Three-dimensional DNA structures: design and biological applications

2014 ◽  
Author(s):  
Hanadi Sleiman
Keyword(s):  
Three Dimensional ◽  
Biological Applications ◽  
Dna Structures

Three-dimensional X-ray microtomography for medical and biological applications

1990 ◽  
Vol 35 (7) ◽  
pp. 805-820 ◽  
Author(s):  
E J Morton ◽  
S Webb ◽  
J E Bateman ◽  
L J Clarke ◽  
C G Shelton
Keyword(s):  
Three Dimensional ◽  
Biological Applications ◽  
X Ray

scholarly journals Stimuli Responsive, Programmable DNA Nanodevices for Biomedical Applications

2021 ◽  
Vol 9 ◽  
Author(s):  
Udisha Singh ◽  
Vinod Morya ◽  
Bhaskar Datta ◽  
Chinmay Ghoroi ◽  
Dhiraj Bhatia
Keyword(s):  
Biomedical Applications ◽  
Recent Progress ◽  
Dna Nanotechnology ◽  
Research Area ◽  
Biological Applications ◽  
Stimuli Responsive ◽  
Future Prospects ◽  
Dna Structures ◽  
Challenges And Opportunities

Of the multiple areas of applications of DNA nanotechnology, stimuli-responsive nanodevices have emerged as an elite branch of research owing to the advantages of molecular programmability of DNA structures and stimuli-responsiveness of motifs and DNA itself. These classes of devices present multiples areas to explore for basic and applied science using dynamic DNA nanotechnology. Herein, we take the stake in the recent progress of this fast-growing sub-area of DNA nanotechnology. We discuss different stimuli, motifs, scaffolds, and mechanisms of stimuli-responsive behaviours of DNA nanodevices with appropriate examples. Similarly, we present a multitude of biological applications that have been explored using DNA nanodevices, such as biosensing, in vivo pH-mapping, drug delivery, and therapy. We conclude by discussing the challenges and opportunities as well as future prospects of this emerging research area within DNA nanotechnology.

Three-Dimensional Microstructures for Biological Applications

2016 ◽  
pp. 355-376 ◽  
Author(s):  
Adriano J. G. Otuka ◽  
Vinicius Tribuzi ◽  
Daniel S. Correa ◽  
Cleber R. Mendonça
Keyword(s):  
Three Dimensional ◽  
Biological Applications

Coaxial-like three-dimensional nanoelectrodes for biological applications

2018 ◽  
Vol 187-188 ◽  
pp. 21-26
Author(s):  
Andrea Cerea ◽  
Valeria Caprettini ◽  
Giovanni Melle ◽  
Giulia Bruno ◽  
Marco Leoncini ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Biological Applications

scholarly journals DNA sequence encodes the position of DNA supercoils

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Sung Hyun Kim ◽  
Mahipal Ganji ◽  
Eugene Kim ◽  
Jaco van der Torre ◽  
Elio Abbondanzieri ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Structural Information ◽  
Three Dimensional ◽  
Decisive Role ◽  
Chromosomal Dna ◽  
Dna Structures ◽  
Cellular Processes ◽  
Specific Sequences ◽  
Good Agreement

The three-dimensional organization of DNA is increasingly understood to play a decisive role in vital cellular processes. Many studies focus on the role of DNA-packaging proteins, crowding, and confinement in arranging chromatin, but structural information might also be directly encoded in bare DNA itself. Here, we visualize plectonemes (extended intertwined DNA structures formed upon supercoiling) on individual DNA molecules. Remarkably, our experiments show that the DNA sequence directly encodes the structure of supercoiled DNA by pinning plectonemes at specific sequences. We develop a physical model that predicts that sequence-dependent intrinsic curvature is the key determinant of pinning strength and demonstrate this simple model provides very good agreement with the data. Analysis of several prokaryotic genomes indicates that plectonemes localize directly upstream of promoters, which we experimentally confirm for selected promotor sequences. Our findings reveal a hidden code in the genome that helps to spatially organize the chromosomal DNA.

scholarly journals The biological applications of DNA nanomaterials: current challenges and future directions

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Wenjuan Ma ◽  
Yuxi Zhan ◽  
Yuxin Zhang ◽  
Chenchen Mao ◽  
Xueping Xie ◽  
...  
Keyword(s):  
Self Assembly ◽  
Drug Carrier ◽  
Genetic Material ◽  
Three Dimensional ◽  
Real Life ◽  
Dna Nanotechnology ◽  
Structural Development ◽  
Biological Applications ◽  
Dna Materials ◽  
Functional Dna

AbstractDNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson–Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.

Modelling Stress Softening and Necking Phenomena in Double Network Hydrogels

2019 ◽  
Author(s):  
Vahid Morovati ◽  
Mohammad Ali Saadat ◽  
Roozbeh Dargazany
Keyword(s):  
Polymer Networks ◽  
Three Dimensional ◽  
Interpenetrating Polymer Networks ◽  
Biological Applications ◽  
Inelastic Behavior ◽  
Interpenetrating Networks ◽  
Double Network ◽  
Stress Softening ◽  
Proposed Model ◽  
Damage Process

Abstract Double network (DN) gels are three-dimensional polymer matrices formed by interpenetrating networks. In contrast to the conventional single-network gels, DN gels have significant toughness, which makes them a promising material for different biomedical and biological applications. However, DN gels show complicated inelastic behavior including the Mullins effect and necking instability. Despite extensive efforts on modelling different aspects of the damage process in gels, the micro-mechanical modelling of the mechanisms that lead to necking in DN gels remains to be a challenging task. Here, a constitutive model is proposed to understand and describe the mechanical behavior of DN gels based on statistical micro-mechanics of interpenetrating polymer networks. DN gels behavior is divided into three parts including pre-necking, necking, and hardening. The first network is dominant in the response of the gel in the pre-necking stage. The breakage of the first network to smaller network fractions (clusters) induces the stress softening observed in this stage. The interaction of both networks and the second network are also considered as main contributors to the response of gel in necking and hardening stages, respectively. The contribution of clusters decreases during the necking as the second network starts hardening. The numerical results of the proposed model are validated and compared by uni-axial cyclic tensile experimental data of DN gels.

Biological Applications of the Scanning Transmitted Electron Microscope

1971 ◽  
Vol 29 ◽  
pp. 474-475
Author(s):  
Tatsuya Matsuo ◽  
Mikio Suzuki
Keyword(s):  
Electron Microscope ◽  
Osmium Tetroxide ◽  
Three Dimensional ◽  
Thick Section ◽  
Biological Applications ◽  
Three Dimensional Model ◽  
Voltage Electron ◽  
Osmium Tetroxide Solution ◽  
High Voltage Electron Microscope ◽  
Mice Liver

Recently, very thick section of biological specimens have been observed by using super high voltage electron microscope to obtain a three dimensional model of a specimen.However, the thicker the section, the more difficult the penetration of staining solution into the depth of thick section. So, it is doutful whether the stain solution fully penetrated into the thick section. This paper reports an observation of various thick unstained sections using scanning transmitted electron microscope(STEM) and conventional electron microscope(CEM).The observed specimen is mice liver cells. The tissue was fixed in cold 1% phosphate-buffered osmium tetroxide solution for 2 hours. After fixation, the tissue was dehydrated in a graded series of ethanols and then embedded in Epon 812. The 500 Å, 5,000 Å and 1μ thick sections were cut, not stained with uranyle and lead, and then examined with STEM and GEM operated at accelerating voltage 80 kV.

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