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https://www.readbyqxmd.com/read/27903819/towards-designing-new-nano-scale-protein-architectures
#1
REVIEW
Jana Aupič, Fabio Lapenta, Žiga Strmšek, Roman Jerala
The complexity of designed bionano-scale architectures is rapidly increasing mainly due to the expanding field of DNA-origami technology and accurate protein design approaches. The major advantage offered by polypeptide nanostructures compared with most other polymers resides in their highly programmable complexity. Proteins allow in vivo formation of well-defined structures with a precise spatial arrangement of functional groups, providing extremely versatile nano-scale scaffolds. Extending beyond existing proteins that perform a wide range of functions in biological systems, it became possible in the last few decades to engineer and predict properties of completely novel protein folds, opening the field of protein nanostructure design...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27893729/programmable-disorder-in-random-dna-tilings
#2
Grigory Tikhomirov, Philip Petersen, Lulu Qian
Scaling up the complexity and diversity of synthetic molecular structures will require strategies that exploit the inherent stochasticity of molecular systems in a controlled fashion. Here we demonstrate a framework for programming random DNA tilings and show how to control the properties of global patterns through simple, local rules. We constructed three general forms of planar network-random loops, mazes and trees-on the surface of self-assembled DNA origami arrays on the micrometre scale with nanometre resolution...
November 28, 2016: Nature Nanotechnology
https://www.readbyqxmd.com/read/27892718/the-utility-of-dna-nanostructures-for-drug-delivery-in-vivo
#3
Anders H Okholm, Jørgen Kjems
No abstract text is available yet for this article.
November 28, 2016: Expert Opinion on Drug Delivery
https://www.readbyqxmd.com/read/27890616/cerium-chloride-stimulated-controlled-conversion-of-b-to-z-dna-in-self-assembled-nanostructures
#4
Madhabi M Bhanjadeo, Ashok K Nayak, Umakanta Subudhi
DNA adopts different conformation not only because of novel base pairs but also while interacting with inorganic or organic compounds. Dynamic origami or self-assembled branched DNA (bDNA) structures that change conformation in response to environmental cues hold great promises in sensing and actuation at the nanoscale. Recently, the B-Z transition in DNA is being explored to design various nanomechanical devices. In this communication we have demonstrated that Cerium chloride binds to the phosphate backbone of self-assembled bDNA structure and induce B-to-Z transition at physiological concentration...
November 24, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27875979/self-assembled-nucleic-acid-nanostructures-for-cancer-theranostic-medicines
#5
Jinglin Fu, Gabriele Stankeviciute, Sung Won Oh, John Collins, Yinghui Zhong, Ting Zhang
Theranostic medicine has become more promising in cancer treatment, where the cancer diagnosis and chemotherapy are combined for early diagnosis and precise treatment with improved efficacy and reduced side effects. Nanotechnology has played a critical role in developing various nanomaterials with engendered smart functions and targeted delivery. The rapid development of structural DNA nanotechnology has enabled the design and fabrication of complex nanostructures with prescribed 1D, 2D and 3D patterns in vitro and in vivo...
November 22, 2016: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/27875975/self-assembly-of-dna-based-nanomaterials-and-potential-application-in-drug-delivery
#6
Zhiyong Zhao, Feng Liang, Simin Liu
DNA molecules can be self-assembled into programmable two-dimensional and three-dimensional nanostructures with arbitrarily predetermined sizes and shapes. Because of the addressable arbitrary size and shape, high capacity of cargo loading, ability to be internalized by cells, structural stability in physiological conditions and excellent biocompatibility, the pristine DNA nanostructures are explored as drug vehicles in drug delivery. In addition, DNA block copolymer and DNA-Dendron hybrid, as new building blocks, can be self-assembled into various ordered structures in aqueous solution, e...
November 22, 2016: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/27869278/cellular-delivery-of-enzyme-loaded-dna-origami
#7
Ari Ora, Erika Järvihaavisto, Hongbo Zhang, Henni Auvinen, Hélder A Santos, Mauri A Kostiainen, Veikko Linko
In this communication, we show that active enzymes can be delivered into HEK293 cells in vitro when they are attached to tubular DNA origami nanostructures. We use bioluminescent enzymes as a cargo and monitor their activity from a cell lysate. The results show that the enzymes stay intact and retain their activity in the transfection process. The method is highly modular, which makes it a compelling candidate for a great variety of delivery applications.
December 1, 2016: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/27866079/multimodal-plasmonic-biosensing-nanostructures-prepared-by-dna-directed-immobilization-of-multifunctional-dna-gold-nanoparticles
#8
Nuria Tort, J-Pablo Salvador, M-Pilar Marco
Biofunctional multimodal plasmonic nanostructures suitable for multiplexed localized surface plasmon resonance (LSPR) biosensing have been created by DNA-directed immobilization (DDI) of two distinct multifunctional biohybrid gold nanoparticles. Gold nanoparticles (AuNP) of distinct sizes, and therefore showing distinct plasmon resonant peaks (RP), have been biofunctionalized and codified with two different single stranded-DNA (ssDNA) chains. One of these oligonucleotide chains has been specifically designed to direct each AuNP to a distinct location of the surface of a DNA microarray chip through specific hybridization with complementary oligonucleotide strands...
November 11, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27856755/controlling-dna-nanoparticle-serum-interactions
#9
Kyryl Zagorovsky, Leo Y T Chou, Warren C W Chan
Understanding the interaction of molecularly assembled nanoparticles with physiological fluids is critical to their use for in vivo delivery of drugs and contrast agents. Here, we systematically investigated the factors and mechanisms that govern the degradation of DNA on the nanoparticle surface in serum. We discovered that a higher DNA density, shorter oligonucleotides, and thicker PEG layer increased protection of DNA against serum degradation. Oligonucleotides on the surface of nanoparticles were highly resistant to DNase I endonucleases, and degradation was carried out exclusively by protein-mediated exonuclease cleavage and full-strand desorption...
November 16, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27853820/antiparallel-d-stable-traces-and-a-stronger-version-of-ore-problem
#10
Jernej Rus
In 2013 a novel self-assembly strategy for polypeptide nanostructure design which could lead to significant developments in biotechnology was presented in Gradišar et al. (Nat Chem Bio 9:362-366, 2013). It was since observed that a polyhedron P can be realized by interlocking pairs of polypeptide chains if its corresponding graph G(P) admits a strong trace. It was since also demonstrated that a similar strategy can also be expanded to self-assembly of designed DNA (Kočar, Nat commun 7:1-8, 2016). In this direction, in the present paper we characterize graphs which admit closed walk which traverses every edge exactly once in each direction and for every vertex v, there is no subset N of its neighbors, with [Formula: see text], such that every time the walk enters v from N, it also exits to a vertex in N...
November 16, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27825888/sdr-elisa-ultrasensitive-and-high-throughput-nucleic-acid-detection-based-on-antibody-like-dna-nanostructure
#11
Junlin Wen, Junhua Chen, Li Zhuang, Shungui Zhou
An ultrasensitive and high-throughput nucleic acid detection system, termed as strand displacement reaction-enzyme linked immunosorbent assay (SDR-ELISA), has been developed on the basis of antibody-like DNA nanostructures. Three digoxigenin or biotin modified hairpin probes are utilized to construct antibody-like DNA nanostructures that feature affinity toward streptavidin and anti-digoxigenin antibody via isothermal target-triggered SDR amplification. These antibody-like nanostructures have been employed to conjugate horseradish-peroxidase-labeled anti-digoxigenin antibody with streptavidin that is immobilized on microliter plate wells for enzyme-linked colorimetric assay...
November 2, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27823668/a-label-free-ultrasensitive-assay-of-8-hydroxy-2-deoxyguanosine-in-human-serum-and-urine-samples-via-polyaniline-deposition-and-tetrahedral-dna-nanostructure
#12
Jiahui Fan, Yuanjian Liu, Ensheng Xu, Yuanjian Zhang, Wei Wei, Lihong Yin, Yuepu Pu, Songqin Liu
Oxidative damage is an important factor in causing various human disease and injury. As an oxidative DNA damage product, 8-hydroxy-2'-deoxyguanosine (8-OHdG) is a key marker, which is widely used to study oxidative damage mechanism in diseases. Most reported electrochemical methods were based on oxidation current of 8-OHdG. In this work, a simple electrochemical biosensor for ultrasensitive detection of 8-OHdG was proposed based on it triggered polyaniline (PANI) deposition on tetrahedral DNA nanostructure (TDN)...
November 23, 2016: Analytica Chimica Acta
https://www.readbyqxmd.com/read/27816585/a-rapid-and-visual-aptasensor-for-lipopolysaccharides-detection-based-on-the-bulb-like-triplex-turn-on-switch-coupled-with-hcr-hrp-nanostructures
#13
Wentao Xu, Jingjing Tian, Xiangli Shao, Longjiao Zhu, Kunlun Huang, Yunbo Luo
For previously reported aptasensor, the sensitivity and selectivity of aptamers to targets were often suppressed due to the reporter label of single-stranded molecular beacon or hindrance of the duplex DNA strand displacement. To solve the affinity declining of aptamers showed in traditional way and realize on-site rapid detection of Lipopolysaccharides (LPS), we developed an ingenious structure-switching aptasensor based on the bulb-like triplex turn-on switch (BTTS) as the effective molecular recognition and signal transduction element and streptavidin-horseradish peroxidase modified hybridization chain reaction (HCR-HRP) nanocomposites as the signal amplifier and signal report element...
October 5, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27813013/dna-directed-self-assembly-of-highly-ordered-and-dense-single-walled-carbon-nanotube-arrays
#14
Hareem Maune, Si-Ping Han
Single-walled carbon nanotubes (SWNT or CNT) have unique and well-known high-performance material properties that can enable revolutionary increases in the performance of electronic devices and architectures. However, fabrication of large-scale SWNT-based ICs is an enormously challenging, unsolved problem, and self-assembly is likely needed for critical steps. Over the past several years, methods have been introduced to created ordered carbon nanotube structures using DNA guided self-assembly. In this chapter, we briefly review the challenges involved in using DNA to assemble SWNT nanostructures, and then give detailed methods to assemble dense, aligned SWNT arrays...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27813011/direct-nanofabrication-using-dna-nanostructure
#15
Feng Zhou, Haitao Liu
Recent advances in DNA nanotechnology make it possible to fabricate arbitrarily shaped 1D, 2D, and 3D DNA nanostructures through controlled folding and/or hierarchical assembly of up to several thousands of unique sequenced DNA strands. Both individual DNA nanostructures and their assembly can be made with almost arbitrarily shaped patterns at a theoretical resolution down to 2 nm. Furthermore, the deposition of DNA nanostructures on a substrate can be made with precise control of their location and orientation, making them ideal templates for bottom-up nanofabrication...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27813009/dna-paint-super-resolution-imaging-for-nucleic-acid-nanostructures
#16
Mingjie Dai
Far-field super-resolution fluorescence microscopy has allowed observation of biomolecular and synthetic nanoscale systems with features on the nanometre scale, with chemical specificity and multiplexing capability. DNA-PAINT (DNA-based point accumulation for imaging in nanoscale topography) is a super-resolution method that exploits programmable transient hybridization between short oligonucleotide strands, and allows multiplexed, single-molecule, single-label visualization with down to ~5-10 nm resolution...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27813008/lipid-membrane-encapsulation-of-a-3d-dna-nano-octahedron
#17
Steven D Perrault, William M Shih
Structural DNA nanotechnology methods such as DNA origami allow for the synthesis of highly precise nanometer-scale materials (Rothemund, Nature 440:297-302, 2006; Douglas et al., Nature 459:414-418, 2009). These offer compelling advantages for biomedical applications. Such materials can suffer from structural instability in biological environments due to denaturation and nuclease digestion (Hahn et al., ACS Nano 2014; Perrault and Shih, ACS Nano 8:5132-5140, 2014). Encapsulation of DNA nanostructures in a lipid membrane compartmentalizes them from their environment and prevents denaturation and nuclease digestion (Perrault and Shih, ACS Nano 8:5132-5140, 2014)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27813007/spatial-organization-of-enzyme-cascade-on-a-dna-origami-nanostructure
#18
Jinglin Fu, Tianran Li
Self-assembled DNA nanostructures hold great promise to organize multi-enzyme systems with the precise control of the geometric arrangements. Enzymes modified with single-stranded DNA anchors are assembled onto the DNA origami tiles by hybridizing with the corresponding complementary strands displayed on the surface of the DNA nanostructures. Here, we describe a protocol of assembling a two-enzyme cascade on a discrete, rectangular DNA origami tile, where the distance between enzymes is precisely controlled for investigating the distance-dependent cascade activities...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27813006/dna-g-quadruplex-based-assay-of-enzyme-activity
#19
Zhuoliang Liu, Kaiyu He, Wang Li, Xin Liu, Xiahong Xu, Zhou Nie, Shouzhuo Yao
DNA G-quadruplexes are special three-dimensional (3D) DNA nanostructures formed by specific G-rich DNA sequences. These 3D DNA nanostructures can bind with hemin and significantly improve the intrinsic peroxidase activity of hemin. Besides this function, they also enhance the fluorescence intensity of some G-quadruplex-specific dyes. Owing to these features, G-quadruplexes possess several superiorities in the detection of enzymes involved in nucleic acid metabolism, including facile probe fabrication without labeling, simple detection process without washing or separation steps, rapid observation by naked eyes, and easy integration with nucleic acid amplification strategies to amplify signals...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27813005/dna-nanostructure-as-smart-carriers-for-drug-delivery
#20
Xiangyuan Ouyang, Jie Chao, Shao Su, Chunhai Fan
Self-assembled DNA nanostructures have recently emerged as a type of drug delivery carriers due to their suitable sizes, well-defined nanoscale shapes, precise spatial addressability, and excellent biocompatibility. Here, we describe practical procedures in detail for the design and construction of DNA nanostructures with different width and patterns by long rolling circle amplification (RCA) strands and a few short staples, and provide practical guidance and troubleshooting advice for delivering CpG immunostimulatory drugs with these RCA based DNA nanostructures...
2017: Methods in Molecular Biology
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