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DNA nanotechnology

Ze Shi, Carlos E Castro, Gaurav Arya
Structural DNA nanotechnology, the assembly of rigid 3D structures of complex yet precise geometries, has recently been used to design dynamic, mechanically-compliant nanostructures with tunable equilibrium conformations and conformational distributions. Here we use coarse-grained molecular dynamics simulations to provide in- sights into the conformational dynamics of a set of mechanically compliant DNA nanostructures-DNA hinges that use single-stranded DNA "springs" to tune the equilibrium conformation of a layered double-stranded DNA "joint" connecting two stiff "arms" constructed from DNA helix bundles...
April 19, 2017: ACS Nano
Larissa Kotelevets, Eric Chastre, Joachim Caron, Julie Mougin, Gerard Bastian, Alain Pineau, Francine Walker, Therese Lehy, Didier Desmaele, Patrick Couvreur
Nanotechnology offers many possibilities to improve drug treatments, including with regard to drug pharmacology. The current study reports a simple approach to improve cisplatin efficacy in the treatment of colon cancer through the creation of orally administered squalenoylated nanoparticles loaded with cisplatin (SQ-CDDP NP). Cytotoxic effects of SQ-CDDP NP were assessed in human colonic cells and in mouse models of intestinal cancer. In cell culture, SQ-CDDP NP exhibited at least 10-fold greater cytotoxic potency compared to uncomplexed cisplatin, reflecting an enhancement in intracellular accumulation and DNA platination...
April 17, 2017: Cancer Research
Jerzy W Kozyra, Alessandro Ceccarelli, Emanuela Torelli, Annunziata Lopiccolo, Jing-Ying Gu, Harold Fellermann, Ulrich Stimming, Natalio Krasnogor
Nanotechnology and synthetic biology are rapidly converging, with DNA origami being one of the leading bridging technologies. DNA origami was shown to work well in a wide array of biotic environments. However, the large majority of extant DNA origami scaffolds utilize bacteriophages or plasmid sequences thus severely limiting its future applicability as bio-orthogonal nanotechnology platform. In this paper we present the design of biologically inert (i.e. "bio-orthogonal") origami scaffolds. The synthetic scaffolds have the additional advantage of being uniquely addressable (unlike biologically derived ones) and hence are better optimised for high-yield folding...
April 17, 2017: ACS Synthetic Biology
Toma E Tomov, Roman Tsukanov, Yair Glick, Yaron Berger, Miran Liber, Dorit Avrahami, Doron Gerber, Eyal Nir
Realization of bioinspired molecular machines that can perform many and diverse operations in response to external chemical commands is a major goal in nanotechnology, but current molecular machines respond to only a few sequential commands. Lack of effective methods for introduction and removal of command compounds and low efficiencies of the reactions involved are major reasons for the limited performance. We introduce here a user interface based on a microfluidics device and single-molecule fluorescence spectroscopy that allows efficient introduction and removal of chemical commands and enables detailed study of the reaction mechanisms involved in the operation of synthetic molecular machines...
April 14, 2017: ACS Nano
Srinivas Chinde, Naresh Dumala, Mohammed Fazlur Rahman, Sarika Srinivas Kalyan Kamal, Srinivas Indu Kumari, Mohammed Mahboob, Paramjit Grover
Advances in and the rapid growth of the nanotechnology sector have escalated manufacture of nanoparticles (NPs), resulting in a significant increase in the probability of exposure of humans and wildlife to these materials. Many NPs have been found to exert genotoxicity. Therefore, genotoxicity studies are mandatory to assess the toxicity of NPs as a concern of succumbing to genetic diseases and cancers are universal. Tungsten oxide (WO3) NPs are being explored extensively in various fields. However, the toxicological data of WO3 NPs by oral route in mammals is limited...
April 8, 2017: Environmental Science and Pollution Research International
Shuzhen Yue, Tingting Zhao, Hongjie Qi, Yongcun Yan, Sai Bi
A toehold-mediated strand displacement (TMSD)-based cross-catalytic hairpin assembly (C-CHA) is demonstrated in this study, achieving exponential amplification of nucleic acids. Functionally, this system consists of four hairpins (H1, H2, H3 and H4) and one single-stranded initiator (I). Upon the introduction of I, the first CHA reaction (CHA1) is triggered, leading to the self-assembly of hybrid H1·H2 that then initiates the second CHA reaction (CHA2) to obtain the hybrid H3·H4. Since the single-stranded region in H3·H4 is identical to I, a new CHA1 is initiated, which thus achieves cross operation of CHA1 and CHA2 and exponential growth kinetics...
April 4, 2017: Biosensors & Bioelectronics
Zhaolu Xie, Xianghui Zeng
To develop a successful formulation for the gene therapy of breast cancer, an effective therapeutic nucleic acid and proper delivery system are essential. Increased understanding of breast cancer, and developments in biotechnology, material science and nanotechnology have provided a major impetus in the development of effective formulations for the gene therapy of breast cancer. Areas covered: We discuss DNA/RNA-based formulations that can inhibit the growth of breast cancer cells and control the progress of breast cancer...
April 7, 2017: Expert Opinion on Drug Delivery
Jae Hyeop Lee, Sook Hee Ku, Min Ju Kim, So Jin Lee, Hyun Cheol Kim, Kwangmeyung Kim, Sun Hwa Kim, Ick Chan Kwon
RNA, one of the major biological macromolecules, has been considered as an attractive building material for bottom-up fabrication of nanostructures in the past few decades due to advancements in RNA biology, RNA chemistry and RNA nanotechnology. Most recently, an isothermal enzymatic nucleic acid amplification method termed rolling circle transcription (RCT), which achieves a large-scale synthesis of RNA nanostructures, has emerged as one of fascinating techniques for RNAi-based therapies. Herein, we proposed a newly designed RCT method for synthesis of polymeric siRNA nanoflower, referred to 'RCT and annealing-generated polymeric siRNA (RAPSI)': (1) Amplification of the antisense strand of siRNA via RCT process and (2) annealing of chimeric sense strand containing 3'-terminal DNA nucleotides that provide enzyme cleavage sites...
March 31, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
Gueven Edgue, Richard M Twyman, Veronique Beiss, Rainer Fischer, Markus Sack
Antibodies are produced as part of the vertebrate adaptive immune response and are not naturally made by plants. However, antibody DNA sequences can be introduced into plants, and together with laboratory technologies that allow the design of antibodies recognizing any conceivable molecular structure, plants can be used as 'green factories' to produce any antibody at all. The advent of plant-based transient expression systems in particular allows the rapid, convenient, and safe production of antibodies, ranging from laboratory-scale expression to industrial-scale manufacturing...
March 27, 2017: Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology
Jose Antonio Garrido-Cardenas, Federico Garcia-Maroto, Jose Antonio Alvarez-Bermejo, Francisco Manzano-Agugliaro
The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger...
March 14, 2017: Sensors
Donglei Yang, Zhenyu Tan, Yongli Mi, Bryan Wei
Earlier studies in DNA self-assembly have foretold the feasibility of building addressable nanostructures with multi-stranded motifs, which is fully validated in this study. In realizing this feasibility in DNA nanotechnology, a diversified set of motifs of modified domain lengths is extended from a classic type. The length of sticky ends can be adjusted to form different dihedral angles between the matching motifs, which corresponds to different connecting patterns. Moreover, the length of rigidity core can also be tuned to result in different dihedral angles between the component helices of a certain motif therefore different numbers of component helices...
April 7, 2017: Nucleic Acids Research
Rainer Joachim Schwarz, Clemens Richert
Designed DNA nanostructures of impressive size have been described, but designed structures of the size of protein enzymes that bind organic ligands with high specificity are rare. Here we report a four-helix motif consisting of three synthetic strands with 65 base pairs and 165 nucleotides in total that folds well. Furthermore, we show that in the interior of this small folded DNA nanostructure, cavities can be set up that bind pyrimidine nucleotides with micromolar affinity. Base-specific binding for both thymidine and cytidine derivatives is demonstrated...
March 22, 2017: Nanoscale
E-C Schöneweiß, B Saccà
Dynamic DNA nanotechnology relies on the integration of small switchable motifs at suitable positions of DNA nanostructures, thus enabling the manipulation of matter with nanometer spatial accuracy in a trigger-dependent fashion. Typical examples of such motifs are hairpins, whose elongation into duplexes can be used to perform long-range, translational movements. In this work, we used temperature-dependent FRET spectroscopy to determine the thermal stabilities of distinct sets of hairpins integrated into the central seam of a DNA origami structure...
March 20, 2017: Nanoscale
Shine K Albert, Hari Veera Prasad Thelu, Murali Golla, Nithiyanandan Krishnan, Reji Varghese
DNA nanostructures have found potential applications in various fields including nanotechnology, materials science and nanomedicine, hence the design and synthesis of DNA nanostructures is extremely important. Self-assembly of DNA amphiphiles provides an efficient strategy for the crafting of soft DNA nanostructures. However, the synthesis of DNA amphiphiles is always challenging. Herein, we show a non-covalent approach based on the host-guest interaction between β-CD and adamantane for the synthesis of DNA amphiphiles, and report their amphiphilicity-driven self-assembly into DNA decorated vesicles...
March 16, 2017: Nanoscale
Nayan P Agarwal, Michael Matthies, Fatih N Gür, Kensuke Osada, Thorsten L Schmidt
DNA nanotechnology enables the synthesis of nanometer-sized objects that can be site-specifically functionalized with a large variety of materials. For these reasons, DNA-based devices such as DNA origami are being considered for applications in molecular biology and nanomedicine. However, many DNA structures need a higher ionic strength than that of common cell culture buffers or bodily fluids to maintain their integrity and can be degraded quickly by nucleases. To overcome these deficiencies, we coated several different DNA origami structures with a cationic poly(ethylene glycol)-polylysine block copolymer, which electrostatically covered the DNA nanostructures to form DNA origami polyplex micelles (DOPMs)...
March 15, 2017: Angewandte Chemie
Aaron M Fleming, Yun Ding, R Aaron Rogers, Judy Zhu, Julia Zhu, Ashlee D Burton, Connor B Carlisle, Cynthia J Burrows
Strands of DNA with four or more contiguous runs of 2'-deoxycytidine (dC) nucleotides have the potential to adopt i-motif folds, generally under mildly acidic conditions. Analysis of dC homo-oligonucleotide strands ranging in length from 10 to 30 nucleotides by five different pH-dependent methods identified a pattern in strand length vs stability. Beginning with dC11, which does not fold, the transition pH (pHT) increased with chain length with the addition of up to four nucleotides, after which the stability dramatically decreased, and the trend repeated this cycle up to dC27...
March 21, 2017: Journal of the American Chemical Society
Jashmini Deka, Aditya Mojumdar, Pietro Parisse, Silvia Onesti, Loredana Casalis
Helicase are essential enzymes which are widespread in all life-forms. Due to their central role in nucleic acid metabolism, they are emerging as important targets for anti-viral, antibacterial and anti-cancer drugs. The development of easy, cheap, fast and robust biochemical assays to measure helicase activity, overcoming the limitations of the current methods, is a pre-requisite for the discovery of helicase inhibitors through high-throughput screenings. We have developed a method which exploits the optical properties of DNA-conjugated gold nanoparticles (AuNP) and meets the required criteria...
March 13, 2017: Scientific Reports
Dimitra Milioni, Achilleas Tsortos, Marisela Velez, Electra Gizeli
The ability to derive information on the conformation of surface attached biomolecules by using simple techniques such as biosensors is currently considered of great importance in the fields of surface science and nanotechnology. Here we present a nanoshape sensitive biosensor where a simple mathematical expression is used to relate acoustic measurements to the geometrical features of a surface-attached biomolecule. The underlying scientific principle is that the acoustic ratio (ΔD/ΔF) is a measure of the hydrodynamic volume of the attached entity, mathematically expressed by its intrinsic viscosity [η]...
March 22, 2017: Analytical Chemistry
Guang Hu, Lei He, Federico Iacovelli, Mattia Falconi
DNA is a fundamental component of living systems where it plays a crucial role at both functional and structural level. The programmable properties of DNA make it an interesting building block for the construction of nanostructures. However, molecular mechanisms for the arrangement of these well-defined DNA assemblies are not fully understood. In this paper, the intrinsic dynamics of a DNA octahedron has been investigated by using two types of Elastic Network Models (ENMs). The application of ENMs to DNA nanocages include the analysis of the intrinsic flexibilities of DNA double-helices and hinge sites through the calculation of the square fluctuations, as well as the intrinsic collective dynamics in terms of cross-collective map calculation coupled with global motions analysis...
January 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Anastasia Mickhailovna Korotkova, Svyatoslav Valeryevich Lebedev, Irina Aleksandrovna Gavrish
The rapid development of nanotechnology raises questions assessment of their impact on living objects. In the present study, we evaluated the impact of nanoparticle (NP) CuO at concentrations ranging from 0.8 to 63.5 g/l in the test on wheat seedlings Triticum vulgare during 1-72 h. In the viability test (WST-test), cells were isolated from the roots of seedlings T. vulgare, 12 h not observed increase reductase activity after 24 h decreased rate of not more than 19% compared with the control. The number of dead cells in seedlings of T...
March 6, 2017: Environmental Science and Pollution Research International
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