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DNA tetrahedron

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)...
June 16, 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...
May 8, 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
Lei He, Dan-Qing Lu, Hao Liang, Sitao Xie, Can Luo, Miaomiao Hu, Liujun Xu, Xiaobing Zhang, Weihong Tan
Accurate detection and imaging of tumor-related mRNA in living cells hold great promise for early cancer detection. However, currently, most probes designed to image intracellular mRNA confront intrinsic interferences arising from complex biological matrices and resulting in inevitable false-positive signals. To circumvent this problem, an intracellular DNA nanoprobe, termed DNA tetrahedron nanotweezer (DTNT), was developed to reliably image tumor-related mRNA in living cells based on the FRET (fluorescence resonance energy transfer) "off" to "on" signal readout mode...
April 25, 2017: ACS Nano
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...
June 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...
March 2017: 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
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