, resulting in a significant signal amplification for sensitive miRNA detection...
December 14, 2016: ACS Applied Materials & Interfaces
Kyoung-Ran Kim, Hyo Young Kim, Yong-Deok Lee, Jong Seong Ha, Ji Hee Kang, Hansaem Jeong, Duhee Bang, Young Tag Ko, Sehoon Kim, Hyukjin Lee, Dae-Ro Ahn
Nanoparticle delivery systems have been extensively investigated for targeted delivery of anticancer drugs over the past decades. However, it is still a great challenge to overcome the drawbacks of conventional nanoparticle systems such as liposomes and micelles. Various novel nanomaterials consist of natural polymers are proposed to enhance the therapeutic efficacy of anticancer drugs. Among them, deoxyribonucleic acid (DNA) has received much attention as an emerging material for preparation of self-assembled nanostructures with precise control of size and shape for tailored uses...
December 10, 2016: Journal of Controlled Release: Official Journal of the Controlled Release Society
Yi-Ning Zhong, Yan Zhang, Yun-Qiong Gu, Shi-Yun Wu, Wen-Ying Shen, Ming-Xiong Tan
Tryptanthrin is one of the most important members of indoloquinoline alkaloids. We obtained this alkaloid from Isatis. Two novel Fe(II) and Co(II) complexes of tryptanthrin were first synthesized. Single-crystal X-ray diffraction analyses show that these complexes display distorted four-coordinated tetrahedron geometry via two heterocyclic nitrogen and oxygen atoms from tryptanthrin ligand. Binding with G-quadruplex DNA properties revealed that both complexes were found to exhibit significant interaction with G-quadruplex DNA...
2016: Bioinorganic Chemistry and Applications
Ping Song, Min Li, Juwen Shen, Hao Pei, Jie Chao, Shao Su, Ali Aldalbahi, Lihua Wang, Jiye Shi, Shiping Song, Lianhui Wang, Chunhai Fan, Xiaolei Zuo
The fixed dynamic range of traditional biosensors limits their utility in several real applications. For example, viral load monitoring requires the dynamic range spans several orders of magnitude; whereas, monitoring of drugs requires extremely narrow dynamic range. To overcome this limitation, here, we devised tunable biosensing interface using allosteric DNA tetrahedral bioprobes to tune the dynamic range of DNA biosensors. Our strategy takes the advantage of the readily and flexible structure design and predictable geometric reconfiguration of DNA nanotechnology...
August 16, 2016: Analytical Chemistry
Larry J Kricka, Paolo Fortina, Jason Y Park
Important and emerging trends at the interface of luminescence, nucleic acids and nanotechnology are: (i) the conventional luminescence labeling of nucleic acid nanostructures (e.g. DNA tetrahedron); (ii) the labeling of bulk nucleic acids (e.g. single-stranded DNA, double-stranded DNA) with nanostructured luminescent labels (e.g. copper nanoclusters); and (iii) the labeling of nucleic acid nanostructures (e.g. origami DNA) with nanostructured luminescent labels (e.g. silver nanoclusters). This review surveys recent advances in these three different approaches to the generation of nanostructured luminescently labeled nucleic acids, and includes both direct and indirect labeling methods...
July 15, 2016: Luminescence: the Journal of Biological and Chemical Luminescence
I P Shabalkin, E Yu Grigor'eva, M V Gudkova, P I Shabalkin
We proposed a new model of supramolecular DNA structure. Similar to the previously developed by us model of primary DNA structure [11-15], 3D structure of DNA molecule is assembled in accordance to a mathematic rule known as Fibonacci sequence. Unlike primary DNA structure, supramolecular 3D structure is assembled from complex moieties including a regular tetrahedron and a regular octahedron consisting of monomers, elements of the primary DNA structure. The moieties of the supramolecular DNA structure forming fragments of regular spatial lattice are bound via linker (joint) sequences of the DNA chain...
May 2016: Bulletin of Experimental Biology and Medicine
Dan Zhu, Hao Pei, Guangbao Yao, Lihua Wang, Shao Su, Jie Chao, Lianhui Wang, Ali Aldalbahi, Shiping Song, Jiye Shi, Jun Hu, Chunhai Fan, Xiaolei Zuo
A proton-driven molecular pump is devised using a surface-confined dynamic 3D DNA scaffold. A dynamic DNA tetrahedral nanostructure is designed by incorporating a pH-sensitive i-motif sequence in one edge, which serves as the scaffold to ensure highly ordered orientation and spatial isolation of this nanomachine on the macroscopic gold surface. It is found that the switching ability of this dynamic tetrahedron is fully maintained on the surface. Importantly, this proton-driven nanomachine can reversibly pump water and ferricynide in response to pH variation in solution...
August 2016: Advanced Materials
Bindong Dai, Yan Hu, JinHong Duan, Xian-Da Yang
Mucin 1 (MUC1) is an important molecular target for cancer treatment because it is overexpressed in most adenocarcinomas. In this study, a new MUC1-targeted drug delivery system was assembled using an aptamer (Apt) that could recognize MUC1 and a DNA tetrahedron (Td) that could carry doxorubicin (Dox) within its DNA structure. The complex thus formed (Apt-Td) had an average size of 12.38 nm and was negatively charged. Similar to the MUC1 aptamer, the Apt-Td could preferentially bind with MUC1-positive MCF-7 breast cancer cells...
June 21, 2016: Oncotarget
Yueran Li, Xifeng Chen, Bidou Wang, Guangxing Liu, Yuguo Tang, Peng Miao
Human immunodeficiency virus (HIV) is a retrovirus which attacks the human body's immune system and further leads to acquired immunodeficiency syndrome (AIDS). Nucleic acid detection is of great importance in the medical diagnosis of such diseases. Herein, we develop a simple and enzyme-free electrochemical method for the target recycling detection of nuclei acid. DNA tetrahedron and star trigon nanostructures are designed and constructed on the electrode interface for target capture and signal enrichment. This strategy is convenient and sensitive, with a limit of detection as low as 1 fM, and can also successfully distinguish single-base mismatched DNA...
June 7, 2016: Analyst
Shunbi Xie, Yongwang Dong, Yali Yuan, Yaqin Chai, Ruo Yuan
The preparation of self-assembled DNA nanostructure with different sizes and shapes has been one of the most promising research areas in recent years, while the application of these DNA nanostructures in biosensors is far from fully developed. Here, we presented a novel carrier system to construct an electrochemiluminescence (ECL) aptasensor for ultrasensitive determination of lipopolysaccharides (LPS) on the basis of self-assembled tetrahedron DNA dendrimers. Doxorubicin (Dox), a well-known intercalator of double stranded DNA (dsDNA), was conjugated with the ECL luminophore of N-(aminobutyl)-N-(ethylisoluminol) (ABEI) to form a new type of ECL indicators (Dox-ABEI), which could noncovalently attach to dsDNA through intercalation...
May 17, 2016: Analytical Chemistry
Cassio Alves, Federico Iacovelli, Mattia Falconi, Francesca Cardamone, Blasco Morozzo Della Rocca, Cristiano L P de Oliveira, Alessandro Desideri
A semiautomatic procedure to build complex atomistic covalently linked DNA nanocages has been implemented in a user-friendly, free, and fast program. As a test set, seven different truncated DNA polyhedra, composed by B-DNA double helices connected through short single-stranded linkers, have been generated. The atomistic structures, including a tetrahedron, a cube, an octahedron, a dodecahedron, a triangular prism, a pentagonal prism, and a hexagonal prism, have been probed through classical molecular dynamics and analyzed to evaluate their structural and dynamical properties and to highlight possible building faults...
May 23, 2016: Journal of Chemical Information and Modeling
Qiu-Mei Feng, Meng-Jiao Zhu, Ting-Ting Zhang, Jing-Juan Xu, Hong-Yuan Chen
A novel three-dimensionally structured DNA probe is reported to realize in situ"off-on" imaging of intracellular telomerase activity. The probe consists of a DNA tetrahedron and a hairpin DNA on one of the vertices of the DNA tetrahedron. It is composed of four modified DNA segments: S1-Au nanoparticle (NP) inserting a telomerase strand primer (TSP) and S2-S4, three Cy5 dye modified DNA segments. Fluorescence of Cy5 at three vertices of the DNA tetrahedron is quenched by the Au NP at the other vertex due to the effective fluorescence resonance energy transfer (FRET) ("off" state)...
April 21, 2016: Analyst
Zhiwei Xia, Ping Wang, Xunwei Liu, Ting Liu, Yinan Yan, Juan Yan, Jian Zhong, Gang Sun, Dannong He
DNA self-assembling nanostructure has been considered as a promising candidate as a drug delivery vehicle because of its compactness, mechanical stability, and noncytotoxicity. In this work, we developed functional, multiform DNA nanostructures by appending a tumor-penetrating peptide to tetrahedral DNA nanostructure (p-TDN). This functional structure is able to efficiently increase the rate of uptake of glioblastoma cell U87MG compared with the DNA tetrahedron and the double-stranded DNA structures. We found that the DNA tetrahedron plays the main role in the endocytosis of U87MG cells, whereas the tumor-penetrating peptide could also bind to transmembrane glycoprotein neuropilin-1 and mediate the endocytosis of the p-TDN nanostructure...
March 8, 2016: Biochemistry
Anna Barth, Daniela Kobbe, Manfred Focke
Kissing-loop annealing of nucleic acids occurs in nature in several viruses and in prokaryotic replication, among other circumstances. Nucleobases of two nucleic acid strands (loops) interact with each other, although the two strands cannot wrap around each other completely because of the adjacent double-stranded regions (stems). In this study, we exploited DNA kissing-loop interaction for nanotechnological application. We functionalized the vertices of DNA tetrahedrons with DNA stem-loop sequences. The complementary loop sequence design allowed the hybridization of different tetrahedrons via kissing-loop interaction, which might be further exploited for nanotechnology applications like cargo transport and logical elements...
February 29, 2016: Nucleic Acids Research
Nuli Xie, Jin Huang, Xiaohai Yang, Yanjing Yang, Ke Quan, He Wang, Le Ying, Min Ou, Kemin Wang
Due to its low cytotoxicity, high resistance to enzymatic degradation, and cellular permeability, a DNA tetrahedron-based molecular beacon (DTMB) is designed for tumor-related TK1 mRNA detection in living cells, where the target sequence can induce the tetrahedron from contraction to extension, resulting in fluorescence restoration.
February 7, 2016: Chemical Communications: Chem Comm
Yuanjian Liu, Min Wei, Xu Liu, Wei Wei, Hongyu Zhao, Yuanjian Zhang, Songqin Liu
Label-free detection of telomerase activity was done by using telomeric hemin/G-quadruplex triggered polyaniline deposition, not only on themselves but also on the DNA tetrahedron-structure (DTS). DTS size has a great impact on telomerase accessibility, reactivity and detection sensitivity. The method has been used to evaluate bladder cancer development.
January 31, 2016: Chemical Communications: Chem Comm
Kyoung-Ran Kim, Duhee Bang, Dae-Ro Ahn
Photodynamic therapy (PDT) is a cytotoxic treatment using singlet oxygen produced by photosensitizers. Approved porphyrinoid PDT still suffers from a lack of robust production methods and low water solubility. Methylene blue (MB) is a good candidate for the PDT drug, because the dye is an effective photosensitizer, can be easily synthesized, and is already being used in other clinical fields. However, its poor cell/tissue penetration and low stability against the reducible biological conditions should be addressed by using a proper delivery vehicle...
April 2016: Biomaterials Science
Manfred Lamprecht, Simon Bogner, Kurt Steinbauer, Burkhard Schuetz, Joachim F Greilberger, Bettina Leber, Bernhard Wagner, Erwin Zinser, Thomas Petek, Sandra Wallner-Liebmann, Tanja Oberwinkler, Norbert Bachl, Gert Schippinger
BACKGROUND: Zeolites are crystalline compounds with microporous structures of Si-tetrahedrons. In the gut, these silicates could act as adsorbents, ion-exchangers, catalysts, detergents or anti-diarrheic agents. This study evaluated whether zeolite supplementation affects biomarkers of intestinal wall permeability and parameters of oxidation and inflammation in aerobically trained individuals, and whether it could improve their performance. METHODS: In a randomized, double-blinded, placebo controlled trial, 52 endurance trained men and women, similar in body fat, non-smokers, 20-50 years, received 1...
2015: Journal of the International Society of Sports Nutrition
Juan Li, Cheng-Yi Hong, Shu-Xian Wu, Hong Liang, Li-Ping Wang, Guoming Huang, Xian Chen, Huang-Hao Yang, Dihua Shangguan, Weihong Tan
Hydrophobic nanoparticles have shown substantial potential for bioanalysis and biomedical applications. However, their use is hindered by complex phase transfer and inefficient surface modification. This paper reports a facile and universal strategy for phase transfer and surface biofunctionalization of hydrophobic nanomaterials using aptamer-pendant DNA tetrahedron nanostructures (Apt-tet). The Janus DNA tetrahedron nanostructures are constructed by three carboxyl group modified DNA strands and one aptamer sequence...
September 9, 2015: Journal of the American Chemical Society
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