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DNA nanotechnology

Mirza Muhammad Faran Ashraf Baig, Sara Khan, Muhammad Ahsan Naeem, Ghulam Jilany Khan, Muhammad Tayyab Ansari
Diabetes mellitus type 2 is a multidimensional disease associated with poor glycemic control through compromised sensitivity of pancreatic islet α and β cells against glucose and dwindled secretion of insulin which is linked with the quantity of incretin hormones that are abridged by dipeptidyl peptidase-4 (DPP-4) in diseased condition. Vildagliptin (VG) inhibits DPP-4 therefore regulates the incretins that conversely maintains glycemic control. The safe reach and absorption of VG from intestine was dubious...
November 13, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Sarah Elisabeth Ochmann, Carolin Vietz, Kateryna Trofymchuk, Guillermo P Acuna, Birka Lalkens, Philip Tinnefeld
Due to the limited signal-to-background ratio, molecular diagnostics requires molecular amplification of the target molecules or molecular signal amplification after target recognition. For direct molecular detection, we demonstrate a purely physical fluorescence enhancement process which can elevate the fluorescence signal of single fluorescent dyes by several orders of magnitude. To this end, DNA origami-based optical antennas with a height of around 125 nm are used, which utilize metallic nanoparticles to create a hotspot where fluorescence signals are enhanced by plasmonic effects...
November 16, 2017: Analytical Chemistry
Pascal Röthlisberger, Cécile Gasse, Marcel Hollenstein
Recent progresses in organic chemistry and molecular biology have allowed the emergence of numerous new applications of nucleic acids that markedly deviate from their natural functions. Particularly, DNA and RNA molecules-coined aptamers-can be brought to bind to specific targets with high affinity and selectivity. While aptamers are mainly applied as biosensors, diagnostic agents, tools in proteomics and biotechnology, and as targeted therapeutics, these chemical antibodies slowly begin to be used in other fields...
November 16, 2017: International Journal of Molecular Sciences
Yan Chen, Ying Zhao, Yan-Bo Li, Yan-Jun Wang, Gui-Zhen Zhang
OBJECTIVE: To establish a high throughput, low cost, and simple nanotechnology-based method for the detection of single nucleotide polymorphism (SNP) loci in type 2 diabetes mellitus (T2DM). METHODS: Multiplex ligase detection reaction (LDR) amplification was performed using fluorescently labeled magnetic nanosphere-bound upstream LDR probes and downstream probes labeled with a unique fluorescent group for each SNP locus. The amplified LDR products were separated by magnetic nanospheres and then scanned by fluorescence spectroscopy...
November 9, 2017: Analytical Biochemistry
Ankur Garg, Udo Heinemann
Wobble base pairs are critical in various physiological functions and have been linked to local structural perturbations in double helical structures of nucleic acids. We report a 1.38-Å resolution crystal structure of an antiparallel octadecamer RNA double helix in overall A conformation, which includes a unique, central stretch of six consecutive wobble base pairs (W helix) with two G·U and four rare C·A(+) wobble pairs. Four adenines within the W helix are N1-protonated and wobble-base-paired with the opposing cytosine through two regular hydrogen bonds...
November 9, 2017: RNA
Farzin Haque, Fengmei Pi, Zhengyi Zhao, Shanqing Gu, Haibo Hu, Hang Yu, Peixuan Guo
In recent years, RNA has attracted widespread attention as a unique biomaterial with distinct biophysical properties for designing sophisticated architectures in the nanometer scale. RNA is much more versatile in structure and function with higher thermodynamic stability compared to its nucleic acid counterpart DNA. Larger RNA molecules can be viewed as a modular structure built from a combination of many 'Lego' building blocks connected via different linker sequences. By exploiting the diversity of RNA motifs and flexibility of structure, varieties of RNA architectures can be fabricated with precise control of shape, size, and stoichiometry...
November 3, 2017: Wiley Interdisciplinary Reviews. RNA
Matan Yah Ben Zion, Xiaojin He, Corinna C Maass, Ruojie Sha, Nadrian C Seeman, Paul M Chaikin
Although stereochemistry has been a central focus of the molecular sciences since Pasteur, its province has previously been restricted to the nanometric scale. We have programmed the self-assembly of micron-sized colloidal clusters with structural information stemming from a nanometric arrangement. This was done by combining DNA nanotechnology with colloidal science. Using the functional flexibility of DNA origami in conjunction with the structural rigidity of colloidal particles, we demonstrate the parallel self-assembly of three-dimensional microconstructs, evincing highly specific geometry that includes control over position, dihedral angles, and cluster chirality...
November 3, 2017: Science
Wenhu Zhou, Juewen Liu
Nucleic acid enzymes (NAEs) are catalytically active RNA and DNA molecules. NAEs with RNA-cleaving activity are most extensively studied for applications in analytical chemistry, gene therapy and nanotechnology. Most NAEs require metal ions for activity. From a biochemical standpoint, these NAEs are reminiscent of metalloprotein enzymes with metal binding sites. While most NAEs require a single metal for the reaction, more and more recent examples have emerged that use two or even three metals for the reaction...
November 2, 2017: Metallomics: Integrated Biometal Science
Elena Pascual, Carlos P Mata, José L Carrascosa, Jose R Caston
Hollow protein containers are widespread in nature, and include virus capsids as well as eukaryotic and bacterial complexes. Protein cages are studied extensively for applications in nanotechnology, nanomedicine and materials science. Their inner and outer surfaces can be modified chemically or genetically, and the internal cavity can be used to template, store and/or arrange molecular cargos. Virus capsids and virus-like particles (VLP, noninfectious particles) provide versatile platforms for nanoscale bioengineering...
October 30, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
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
Jiang Li, Alexander A Green, Hao Yan, Chunhai Fan
Nucleic acids have attracted widespread attention due to the simplicity with which they can be designed to form discrete structures and programmed to perform specific functions at the nanoscale. The advantages of DNA/RNA nanotechnology offer numerous opportunities for in-cell and in-vivo applications, and the technology holds great promise to advance the growing field of synthetic biology. Many elegant examples have revealed the potential in integrating nucleic acid nanostructures in cells and in vivo where they can perform important physiological functions...
November 2017: Nature Chemistry
Guido Grossi, Mette Dalgaard Ebbesen Jepsen, Jørgen Kjems, Ebbe Sloth Andersen
Biological systems use compartmentalisation as a general strategy to control enzymatic reactions by precisely regulating enzyme-substrate interactions. With the advent of DNA nanotechnology, it has become possible to rationally design DNA-based nano-containers with programmable structural and dynamic properties. These DNA nanostructures have been used to cage enzymes, but control over enzyme-substrate interactions using a dynamic DNA nanostructure has not been achieved yet. Here we introduce a DNA origami device that functions as a nanoscale vault: an enzyme is loaded in an isolated cavity and the access to free substrate molecules is controlled by a multi-lock mechanism...
October 19, 2017: Nature Communications
Xijun Piao, Hongzhi Wang, Daniel W Binzel, Peixuan Guo
The question of whether RNA is more stable or unstable comparing to DNA or other nucleic acids has long been an extensive scrutiny and public attention. In these days, thermodynamically-stable and degradation-resistant RNA motifs have been utilized in RNA nanotechnology to build desired architectures and integrate multiple functional groups. Here we report the effects of phosphorothioate deoxyribonucleotides (PS-DNA), deoxyribonucleotides (DNA), ribonucleotides (RNA), 2'-F nucleotides (2'-F) and locked nucleic acids (LNA) on the thermal and in vivo stability of RNA and the three-way junction (3WJ) of bacteriophage phi29 motor pRNA...
October 19, 2017: RNA
Yuan Liu, Sik Lok Lam
The DNA minidumbbell (MDB) is a recently identified non-B structure. The reported MDBs contain two TTTA, CCTG, or CTTG type II loops. At present, the knowledge and understanding of the sequence criteria for MDB formation are still limited. In this study, we performed a systematic high-resolution nuclear magnetic resonance (NMR) and native gel study to investigate the effect of sequence variations in tandem repeats on the formation of MDBs. Our NMR results reveal the importance of hydrogen bonds, base-base stacking, and hydrophobic interactions from each of the participating residues...
November 2, 2017: Journal of Physical Chemistry. B
James Joseph, Kevin N Baumann, Philipp Koehler, Tim J Zuehlsdorff, Daniel J Cole, Judith Weber, Sarah E Bohndiek, Silvia Hernández-Ainsa
Molecular rulers that rely on the Förster resonance energy transfer (FRET) mechanism are widely used to investigate dynamic molecular processes that occur on the nanometer scale. However, the capabilities of these fluorescence molecular rulers are fundamentally limited to shallow imaging depths by light scattering in biological samples. Photoacoustic tomography (PAT) has recently emerged as a high resolution modality for in vivo imaging, coupling optical excitation with ultrasound detection. In this paper, we report the capability of PAT to probe distance-dependent FRET at centimeter depths...
November 2, 2017: Nanoscale
T Klingelfus, J R Lirola, L F Oya Silva, G R Disner, M Vicentini, M J B Nadaline, J C Z Robles, L M Trein, C L Voigt, H C Silva de Assis, M Mela, D M Leme, M M Cestari
Nanotechnologies are at the center of societal interest, due to their broad spectrum of application in different industrial products. The current concern about nanomaterials (NMs) is the potential risks they carry for human health and the environment. Considering that NMs can reach bodies of water, there is a need for studying the toxic effects of NMs on aquatic organisms. Among the NMs' toxic effects on fish, the interactions between NMs and the nervous system are yet to be understood. For this reason, our goal was to assess the neurotoxicity of polyvinylpyrrolidone coated silver nanospheres [AgNS (PVP coated)] and compare their effects in relation to silver ions (Ag(+)) in carnivorous Hoplias intermedius fish after acute and subchronic trophic exposure through the analysis of morphological (retina), biochemical (brain) and genetic biomarkers (brain and blood)...
October 12, 2017: Neurotoxicology
Carina Hernandez, Jens J Birktoft, Yoel P Ohayon, Arun Richard Chandrasekaran, Hatem Abdallah, Ruojie Sha, Vivian Stojanoff, Chengde Mao, Nadrian C Seeman
There is an increasing appreciation for structural diversity of DNA that is of interest to both DNA nanotechnology and basic biology. Here, we have explored how DNA responds to torsional stress by building on a previously reported two-turn DNA tensegrity triangle and demonstrating that we could introduce an extra nucleotide pair (np) into the original sequence without affecting assembly and crystallization. The extra np imposes a significant torsional stress, which is accommodated by global changes throughout the B-DNA duplex and the DNA lattice...
November 16, 2017: Cell Chemical Biology
Zuzana Benková, Lucia Rišpanová, Peter Cifra
Equilibrium conformation of a semiflexible macromolecule in an array of nanoposts exhibits a non-monotonic behavior both at variation of the chain stiffness and increased crowding imposed by nanoposts. This is a result of the competition between the axial chain extension in channel-like interstitial volumes between nanoposts and the chain partitioning among these volumes. The approximation of a nanopost array as a combination of a quasi-channel and a quasi-slit like geometry semi-qualitatively explains the behavior of a chain in the array...
October 7, 2017: Journal of Chemical Physics
Nan Zheng, Xing Wang, Yaoqi Wang, Guobing Xu, Hua Zhang, Wenbing Dai, Bing He, Qiang Zhang, Jiafu Ji, Xueqing Wang
In recent years, drug conjugates as a prodrug strategy have been widely studied, especially combined with nanotechnology. Disulfide-linked doxorubicin drug-drug conjugate (DOX-S-S-DOX) nanoparticles, have recently been developed as a doxorubicin prodrug nanoparticles with greater anticancer activity and less toxicity than doxorubicin in vivo, while its intracellular kinetics and metabolism is unclear which may provide us with a deeper understanding of its pharmacological mechanism and antitumor effect. Hence, in this study, a rapid and sensitive ultra high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method was developed to detect doxorubicin (DOX) activated from DOX-S-S-DOX, as well as the prodrug itself in human breast cancer tumor cells (MCF-7)...
October 15, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
Chao Zhou, Xiaoyang Duan, Na Liu
The development of DNA nanotechnology, especially the advent of DNA origami, has made DNA ideally suited to construct nanostructures with unprecedented complexity and arbitrariness. As a fully addressable platform, DNA origami can be used to organize discrete entities in space through DNA hybridization with nanometer accuracy. Among a variety of functionalized particles, metal nanoparticles such as gold nanoparticles (AuNPs) feature an important pathway to endow DNA-origami-assembled nanostructures with tailored optical functionalities...
September 27, 2017: Accounts of Chemical Research
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