scholarly journals Adenita: Interactive 3D modeling and visualization of DNA Nanostructures

2019 ◽  
Author(s):  
Elisa de Llano ◽  
Haichao Miao ◽  
Yasaman Ahmadi ◽  
Amanda J. Wilson ◽  
Morgan Beeby ◽  
...  
Keyword(s):  
Software Tool ◽  
Building Blocks ◽  
Dna Origami ◽  
Dna Nanostructures ◽  
User Interactions ◽  
Dna Nanostructure ◽  
Dna Tiles ◽  
Integrated Environment ◽  
Interactive 3D ◽  
User Friendly

AbstractWe present Adenita, a novel software tool for the design of DNA nanostructures in a user-friendly integrated environment for molecular modeling. Adenita is capable of handling large DNA origami structures, re-use them as building blocks of new designs and provide on demand feedback, thus overcoming effectively some of the limitations of existing tools. Additionally, it integrates all major established approaches to DNA nanostructure design (DNA origami, wireframe nanostructures and DNA tiles) and allows to combine them. We show-case Adenita by re-using a large nanorod designed with Cadnano [1] to create a new nanostructure through user interactions that employ different editors to modify the original nanorod.

scholarly journals Adenita: interactive 3D modelling and visualization of DNA nanostructures

2020 ◽  
Vol 48 (15) ◽  
pp. 8269-8275 ◽  
Author(s):  
Elisa de Llano ◽  
Haichao Miao ◽  
Yasaman Ahmadi ◽  
Amanda J Wilson ◽  
Morgan Beeby ◽  
...  
Keyword(s):  
Dna Nanotechnology ◽  
Software Tool ◽  
Building Blocks ◽  
Dna Origami ◽  
Dna Nanostructures ◽  
User Interactions ◽  
Dna Nanostructure ◽  
Dna Tiles ◽  
The Creation ◽  
Interactive 3D

Abstract DNA nanotechnology is a rapidly advancing field, which increasingly attracts interest in many different disciplines, such as medicine, biotechnology, physics and biocomputing. The increasing complexity of novel applications requires significant computational support for the design, modelling and analysis of DNA nanostructures. However, current in silico design tools have not been developed in view of these new applications and their requirements. Here, we present Adenita, a novel software tool for the modelling of DNA nanostructures in a user-friendly environment. A data model supporting different DNA nanostructure concepts (multilayer DNA origami, wireframe DNA origami, DNA tiles etc.) has been developed allowing the creation of new and the import of existing DNA nanostructures. In addition, the nanostructures can be modified and analysed on-the-fly using an intuitive toolset. The possibility to combine and re-use existing nanostructures as building blocks for the creation of new superstructures, the integration of alternative molecules (e.g. proteins, aptamers) during the design process, and the export option for oxDNA simulations are outstanding features of Adenita, which spearheads a new generation of DNA nanostructure modelling software. We showcase Adenita by re-using a large nanorod to create a new nanostructure through user interactions that employ different editors to modify the original nanorod.

scholarly journals Constructing Large 2D Lattices Out of DNA-Tiles

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1502
Author(s):  
Johannes M. Parikka ◽  
Karolina Sokołowska ◽  
Nemanja Markešević ◽  
J. Jussi Toppari
Keyword(s):  
Self Assembly ◽  
Dna Nanotechnology ◽  
Building Blocks ◽  
High Yield ◽  
Dna Nanostructures ◽  
Liquid Interfaces ◽  
Basic Principles ◽  
Dna Tiles ◽  
One Step ◽  
Solid Liquid

The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices.

scholarly journals Choice of fluorophore affects dynamic DNA nanostructures

2020 ◽  
Author(s):  
Kevin Jahnke ◽  
Helmut Grubmüller ◽  
Maxim Igaev ◽  
Kerstin Göpfrich
Keyword(s):  
Energy Landscape ◽  
Dna Nanotechnology ◽  
Reaction Diffusion ◽  
Md Simulations ◽  
Dna Origami ◽  
Dna Nanostructures ◽  
Diffusion Modeling ◽  
Ph Responsive ◽  
Dna Nanostructure ◽  
Potential Impact

The ability to dynamically remodel DNA origami structures or functional nanodevices is highly desired in the field of DNA nanotechnology. Concomitantly, the use of fluorophores to track and validate the dynamics of such DNA-based architectures is commonplace and often unavoidable. It is therefore crucial to be aware of the side effects of popular fluorophores, which are often exchanged without considering the potential impact on the system. Here, we show that the choice of fluorophore can strongly affect the reconfiguration of DNA nanostructures. To this end, we encapsulate a triple-stranded DNA (tsDNA) into water-in-oil compartments and functionalize their periphery with a single-stranded DNA handle (ssDNA). Thus, the tsDNA can bind and unbind from the periphery by reversible opening of the triplex and subsequent strand displacement. Using a combination of experiments, molecular dynamics (MD) simulations, and reaction-diffusion modeling, we demonstrate for twelve different fluorophore combinations that it is possible to alter or even inhibit the DNA nanostructure formation - without changing the DNA sequence. Besides its immediate importance for the design of pH-responsive switches and fluorophore labelling, our work presents a strategy to precisely tune the energy landscape of dynamic DNA nanodevices.

scholarly journals Hierarchical coassembly of DNA–triptycene hybrid molecular building blocks and zinc protoporphyrin IX

2016 ◽  
Vol 7 ◽  
pp. 697-707 ◽  
Author(s):  
Rina Kumari ◽  
Sumit Singh ◽  
Mohan Monisha ◽  
Sourav Bhowmick ◽  
Anindya Roy ◽  
...  
Keyword(s):  
Self Assembly ◽  
Polyacrylamide Gel Electrophoresis ◽  
Protoporphyrin Ix ◽  
Building Blocks ◽  
Ros Generation ◽  
Zinc Protoporphyrin ◽  
Dna Nanostructures ◽  
Native Page ◽  
Dna Nanostructure ◽  
Molecular Building Blocks

Herein, we describe the successful construction of composite DNA nanostructures by the self-assembly of complementary symmetrical 2,6,14-triptycenetripropiolic acid (TPA)–DNA building blocks and zinc protoporphyrin IX (Zn PpIX). DNA–organic molecule scaffolds for the composite DNA nanostructure were constructed through covalent conjugation of TPA with 5′-C12-amine-terminated modified single strand DNA (ssDNA) and its complementary strand. The repeated covalent conjugation of TPA with DNA was confirmed by using denaturing polyacrylamide gel electrophoresis (PAGE), reverse-phase high-performance liquid chromatography (RP-HPLC) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). The biologically relevant photosensitizer Zn PpIX was used to direct the hybridization-mediated self-assembly of DNA–TPA molecular building blocks as well as a model guest molecule within the DNA–TPA supramolecular self-assembly. The formation of fiber-like composite DNA nanostructures was observed. Native PAGE, circular dichroism (CD) and atomic force microscopy (AFM) have been utilized for analyzing the formation of DNA nanofibers after the coassembly. Computational methods were applied to discern the theoretical dimension of the DNA–TPA molecular building block of the nanofibers. A notable change in photocatalytic efficiency of Zn PpIX was observed when it was inside the TPA–DNA scaffold. The significant increase in ROS generation by Zn PpIX when trapped in this biocompatible DNA–TPA hybrid nanofiber may be an effective tool to explore photodynamic therapy (PDT) applications as well as photocatalytic reactions.

Structural DNA nanotechnology: Immobile Holliday junctions to artificial robots

2022 ◽  
Vol 22 ◽  
Author(s):  
Raghu Pradeep Narayanan ◽  
Leeza Abraham
Keyword(s):  
Dna Nanotechnology ◽  
Building Blocks ◽  
Holliday Junctions ◽  
Dna Origami ◽  
Building Structures ◽  
Dna Nanostructures ◽  
3 Dimensional ◽  
Scientific World ◽  
2D And 3D ◽  
Structural Dna Nanotechnology

Abstreact: DNA nanotechnology marvels the scientific world with its capabilities to design, engineer, and demonstrate nanoscale shapes. This review is a condensed version walking the reader through the structural developments in the field over the past 40 years starting from the basic design rules of the double-stranded building block to the most recent advancements in self-assembled hierarchically achieved structures to date. It builds off from the fundamental motivation of building 3-dimensional (3D) lattice structures of tunable cavities going all the way up to artificial nanorobots fighting cancer. The review starts by covering the most important developments from the fundamental bottom-up approach of building structures, which is the ‘tile’ based approach covering 1D, 2D, and 3D building blocks, after which, the top-down approach using DNA origami and DNA bricks is also covered. Thereafter, DNA nanostructures assembled using not so commonly used (yet promising) techniques like i-motifs, quadruplexes, and kissing loops are covered. Highlights from the field of dynamic DNA nanostructures have been covered as well, walking the reader through the various approaches used within the field to achieve movement. The article finally concludes by giving the authors a view of what the future of the field might look like while suggesting in parallel new directions that fellow/future DNA nanotechnologists could think about.

scholarly journals Nanomechanics of self-assembled DNA building blocks

Nanoscale ◽  
2021 ◽  
Author(s):  
Michael Penth ◽  
Kordula Schellnhuber ◽  
Roland Bennewitz ◽  
Johanna Blass
Keyword(s):  
Structural Dynamics ◽  
Force Spectroscopy ◽  
Building Blocks ◽  
Dna Origami ◽  
Self Assembled ◽  
High Flexibility

Massive parallel force spectroscopy reveals a surprisingly high flexibility for DNA constructs used in DNA origami. The high flexibility is attributed to the structural dynamics of DNA self-assemblies.

scholarly journals A Structurally Variable Hinged Tetrahedron Framework from DNA Origami

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
David M. Smith ◽  
Verena Schüller ◽  
Carsten Forthmann ◽  
Robert Schreiber ◽  
Philip Tinnefeld ◽  
...  
Keyword(s):  
Self Assembly ◽  
Gel Electrophoresis ◽  
Imaging Techniques ◽  
Building Blocks ◽  
Dna Origami ◽  
Microscopy Technique ◽  
Wire Frame ◽  
Wide Range ◽  
Potential Applications ◽  
Linker Molecules

Nanometer-sized polyhedral wire-frame objects hold a wide range of potential applications both as structural scaffolds as well as a basis for synthetic nanocontainers. The utilization of DNA as basic building blocks for such structures allows the exploitation of bottom-up self-assembly in order to achieve molecular programmability through the pairing of complementary bases. In this work, we report on a hollow but rigid tetrahedron framework of 75 nm strut length constructed with the DNA origami method. Flexible hinges at each of their four joints provide a means for structural variability of the object. Through the opening of gaps along the struts, four variants can be created as confirmed by both gel electrophoresis and direct imaging techniques. The intrinsic site addressability provided by this technique allows the unique targeted attachment of dye and/or linker molecules at any point on the structure's surface, which we prove through the superresolution fluorescence microscopy technique DNA PAINT.

scholarly journals Biophysical characterization of DNA origami nanostructures reveals inaccessibility to intercalation binding sites

2019 ◽  
Author(s):  
Helen L. Miller ◽  
Sonia Contera ◽  
Adam J.M. Wollman ◽  
Adam Hirst ◽  
Katherine E. Dunn ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Single Molecule ◽  
Targeted Drug Delivery ◽  
Binding Sites ◽  
Dna Origami ◽  
Target Cells ◽  
Dna Nanostructures ◽  
Synthetic Dna ◽  
Drug Molecules ◽  
Targeted Drug

AbstractIntercalation of drug molecules into synthetic DNA nanostructures formed through self-assembled origami has been postulated as a valuable future method for targeted drug delivery. This is due to the excellent biocompatibility of synthetic DNA nanostructures, and high potential for flexible programmability including facile drug release into or near to target cells. Such favourable properties may enable high initial loading and efficient release for a predictable number of drug molecules per nanostructure carrier, important for efficient delivery of safe and effective drug doses to minimise non-specific release away from target cells. However, basic questions remain as to how intercalation-mediated loading depends on the DNA carrier structure. Here we use the interaction of dyes YOYO-1 and acridine orange with a tightly-packed 2D DNA origami tile as a simple model system to investigate intercalation-mediated loading. We employed multiple biophysical techniques including single-molecule fluorescence microscopy, atomic force microscopy, gel electrophoresis and controllable damage using low temperature plasma on synthetic DNA origami samples. Our results indicate that not all potential DNA binding sites are accessible for dye intercalation, which has implications for future DNA nanostructures designed for targeted drug delivery.

scholarly journals CHR: An Integrated Software Tool for chilling requirements

2020 ◽  
Author(s):  
Chen Chen ◽  
Wanyu Xu ◽  
Ningning Gou ◽  
Lasu Bai ◽  
Lin Wang ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Software Tool ◽  
Fruit Trees ◽  
Cold Weather ◽  
Chilling Requirements ◽  
Deciduous Fruit ◽  
Heat Requirement ◽  
Integrated Software ◽  
User Friendly ◽  
Analyze Data

Abstract Background Bud dormancy in deciduous fruit trees enables plants to survive cold weather. The buds adopt dormant state and resume growth after satisfying the chilling requirements. Chilling requirements play a key role in flowering time. So far, several chilling models, including ≤ 7.2 °C model, the 0–7.2 °C model, Utah model, and Dynamic Model, have been developed; however, it is still time-consuming to determine the chilling requirements employing any model. This calls for efficient tools that can analyze data. Results In this study, we developed novel software Chilling and Heat Requirement (CHR), by flexibly integrating data conversions, model selection, calculations, statistical analysis, and plotting. Conclusion CHR is a tool for chilling requirements estimation, which will be very useful to researchers. It is very simple, easy, and user-friendly.

Quantification Methods for Construction Waste Generation at Construction Sites: A Review

2010 ◽  
Vol 163-167 ◽  
pp. 4564-4569 ◽  
Author(s):  
Ahmad Firman Masudi ◽  
Che Rosmani Che Hassan ◽  
Noor Zalina Mahmood ◽  
Siti Nazziera Mokhtar ◽  
Nik Meriam Sulaiman
Keyword(s):  
Construction Projects ◽  
Software Tool ◽  
Waste Reduction ◽  
Building Construction ◽  
Civil Infrastructure ◽  
Waste Generation ◽  
Construction Sites ◽  
Construction Waste ◽  
Future Direction ◽  
User Friendly

Estimation of construction and demolition (C&D) waste amount is crucial for implementing waste minimization program. Estimation of C&D waste amount generated is a mean in assessing the potential for waste reduction. Thus, a better understanding of C&D waste generation in terms of causes and sources can be achieved. The aim of this paper is to conduct a review on available construction waste quantification methods from previous studies, which have been utilized in certain countries, while attempting to choose the most suitable and applicable method, and to direct future studies for better quantification methods. This review is applicable only for building construction projects and did not include civil/infrastructure, demolition, renovation, and excavation projects. Six quantification methods and/or waste audit tool available from literatures are discussed, which include their limitation and future direction for this study. It is believed that some combination of these quantification methods could make a good impact in accurate numerical estimation of construction waste amount generated in building construction projects. A strong and accurate database as presented by Soliz-Guzman, combined with effective, vital, and resourceful estimation suggested by Jalali’s Global Index (GI), also with the aid of user-friendly software tool like the SMARTAudit could provide an effective and reliable waste quantification.

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