scholarly journals Conformational Control of DNA Origami by DNA Oligomers, Intercalators and UV Light

2021 ◽  
Vol 4 (2) ◽  
pp. 38
Author(s):  
Ruixin Li ◽  
Haorong Chen ◽  
Hyeongwoon Lee ◽  
Jong Hyun Choi
Keyword(s):  
Uv Light ◽  
Dna Nanotechnology ◽  
Dna Origami ◽  
Conformational Control ◽  
Dna Oligomers ◽  
On Demand ◽  
Powerful Means ◽  
External Signals ◽  
Shape Changes ◽  
Complex Nanostructures

DNA origami has garnered great attention due to its excellent programmability and precision. It offers a powerful means to create complex nanostructures which may not be possible by other methods. The macromolecular structures may be used as static templates for arranging proteins and other molecules. They are also capable of undergoing structural transformation in response to external signals, which may be exploited for sensing and actuation at the nanoscale. Such on-demand reconfigurations are executed mostly by DNA oligomers through base-pairing and/or strand displacement, demonstrating drastic shape changes between two different states, for example, open and close. Recent studies have developed new mechanisms to modulate the origami conformation in a controllable, progressive manner. Here we present several methods for conformational control of DNA origami nanostructures including chemical adducts and UV light as well as widely applied DNA oligomers. The detailed methods should be useful for beginners in the field of DNA nanotechnology.

scholarly journals Dynamic DNA Origami Devices: from Strand-Displacement Reactions to External-Stimuli Responsive Systems

2018 ◽  
Vol 19 (7) ◽  
pp. 2114 ◽  
Author(s):  
Heini Ijäs ◽  
Sami Nummelin ◽  
Boxuan Shen ◽  
Mauri Kostiainen ◽  
Veikko Linko
Keyword(s):  
Dna Sequences ◽  
Rapid Evolution ◽  
Dna Nanotechnology ◽  
Dna Origami ◽  
Dna Assembly ◽  
Stimuli Responsive ◽  
Nanoscale Structures ◽  
Displacement Reactions ◽  
Materials Research ◽  
External Stimuli

DNA nanotechnology provides an excellent foundation for diverse nanoscale structures that can be used in various bioapplications and materials research. Among all existing DNA assembly techniques, DNA origami proves to be the most robust one for creating custom nanoshapes. Since its invention in 2006, building from the bottom up using DNA advanced drastically, and therefore, more and more complex DNA-based systems became accessible. So far, the vast majority of the demonstrated DNA origami frameworks are static by nature; however, there also exist dynamic DNA origami devices that are increasingly coming into view. In this review, we discuss DNA origami nanostructures that exhibit controlled translational or rotational movement when triggered by predefined DNA sequences, various molecular interactions, and/or external stimuli such as light, pH, temperature, and electromagnetic fields. The rapid evolution of such dynamic DNA origami tools will undoubtedly have a significant impact on molecular-scale precision measurements, targeted drug delivery and diagnostics; however, they can also play a role in the development of optical/plasmonic sensors, nanophotonic devices, and nanorobotics for numerous different tasks.

scholarly journals Evaluating Energy and Cost Requirements for Different Configurations of Off-Grid Rainwater Harvesting Systems

Water ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 1024
Author(s):  
Heather Rose ◽  
Charles Upshaw ◽  
Michael Webber
Keyword(s):  
Rainwater Harvesting ◽  
Uv Light ◽  
Storage System ◽  
Energy Storage System ◽  
System Model ◽  
Demand System ◽  
Solar Pv ◽  
On Demand ◽  
Harvesting Systems ◽  
System Configurations

The goal of this analysis was to evaluate energy and cost requirements for different configurations of a rainwater harvesting (RWH) system in conjunction with a solar PV and energy storage system for an off-grid house. Using models in fluid mechanics, we evaluated energy and power requirements for four different system configurations: 1. An On-Demand System containing a single speed pump (OD-SS), 2. An On-Demand System containing a variable speed pump (OD-VS), 3. A Pressurized Storage System where water is pumped once during the day into a large pressurized tank for later consumption and treated on demand via UV light (PS-AOT), and 4. A Pressurized Storage System where water is treated once per day via UV light and then stored for later consumption (PS-TO). Our analysis showed that the OD-SS system model requires 2.63 kWh per day, the OD-VS system model requires a total energy of 1.65 kWh per day, and the PS-AOT requires 1.67–1.69 kWh per day depending on the pump size, and the PS-TO system requires 0.19–0.36 kWh per day depending on the pump size. When comparing estimated cost between systems, we found the OD-SS system to be the most expensive. With the OD-SS system as a base for system costs, we found the OD-VS system to be 39% less expensive, the PS-AOT system to be 21% less expensive, and the PS-TO system to be 60% less expensive than the base OD-SS system.

scholarly journals DNA nanotechnology approaches for microRNA detection and diagnosis

2019 ◽  
Vol 47 (20) ◽  
pp. 10489-10505 ◽  
Author(s):  
Arun Richard Chandrasekaran ◽  
Jibin Abraham Punnoose ◽  
Lifeng Zhou ◽  
Paromita Dey ◽  
Bijan K Dey ◽  
...  
Keyword(s):  
Dna Nanotechnology ◽  
Dna Origami ◽  
Great Promise ◽  
Dna Nanostructures ◽  
New Class ◽  
Advantages And Disadvantages ◽  
Critical Comparison ◽  
Microrna Detection ◽  
Disease Diagnostics ◽  
Detection And Diagnosis

Abstract MicroRNAs are involved in the crucial processes of development and diseases and have emerged as a new class of biomarkers. The field of DNA nanotechnology has shown great promise in the creation of novel microRNA biosensors that have utility in lab-based biosensing and potential for disease diagnostics. In this Survey and Summary, we explore and review DNA nanotechnology approaches for microRNA detection, surveying the literature for microRNA detection in three main areas of DNA nanostructures: DNA tetrahedra, DNA origami, and DNA devices and motifs. We take a critical look at the reviewed approaches, advantages and disadvantages of these methods in general, and a critical comparison of specific approaches. We conclude with a brief outlook on the future of DNA nanotechnology in biosensing for microRNA and beyond.

scholarly journals Programming Structured DNA Assemblies to Probe Biophysical Processes

2019 ◽  
Vol 48 (1) ◽  
pp. 395-419 ◽  
Author(s):  
Eike-Christian Wamhoff ◽  
James L. Banal ◽  
William P. Bricker ◽  
Tyson R. Shepherd ◽  
Molly F. Parsons ◽  
...  
Keyword(s):  
Structural Biology ◽  
Energy Transport ◽  
Dna Nanotechnology ◽  
Dna Origami ◽  
Design And Synthesis ◽  
Copy Numbers ◽  
Target Nucleic Acid ◽  
Biophysical Processes ◽  
Fully Automatic ◽  
Structural Dna Nanotechnology

Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to interface with biology on the 1–100-nm scale. Here, we review the major design and synthesis principles that have enabled the fabrication of a specific subclass of scaffolded DNA origami objects called wireframe assemblies. These objects offer unprecedented control over the nanoscale organization of biomolecules, including biomolecular copy numbers, presentation on convex or concave geometries, and internal versus external functionalization, in addition to stability in physiological buffer. To highlight the power and versatility of this synthetic structural biology approach to probing molecular and cellular biophysics, we feature its application to three leading areas of investigation: light harvesting and nanoscale energy transport, RNA structural biology, and immune receptor signaling, with an outlook toward unique mechanistic insight that may be gained in these areas in the coming decade.

Optical Adhesion Control of Hydrogel Microtools for On-Demand Immobilization and Measurement of Cells on a Microfluidic Chip

2010 ◽  
Vol 22 (5) ◽  
pp. 631-638 ◽  
Author(s):  
Hisataka Maruyama ◽  
◽  
Toshio Fukuda ◽  
Fumihito Arai ◽  
Keyword(s):  
Optical Tweezers ◽  
Microfluidic Chip ◽  
Electrolyte Concentration ◽  
Ph Value ◽  
Uv Light ◽  
Yeast Cells ◽  
Light Illumination ◽  
Local Conditions ◽  
On Demand ◽  
Adhesion Control

Optical adhesion control of hydrogel microtools, made of hydrophilic photo-crosslinkable resin, was developed for on-demand immobilization and measurement of cells on a microfluidic chip. The hydrogel microtool was manipulated by optical tweezers and modified by spiropyran chromospheres, which was a photochromic polymer. We developed on-demand control of uni/bidirectional adhesiveness of the microtool by control of electrolyte concentration in a solution. Photo illumination controls the adhesiveness of the microtools. In case of unidirectional control of adhesiveness, the microtools adhere to glass, other microtools and cells by illumination of ultraviolet (UV) light. Spiropyran chromospheres were used for bidirectional control of adhesiveness to cell. In case of bidirectional control of adhesiveness, the microtools adhere to cells by UV illumination. On the other hand, the microtool detaches from the adhered cells by visible (VIS) light illumination. Electrolyte concentration in the solution controlled these adhesiveness controls. Adherence of the microtool was enough to keep its position on a microfluidic chip. We applied these immobilization methods to measure the local conditions around cells by modifying the microtool with a pH indicator, bromothymol blue (BTB). Local measurements of the ambient pH value of yeast cells were performed by immobilizing the cell on the surface of the pH sensing microtool. Moreover, culture monitoring of a single yeast cell was demonstrated by immobilization to the microtool.

scholarly journals Engineered Th17 cell differentiation using a photo-activatable immune modulator

2019 ◽  
Author(s):  
Bibudha Parasar ◽  
Pamela V. Chang
Keyword(s):  
Cell Differentiation ◽  
Th17 Cell ◽  
Th17 Cells ◽  
Uv Light ◽  
T Cell Subsets ◽  
Light Illumination ◽  
Immune Modulator ◽  
On Demand ◽  
Th17 Cell Differentiation

AbstractT helper 17 (Th17) cells, an important subset of CD4+ T cells, help to eliminate extracellular infectious pathogens that have invaded our tissues. Despite the critical roles of Th17 cells in immunity, how the immune system regulates the production and maintenance of this cell type remains poorly understood. In particular, the plasticity of these cells, or their dynamic ability to trans-differentiate into other CD4+ T cell subsets, remains mostly uncharacterized. Here, we report a synthetic immunology approach using a photo-activatable immune modulator (PIM) to increase Th17 cell differentiation on demand with spatial and temporal precision to help elucidate this important and dynamic process. In this chemical strategy, we developed a latent agonist that, upon photochemical activation, releases a small-molecule ligand that targets the aryl hydrocarbon receptor (AhR) and ultimately induces Th17 cell differentiation. We used this chemical tool to control AhR activation with spatiotemporal precision within cells and to modulate Th17 cell differentiation on demand by using UV light illumination. We envision that this approach will enable an understanding of the dynamic functions and behaviors of Th17 cells in vivo during immune responses and in mouse models of inflammatory disease.

scholarly journals Complex multicomponent patterns rendered on a 3D DNA-barrel pegboard

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Shelley F. J. Wickham ◽  
Alexander Auer ◽  
Jianghong Min ◽  
Nandhini Ponnuswamy ◽  
Johannes B. Woehrstein ◽  
...  
Keyword(s):  
Dna Nanotechnology ◽  
Super Resolution ◽  
Dna Origami ◽  
Design And Optimization ◽  
Hierarchical Assembly ◽  
Double Helices ◽  
Specialist Groups ◽  
Parallel Arrays ◽  
Super Resolution Microscopy ◽  
Rhombic Lattice

AbstractDNA origami, in which a long scaffold strand is assembled with a many short staple strands into parallel arrays of double helices, has proven a powerful method for custom nanofabrication. However, currently the design and optimization of custom 3D DNA-origami shapes is a barrier to rapid application to new areas. Here we introduce a modular barrel architecture, and demonstrate hierarchical assembly of a 100 megadalton DNA-origami barrel of ~90 nm diameter and ~250 nm height, that provides a rhombic-lattice canvas of a thousand pixels each, with pitch of ~8 nm, on its inner and outer surfaces. Complex patterns rendered on these surfaces were resolved using up to twelve rounds of Exchange-PAINT super-resolution microscopy. We envision these structures as versatile nanoscale pegboards for applications requiring complex 3D arrangements of matter, which will serve to promote rapid uptake of this technology in diverse fields beyond specialist groups working in DNA nanotechnology.

DNA Origami Nanoplate-Based Emulsion with Designed Nanopore Function

2018 ◽  
Author(s):  
Daisuke Ishikawa ◽  
Yuki Suzuki ◽  
Chikako Kurokawa ◽  
Masayuki Ohara ◽  
Misato Tsuchiya ◽  
...  
Keyword(s):  
Shape Control ◽  
Dna Nanotechnology ◽  
Dna Origami ◽  
Cell Engineering ◽  
General Strategy ◽  
Surface Chemical ◽  
Artificial Cell ◽  
Physical Chemical ◽  
Oil Water ◽  
Molecular Robots

Bio-inspired functional microcapsules stabilised with surfactants, copolymers, and nano/microparticles have attracted much attention in many fields from physical/chemical science to artificial cell engineering. Although the particle-stabilized microcapsules have advantages for their stability and rich ways for functionalisation such as surface chemical modifications and shape control of particles, versatile methods for their designable functionalisation are desired to expand their possibilities. Here, we report a DNA-based microcapsule composed of a water-in-oil microdroplet stabilised with amphiphilised DNA origami nanoplates. By utilising function programmability achieved by DNA nanotechnology, the DNA nanoplates were designed as a nanopore device for ion transportation as well as the interface stabiliser. Microscopic observations showed that the microcapsule formed by amphiphilic DNA nanoplates accumulated at the oil-water interface. Ion current measurements demonstrated that pores in the nanoplates functioned as ion channels. These findings provide a general strategy for programmable designing of microcapsules for engineering artificial cells and molecular robots.<br>

scholarly journals Recent Advances in Novel DNA Guiding Nanofabrication and Nanotechnology

2018 ◽  
Vol 4 (1) ◽  
pp. 32-52 ◽  
Author(s):  
Zhiguang Suo ◽  
Jingqi Chen ◽  
Ziheng Hu ◽  
Yihao Liu ◽  
Feifei Xing ◽  
...  
Keyword(s):  
Dna Recognition ◽  
Genetic Material ◽  
Dna Nanotechnology ◽  
Structural Features ◽  
Dna Origami ◽  
Site Specific ◽  
Metal Organic ◽  
Nanomaterials Synthesis ◽  
Promising Development ◽  
3D Topology

Abstract DNA as life’s genetic material has been widely investigated around the world. In recent years, with the fiery researches on nanomaterials, it also plays an important role in the development of material science due to its extraordinary molecular recognition capability and prominent structural features. In this mini review, we mainly overview the recent progresses of DNA guiding self-assembled nanostructures and nanofabrication. Typical DNA tile-based assembly and DNA origami nanotechnologies are presented, utilizing the recent 3D topology methods to fabricate multidimensional structures with unique properties. Then the site-specific nanomaterials synthesis and nano-DNA recognition on different DNA scaffolds/templates are demonstrated with excellent addressability, biocompatibility and structural programmability. Various nanomaterials, such as metals, carbon family materials, quantum dots, metal-organic frameworks, and DNA-based liquid crystals are briefly summarized. Finally, the present limitation and future promising development directions are discussed in conclusion and perspective. We wish this review would provide useful information toward the broader scientific interests in DNA nanotechnology.

scholarly journals DNA Nanotechnology: 3D DNA Origami Crystals (Adv. Mater. 28/2018)

2018 ◽  
Vol 30 (28) ◽  
pp. 1870203 ◽  
Author(s):  
Tao Zhang ◽  
Caroline Hartl ◽  
Kilian Frank ◽  
Amelie Heuer-Jungemann ◽  
Stefan Fischer ◽  
...  
Keyword(s):  
Dna Nanotechnology ◽  
Dna Origami
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