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DNA nanotechnology

Vanessa Koehlé-Divo, Carole Cossu-Leguille, Sandrine Pain-Devin, Cécile Simonin, Carole Bertrand, Bénédicte Sohm, Catherine Mouneyrac, Simon Devin, Laure Giambérini
The rapid development of nanotechnology and the increased use of nanomaterials in products used in everyday life have raised the question of the potential release of nanoparticles into the aquatic environment. Their fate and effects in natural ecosystems are not currently well understood but harmful effects of nanoparticles have been demonstrated at low concentrations on some freshwater and marine species. Cerium dioxide nanoparticles (CeO2 NPs) are produced in large quantities and used in products in many different fields, such as automotives or optics...
February 27, 2018: Aquatic Toxicology
Akram Norouzi, Hadi Ravan, Abbas Mohammadi, Elyas Hosseinzadeh, Mahdieh Norouzi, Tahereh Fozooni
The development of powerful techniques to detect cancer cells at early stages plays a notable role in diagnosing and prognosing cancer patients and reducing mortality. This paper reports on a novel functional DNA nanoassembly capable of detecting cancer cells based on structural DNA nanotechnology. DNA nanoassemblies were constructed by the self-assembly of a DNA concatemer to a plenty of sticky-ended three-way junctions. While an aptamer moiety guided the nanoassembly to the target cancer cell, the peroxidase-mimicking DNAzymes embedded in the nanoassemblies were used as the sensing element to produce colorimetric signals...
August 9, 2018: Analytica Chimica Acta
Sijin Guo, Xijun Piao, Hui Li, Peixuan Guo
The field of RNA nanotechnology has developed rapidly over the last decade, as more elaborate RNA nanoarchitectures and therapeutic RNA nanoparticles have been constructed, and their applications have been extensively explored. Now it is time to offer different levels of RNA construction methods for both the beginners and the experienced researchers or enterprisers. The first and second parts of this article will provide instructions on basic and simple methods for the assembly and characterization of RNA nanoparticles, mainly based on the pRNA three-way junction (pRNA-3WJ) of phi29 DNA packaging motor...
March 9, 2018: Methods: a Companion to Methods in Enzymology
Dinesh Pratap Singh, Carlos Eugenio Herrera, Brijesh Singh, Shipra Singh, Rajesh Kumar Singh, Rajesh Kumar
The two-dimensional (2D) derivative of graphite termed graphene has widespread applications in various frontiers areas of nanoscience and nanotechnologies. Graphene in its oxidized form named as graphene oxide (GO) has a mixed structure equipped with various oxygen containing functional groups (epoxy, hydroxyl, carboxylic and carbonyl etc.) provides attachment sites to various biological molecules including protein, deoxyribonucleic acid (DNA), ribonucleic acid (RNA) etc. The attached biological molecules with the help of functional groups make it a promising candidate in research field of biotechnological and biomedical applications...
May 1, 2018: Materials Science & Engineering. C, Materials for Biological Applications
Rongrong Huang, Nongyue He, Zhiyang Li
DNA has emerged as a promising biomaterial for assembling a variety of nanostructures based on its programmable base pairing. It also has other remarkable properties including stability, prominent biocompatibility, and can easily be modified with functional groups for further applications. In the past few decades, researchers have established various design rules and assembly technologies to improve the stability and complexity of DNA nanostructures. The detection of cancer-associated biomarkers has significant importance in identifying patients with different clinical stages and also in developing adaptive therapeutic strategies...
March 6, 2018: Biosensors & Bioelectronics
Hang-Soo Park, Hyosung Kwon, Jewon Yu, Yeonju Bae, Jae-Yong Park, Kyung-Ah Choi, Yeonho Choi, Sunghoi Hong
Direct conversion is a powerful approach to safely generate mature neural lineages with potential for treatment of neurological disorders. Astrocytes play a crucial role in neuronal homeostasis and their dysfunctions contribute to several neurodegenerative diseases. Using a single-cell approach for precision, we describe here a robust method using optimized DNA amounts for the direct conversion of mouse fibroblasts to astrocytes. Controlled amount of the reprogramming factors Oct4, Sox2, Klf4 and cMyc was directly delivered into a single fibroblast cell...
March 6, 2018: Artificial Cells, Nanomedicine, and Biotechnology
Jonathan R Burns, Stefan Howorka
DNA nanopores are a recent class of bilayer-puncturing nanodevices that can help advance biosensing, synthetic biology, and nanofluidics. Here, we create archetypal lipid-anchored DNA nanopores and characterize them with a nanoprobe-based approach to gain essential information about their interactions with bilayers. The strategy determines the molecular accessibility of DNA pores with a nuclease and can thus distinguish between the nanopores' membrane-adhering and membrane-spanning states. The analysis reveals, for example, that pores interact with bilayers in two steps whereby fast initial membrane tethering is followed by slower reorientation to the puncturing state...
March 1, 2018: ACS Nano
Dekai Ye, Xiaolei Zuo, Chunhai Fan
Biosensors represent biomimetic analytical tools for addressing increasing needs in medical diagnosis, environmental monitoring, security, and biodefense. Nevertheless, widespread real-world applications of biosensors remain challenging due to limitations of performance, including sensitivity, specificity, speed, and reproducibility. In this review, we present a DNA nanotechnology-enabled interfacial engineering approach for improving the performance of biosensors. We first introduce the main challenges of the biosensing interfaces, especially under the context of controlling the DNA interfacial assembly...
February 28, 2018: Annual Review of Analytical Chemistry
Vladimir B Tsvetkov, Timofei S Zatsepin, Evgeny S Belyaev, Yury I Kostyukevich, George V Shpakovski, Victor V Podgorsky, Galina E Pozmogova, Anna M Varizhuk, Andrey V Aralov
Non-canonical DNA structures are widely used for regulation of gene expression, in DNA nanotechnology and for the development of new DNA-based sensors. I-motifs (iMs) are two intercalated parallel duplexes that are held together by hemiprotonated C-C base pairs. Previously, iMs were used as an accurate sensor for intracellular pH measurements. However, iM stability is moderate, which in turn limits its in vivo applications. Here, we report the rational design of a new substituted phenoxazine 2'-deoxynucleotide (i-clamp) for iM stabilization...
February 21, 2018: Nucleic Acids Research
Scott G Harroun, Carl Prévost-Tremblay, Dominic Lauzon, Arnaud Desrosiers, Xiaomeng Wang, Liliana Pedro, Alexis Vallée-Bélisle
DNA switches are ideally suited for numerous nanotechnological applications, and increasing efforts are being directed toward their engineering. In this review, we discuss how to engineer these switches starting from the selection of a specific DNA-based recognition element, to its adaptation and optimisation into a switch, with applications ranging from sensing to drug delivery, smart materials, molecular transporters, logic gates and others. We provide many examples showcasing their high programmability and recent advances towards their real life applications...
February 21, 2018: Nanoscale
Qinqin Hu, Hua Li, Lihua Wang, Hongzhou Gu, Chunhai Fan
Over the past decade, we have seen rapid advances in applying nanotechnology in biomedical areas including bioimaging, biodetection, and drug delivery. As an emerging field, DNA nanotechnology offers simple yet powerful design techniques for self-assembly of nanostructures with unique advantages and high potential in enhancing drug targeting and reducing drug toxicity. Various sequence programming and optimization approaches have been developed to design DNA nanostructures with precisely engineered, controllable size, shape, surface chemistry, and function...
February 21, 2018: Chemical Reviews
Ismail Ocsoy, Didar Tasdemir, Sumeyye Mazicioglu, Weihong Tan
The integration of nanotechnology in medicine has had a tremendous impact in the past few decades. The discovery of synthesis of nanomaterials (NMs) and their functions as versatile tools promoted various applications in nano-biotechnology and nanomedicine. Although the physical and chemical methods are still considered as commonly used methods, they introduce several drawbacks such as the use of toxic chemicals (solvent, reducing, and capping agents) and poor control of size, size distribution, and morphology, respectively...
February 21, 2018: Advances in Biochemical Engineering/biotechnology
Nayan P Agarwal, Michael Matthies, Bastian Joffroy, Thorsten L Schmidt
The programmability of DNA enables constructing nanostructures with almost any arbitrary shape, which can be decorated with many functional materials. Moreover, dynamic structures can be realized such as molecular motors and walkers. In this work, we have explored the possibility to synthesize the complementary sequences to single-stranded gap regions in the DNA origami scaffold cost effectively by a DNA polymerase rather than by a DNA synthesizer. For this purpose, four different wireframe DNA origami structures were designed to have single-stranded gap regions...
February 16, 2018: ACS Nano
Weiyu Ning, Zhenghan Di, Yingjie Yu, Pingmei Zeng, Chunzhi Di, Daquan Chen, Xueqian Kong, Guangjun Nie, Yuliang Zhao, Lele Li
Surface functionality is an essential component for processing and application of metal-organic frameworks (MOFs). A simple and cost-effective strategy for DNA-mediated surface engineering of zirconium-based nanoscale MOFs (NMOFs) is presented, capable of endowing them with specific molecular recognition properties and thus expanding their potential for applications in nanotechnology and biotechnology. It is shown that efficient immobilization of functional DNA on NMOFs can be achieved via surface coordination chemistry...
February 16, 2018: Small
Dan Wu, Ya-Ting Wang, Wei-Hai Fang, Ganglong Cui, Walter Thiel
The photoresponsive azobenzene-tethered DNAs have received growing experimental attention because of their potential applications in biotechnology and nanotechnology; however, little is known about the initial photoisomerization of azobenzene in these systems. Herein we have employed quantum mechanics/molecular mechanics (QM/MM) methods to explore the photoisomerization dynamics of an azobenzene-tethered DNA duplex. We find that in the S₁ state the trans-cis photoisomerization path is much steeper in DNA than in vacuo, which makes the photoisomerization much faster in the DNA environment...
February 15, 2018: Chemistry, An Asian Journal
Renu A Kowluru, Manish Mishra
Retinopathy remains as one of the most feared blinding complications of diabetes, and with the prevalence of this life-long disease escalating at an alarming rate, the incidence of retinopathy is also climbing. Although the cutting edge research has identified many molecular mechanisms associated with its development, the exact mechanism how diabetes damages the retina remains obscure, limiting therapeutic options for this devastating disease. Areas covered: This review focuses on the central role of mitochondrial dysfunction/damage in the pathogenesis of diabetic retinopathy, and how damaged mitochondria initiates a self-perpetuating vicious cycles of free radicals...
February 13, 2018: Expert Opinion on Therapeutic Targets
Elisa Alina Hemmig, Clare Fitzgerald, Christopher Maffeo, Lisa Hecker, Sarah Elisabeth Ochmann, Aleksei Aksimentiev, Philip Tinnefeld, Ulrich F Keyser
We explore the potential of DNA nanotechnology for developing novel optical voltage sensing nano-devices that convert a local change of electric potential into optical signals. As a proof-of-concept of the sensing mechanism, we assembled voltage responsive DNA origami structures labelled with a single pair of FRET dyes. The DNA structures were reversibly immobilised on a nanocapillary tip and underwent controlled structural changes upon application of an electric field. The applied field was monitored through a change in FRET efficiency...
February 12, 2018: Nano Letters
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
Samaresh Sau, Hashem O Alsaab, Ketki Bhise, Rami Alzhrani, Ghazal Nabil, Arun K Iyer
Several cancer immunotherapy approaches have been recently introduced into the clinics and they have shown remarkable therapeutic potentials. The groundbreaking cancer immunotherapeutic agents function as a stimulant or modulator of the body immune system to fight against or kill cancers. Although targeted immunotherapies such as immune check point inhibitors (CTLA-4 or PD-1/PD-L1), DNA vaccination and CAR-T therapy are revolutionizing cancer treatment, the delivery efficacy can be further improved while their off-target toxicity can be mitigated through nanotechnology approaches...
January 29, 2018: Journal of Controlled Release: Official Journal of the Controlled Release Society
Yan Wen, Yingze Wang, Xiaoli Liu, Wei Zhang, Xinhe Xiong, Zhongxiao Han, Xingjie Liang
The drug camptothecin has a wide range of antitumor effects in cancers including gastric cancer, rectal and colon cancer, liver cancer, and lung cancer. Camptothecin-based drugs inhibit topoisomerase 1 (Topo 1), leading to destruction of DNA, and are currently being used as important chemotherapeutic agents in clinical antitumor treatment. However, the main obstacle associated with cancer therapy is represented by systemic toxicity of conventional anticancer drugs and their low accumulation at the tumor site...
November 2017: Cancer Biology & Medicine
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