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DNA nanotechnology

Rebekah J Karadeema, Maria Stancescu, Tyler P Steidl, Sophia C Bertot, Dmitry M Kolpashchikov
Analysis of single nucleotide variations (SNVs) in DNA and RNA sequences is instrumental in healthcare for the detection of genetic and infectious diseases and drug-resistant pathogens. Here we took advantage of the developments in DNA nanotechnology to design a hybridization sensor, named the 'owl sensor', which produces a fluorescence signal only when it complexes with fully complementary DNA or RNA analytes. The novelty of the owl sensor operation is that the selectivity of analyte recognition is, at least in part, determined by the structural rigidity and stability of the entire DNA nanostructure rather than exclusively by the stability of the analyte-probe duplex, as is the case for conventional hybridization probes...
May 21, 2018: Nanoscale
Ilham F Osman, Mojgan Najafzadeh, Vyom Sharma, Ritesh K Shukla, B K Jacob, Alok Dhawan, D Anderson
Little is known of the effects of nanoparticles in human systems, let alone in diseased individuals and nanotechnology has preceded nanotoxicology. Therefore, the effects of titanium dioxide (TiO2) nanoparticles in peripheral blood lymphocytes from patients with respiratory diseases [lung cancer, chronic obstructive pulmonary disease (COPD) and asthma] were compared with those in healthy Individuals, to determine differences in sensitivity to nanochemical insult. The Comet assay was performed according to recommended guidelines...
January 1, 2018: Journal of Nanoscience and Nanotechnology
A T Saber, A Mortensen, J Szarek, N R Jacobsen, M Levin, I K Koponen, K A Jensen, U Vogel, H Wallin
Little is known on the toxicity of nanomaterials in the user phase. Inclusion of nanomaterials in paints is a common nanotechnology application. This study focuses on the toxicity of dusts from sanding of paints containing nanomaterials. We compared the toxicity of titanium dioxide nanomaterials (TiO2 NMs) and dusts generated by sanding boards coated with paints with different amounts of two different types of uncoated TiO2 NMs (diameters:10.5 nm and 38 nm). Mice were intratracheally instilled with a single dose of 18, 54 and 162 µg of TiO2 NMs or 54, 162 and 486 µg of sanding dusts...
January 1, 2018: Human & Experimental Toxicology
Denis Selnihhin, Steffen Møller Sparvath, Søren Preus, Victoria Birkedal, Ebbe Sloth Andersen
Biosensors play increasingly important roles in many fields, from clinical diagnosis to environmental monitoring, and there is a growing need for cheap and simple analytical devices. DNA nanotechnology provides methods for the creation of sophisticated biosensors, however many of the developed DNA-based sensors are limited by cumbersome and time-consuming readouts involving advanced experimental techniques. Here we describe design, construction and characterization of an optical DNA origami nano-biosensor device exploiting arrays of precisely positioned organic fluorophores...
May 15, 2018: ACS Nano
Allan Radaic, Marcelo B de Jesus
Nanotechnology can produce materials with unique features compared to the bulk counterparts, which can be useful for medical applications (i.e., nanomedicine). Among the therapeutic agents used in nanomedicine, small molecules or biomacromolecules, such as proteins or genetic materials, can be designed for disease diagnostics and treatment. To transport these biomacromolecules to the target cells, nanomedicine requires nanocarriers. Solid lipid nanoparticles (SLNs) are one of the promising nanocarriers available, because they can be made of biocompatible materials and present high stability (over one year)...
May 14, 2018: Nanotechnology
Maartje Bastings, Frances Anastassacos, Nandhini Ponnuswamy, Franziska Leifer, Garry Cuneo, Chenxiang Lin, Donald E Ingber, Ju Hee Ryu, William M Shih
Designer nanoparticles with controlled shape and size are increasingly popular vehicles for therapeutic delivery due to their enhanced cell delivery performance. However, our ability to fashion nanoparticles has offered only limited control over these parameters. Structural DNA nanotechnology has an unparalleled ability to self-assemble three-dimensional nanostructures with near-atomic resolution features and thus, it offers an attractive platform for systematic exploration of the parameter space relevant to nanoparticle uptake by living cells...
May 14, 2018: Nano Letters
Pongphak Chidchob, Hanadi F Sleiman
DNA is a powerful guiding molecule to achieve the precise construction of arbitrary structures and high-resolution organization of functional materials. The combination of sequence programmability, rigidity and highly specific molecular recognition in this molecule has resulted in a wide range of exquisitely designed DNA frameworks. To date, the impressive potential of DNA nanomaterials has been demonstrated from fundamental research to technological advancements in materials science and biomedicine. This review presents a summary of some of the most recent developments in structural DNA nanotechnology regarding new assembly approaches and efforts in translating DNA nanomaterials into practical use...
May 8, 2018: Current Opinion in Chemical Biology
Jieming Li, Alexander Johnson-Buck, Yuhe Renee Yang, William M Shih, Hao Yan, Nils G Walter
Dynamic DNA nanotechnology has yielded nontrivial autonomous behaviours such as stimulus-guided locomotion, computation and programmable molecular assembly. Despite these successes, DNA-based nanomachines suffer from slow kinetics, requiring several minutes or longer to carry out a handful of operations. Here, we pursue the speed limit of an important class of reactions in DNA nanotechnology-toehold exchange-through the single-molecule optimization of a novel class of DNA walker that undergoes cartwheeling movements over a field of complementary oligonucleotides...
May 7, 2018: Nature Nanotechnology
Jun Yao, Pingfan Li, Lin Li, Mei Yang
According to recent research, nanotechnology based on quantum dots (QDs) has been widely applied in the field of bioimaging, drug delivery, and drug analysis. Therefore, it has become one of the major forces driving basic and applied research. The application of nanotechnology in bioimaging has been of concern. Through in vitro labeling, it was found that luminescent QDs possess many properties such as narrow emission, broad UV excitation, bright fluorescence, and high photostability. The QDs also show great potential in whole-body imaging...
May 4, 2018: Acta Biomaterialia
Erik E Augspurger, Muhit Rana, Mehmet Veysel Yigit
Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. DNA-based technologies' recent prominence in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions and solvent types...
May 7, 2018: ACS Sensors
Xun Zhang, Fei Wang, Jin-Liang Sheng, Min-Xuan Sun
DNA-functionalized nanoparticle (DfNP) technology, the integration of DNA with nanotechnology, has emerged over recent decades as a promising biofunctionalization tool in the light of biotechnological approaches. The development of DfNPs has exhibited significant potential for several biological and biomedical applications. In this review, we focus on the mechanism of a series of DNA-NP nanocomposites and highlight the superstructures of DNA-based NPs. We also summarize its applications of these nanocomposites in cell imaging, cancer therapy and bioanalytical detection...
April 30, 2018: Current Medicinal Chemistry
Hisae Tateishi-Karimata, Naoki Sugimoto
Nucleic acids have emerged as powerful biological and nanotechnological tools. In biological and nanotechnological experiments, methods of extracting and purifying nucleic acids from various types of cells and their storage are critical for obtaining reproducible experimental results. In nanotechnological experiments, methods for regulating the conformational polymorphism of nucleic acids and increasing sequence selectivity for base pairing of nucleic acids are important for developing nucleic acid-based nanomaterials...
April 23, 2018: Biophysical Reviews
Kerstin Göpfrich, Ilia Platzman, Joachim P Spatz
With the ultimate aim to construct a living cell, bottom-up synthetic biology strives to reconstitute cellular phenomena in vitro - disentangled from the complex environment of a cell. Recent work towards this ambitious goal has provided new insights into the mechanisms governing life. With the fast-growing library of functional modules for synthetic cells, their classification and integration become increasingly important. We discuss strategies to reverse-engineer and recombine functional parts for synthetic eukaryotes, mimicking the characteristics of nature's own prototype...
April 21, 2018: Trends in Biotechnology
Hyunjae Cho, Sekhar Babu Mitta, Yongwoo Song, Junyoung Son, Suyoun Park, Tai Hwan Ha, Sung Ha Park
Although structural DNA nanotechnology is a well-established field, computations performed using DNA algorithmic self-assembly is still in the primitive stages in terms of its adaptability of rule implementation and experimental complexity. Here, we discuss the feasibility of constructing an M-input/N-output logic gate implemented into simple DNA building blocks. To date, no experimental demonstrations have been reported with M > 2 owing to the difficulty of tile design. To overcome this problem, we introduce a special tile referred to as an operator...
April 23, 2018: ACS Nano
Yongfei Li, Lei Song, Bang Wang, Jianbo He, Yulin Li, Zhaoxiang Deng, Chengde Mao
pH-responsivity has been widely pursued in dynamic DNA nanotechnology, due to its great potential in biosensing, controlled release and nanomachinery. Previously developed pH-triggering systems mostly depend on specific designs of DNA sequences. However, sequence-independent regulation could provide a more general tool to achieve pH-responsive DNA assembly, which has yet to be developed. Herein, we propose a mechanism for dynamic DNA assembly by utilizing ethylenediamine (EN) as a reversibly chargeable (via protonation) cation to overcome electrostatic repulsions...
April 23, 2018: Angewandte Chemie
Mustafa Salih Hizir, Nidhi Nandu, Mehmet Veysel Yigit
A novel combinatorial nanosensor array for miRNA analyses was assembled using the intrinsic non-covalent interactions of unmodified two-dimensional nanoparticles. Discrimination of nine miRNA analogs with as little as a single nucleotide difference was demonstrated under four hours. All nine targets were identified simultaneously with 95% confidence. The developed nanotechnology offered identification and quantification of unknown targets with unknown concentration. Discrimination of target mixtures from low-to-high ratios was demonstrated...
April 20, 2018: Analytical Chemistry
Ana-Maria Chiorcea-Paquim, Ramon Eritja, Ana Maria Oliveira-Brett
Guanine-rich DNA sequences are able to form G-quadruplexes, being involved in important biological processes and representing smart self-assembling nanomaterials that are increasingly used in DNA nanotechnology and biosensor technology. G-quadruplex electrochemical biosensors have received particular attention, since the electrochemical response is particularly sensitive to the DNA structural changes from single-stranded, double-stranded, or hairpin into a G-quadruplex configuration. Furthermore, the development of an increased number of G-quadruplex aptamers that combine the G-quadruplex stiffness and self-assembling versatility with the aptamer high specificity of binding to a variety of molecular targets allowed the construction of biosensors with increased selectivity and sensitivity...
2018: Journal of Nucleic Acids
Xin Guo, Xue-Mei Wang, Shuai Wei, Shou-Jun Xiao
Design rules for DNA nanotechnology have been mostly learnt from using linear single stranded (ss) DNAs as the source materials. For example, a typical DAO (Double crossover, Antiparallel, Odd half turns) tile for assembling two-dimensional (2D) lattices is built by only two linear ss-oligonucleotide scaffold strands, like two ropes making a square knot. We demonstrate here a new type of coupled DAO (cDAO) tiles and their 2D lattices using small circular ss-oligonucleotides as scaffold strands and linear ss-oligonucleotides as staple strands...
April 12, 2018: Chembiochem: a European Journal of Chemical Biology
Shu-Ichi Nakano, Daisuke Yamaguchi, Naoki Sugimoto
Spatially confined environments are seen in biological systems and in the fields of biotechnology and nanotechnology. The confinement restricts the conformational space of polymeric molecules and increasing the degree of molecular crowding. Here, we developed preparation methods for agarose and polyacrylamide gels applicable to UV spectroscopy that can evaluate the confinement effects on DNA and protein structures. Measurements of UV absorbance and CD spectra showed no significant effect of the confinement in the porous media of agarose gels on the base-pair stability of DNA polynucleotides [poly(dA)/poly(dT)] and oligonucleotides (hairpin, duplex, and triplex structures)...
April 6, 2018: Molecular Biology Reports
Yonggang Ke, Carlos Castro, Jong Hyun Choi
Structural DNA nanotechnology utilizes synthetic or biologic DNA as designer molecules for the self-assembly of artificial nanostructures. The field is founded upon the specific interactions between DNA molecules, known as Watson-Crick base pairing. After decades of active pursuit, DNA has demonstrated unprecedented versatility in constructing artificial nanostructures with significant complexity and programmability. The nanostructures could be either static, with well-controlled physicochemical properties, or dynamic, with the ability to reconfigure upon external stimuli...
April 4, 2018: Annual Review of Biomedical Engineering
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