scholarly journals Automated exploration of DNA-based structure self-assembly networks

2021 ◽  
Vol 8 (10) ◽  
Author(s):  
L. Cazenille ◽  
A. Baccouche ◽  
N. Aubert-Kato
Keyword(s):  
Dna Sequences ◽  
Self Assembly ◽  
Search Space ◽  
Dna Origami ◽  
Reaction Pathways ◽  
Reaction Networks ◽  
Dna Structures ◽  
Search Spaces ◽  
Dna Strands ◽  
Domain Level

Finding DNA sequences capable of folding into specific nanostructures is a hard problem, as it involves very large search spaces and complex nonlinear dynamics. Typical methods to solve it aim to reduce the search space by minimizing unwanted interactions through restrictions on the design (e.g. staples in DNA origami or voxel-based designs in DNA Bricks). Here, we present a novel methodology that aims to reduce this search space by identifying the relevant properties of a given assembly system to the emergence of various families of structures (e.g. simple structures, polymers, branched structures). For a given set of DNA strands, our approach automatically finds chemical reaction networks (CRNs) that generate sets of structures exhibiting ranges of specific user-specified properties, such as length and type of structures or their frequency of occurrence. For each set, we enumerate the possible DNA structures that can be generated through domain-level interactions, identify the most prevalent structures, find the best-performing sequence sets to the emergence of target structures, and assess CRNs' robustness to the removal of reaction pathways. Our results suggest a connection between the characteristics of DNA strands and the distribution of generated structure families.

scholarly journals Modelling DNA origami self-assembly at the domain level

2015 ◽  
Vol 143 (16) ◽  
pp. 165102 ◽  
Author(s):  
Frits Dannenberg ◽  
Katherine E. Dunn ◽  
Jonathan Bath ◽  
Marta Kwiatkowska ◽  
Andrew J. Turberfield ◽  
...  
Keyword(s):  
Self Assembly ◽  
Dna Origami ◽  
Domain Level

scholarly journals DNA Origami Nanomachines

Molecules ◽  
2018 ◽  
Vol 23 (7) ◽  
pp. 1766 ◽  
Author(s):  
Masayuki Endo ◽  
Hiroshi Sugiyama
Keyword(s):  
Dna Sequences ◽  
Molecular Motors ◽  
Molecular Machines ◽  
Dna Origami ◽  
Dna Nanostructures ◽  
Molecular Systems ◽  
Nanoscale Structures ◽  
Research Fields ◽  
Dna Strands ◽  
External Stimuli

DNA can assemble various molecules and nanomaterials in a programmed fashion and is a powerful tool in the nanotechnology and biology research fields. DNA also allows the construction of desired nanoscale structures via the design of DNA sequences. Structural nanotechnology, especially DNA origami, is widely used to design and create functionalized nanostructures and devices. In addition, DNA molecular machines have been created and are operated by specific DNA strands and external stimuli to perform linear, rotational, and reciprocating movements. Furthermore, complicated molecular systems have been created on DNA nanostructures by arranging multiple molecules and molecular machines precisely to mimic biological systems. Currently, DNA nanomachines, such as molecular motors, are operated on DNA nanostructures. Dynamic DNA nanostructures that have a mechanically controllable system have also been developed. In this review, we describe recent research on new DNA nanomachines and nanosystems that were built on designed DNA nanostructures.

DNA as an Engineering Material: From Assembly to Computation on Silicon

2011 ◽  
Vol 1346 ◽  
Author(s):  
Hayri E. Akin ◽  
Jiebin Zhong ◽  
Miroslav Penchev ◽  
Cengiz S. Ozkan ◽  
Mihrimah Ozkan
Keyword(s):  
Dna Sequences ◽  
Self Assembly ◽  
Dna Computing ◽  
Microarray Platform ◽  
Differential Resistance ◽  
Building Blocks ◽  
Boolean Formula ◽  
Electrical Measurements ◽  
Tunneling Diodes ◽  
Dna Strands

ABSTRACTDNA possesses inherent recognition and self-assembly capabilities, making it attractive templates for constructing functional material structures as building blocks for nanoelectronics. Here we report the use of DNA towards the assembly and electronic functionality of nanoarchitectures based on conjugates of carbon nanotubes (CNTs), nanowires (NWs) and DNA computing on Si-CMOS platform. First, assembly of CNTs with DNA is demonstrated and electrical measurements of these nanoarchitectures demonstrate negative differential resistance in the presence of CNT/DNA interfaces, which indicates a biomimetic route to fabricating resonant tunneling diodes. End-to-end assembly of NWs is realized with designed DNA sequences and process is carried on silicon CMOS based microarray platform. Second, this microarray platform is adopted to perform DNA computing. To begin with, the information present in an image is encoded through the concentrations of various DNA strands via selective hybridization and decoded on microarray to recreate the original image. Lately, various satisfiability (SAT) problems, which has long served as a benchmark problem in DNA computing, are solved on this platform via DNA. The goal in a SAT Problem is to determine appropriate assignments of a set of Boolean variables with values of either “true” or “false” such that the output of the whole Boolean formula is true. Other than making 1st time silicon compatible DNA computing, our studies make us understand bio molecules, especially DNA has various advantages for future hybrid technologies.

Automated Quantification of the Impact of Defects on the Mechanical Behavior of Deoxyribonucleic Acid Origami Nanoplates

2017 ◽  
Vol 139 (4) ◽  
Author(s):  
Bowen Liang ◽  
Anand Nagarajan ◽  
Michael W. Hudoba ◽  
Ricardo Alvarez ◽  
Carlos E. Castro ◽  
...  
Keyword(s):  
Mechanical Behavior ◽  
Self Assembly ◽  
Adaptive Mesh Refinement ◽  
Deoxyribonucleic Acid ◽  
Structural Integrity ◽  
Adaptive Mesh ◽  
Dna Origami ◽  
Structured Adaptive Mesh Refinement ◽  
Dna Strands ◽  
The Impact

Deoxyribonucleic acid (DNA) origami is a method for the bottom-up self-assembly of complex nanostructures for applications, such as biosensing, drug delivery, nanopore technologies, and nanomechanical devices. Effective design of such nanostructures requires a good understanding of their mechanical behavior. While a number of studies have focused on the mechanical properties of DNA origami structures, considering defects arising from molecular self-assembly is largely unexplored. In this paper, we present an automated computational framework to analyze the impact of such defects on the structural integrity of a model DNA origami nanoplate. The proposed computational approach relies on a noniterative conforming to interface-structured adaptive mesh refinement (CISAMR) algorithm, which enables the automated transformation of a binary image of the nanoplate into a high fidelity finite element model. We implement this technique to quantify the impact of defects on the mechanical behavior of the nanoplate by performing multiple simulations taking into account varying numbers and spatial arrangements of missing DNA strands. The analyses are carried out for two types of loading: uniform tensile displacement applied on all the DNA strands and asymmetric tensile displacement applied to strands at diagonal corners of the nanoplate.

scholarly journals Using MAP-Elites to Optimize Self-Assembling Behaviors in a Swarm of Bio-micro-robots

2019 ◽  
Author(s):  
Leo Cazenille ◽  
Nicolas Bredeche ◽  
Nathanael Aubert-Kato
Keyword(s):  
Self Assembly ◽  
State Of The Art ◽  
Optimization Methods ◽  
Search Space ◽  
Reaction Networks ◽  
High Performing ◽  
Robot Swarms ◽  
Self Assembling ◽  
Previous State ◽  
Molecular Robots

AbstractWe are interested in programming a swarm of molecular robots that can perform self-assembly to form specific shapes at a specific location. Programming such robot swarms is challenging for two reasons. First, the goal is to optimize both the parameters and the structure of chemical reaction networks. Second, the search space is both high-dimensional and deceptive. In this paper, we show that MAP-Elites, an algorithm that searches for both high-performing and diverse solutions, outperforms previous state-of-the-art optimization methods.

Factors Affecting Molecular Self-Assembly and Its Mechanism

2012 ◽  
Vol 9 (1) ◽  
pp. 43 ◽  
Author(s):  
Hueyling Tan
Keyword(s):  
Self Assembly ◽  
Building Blocks ◽  
Molecular Engineering ◽  
Molecular Structures ◽  
Polymer Science ◽  
New Approach ◽  
Factors Affecting ◽  
Dna Structures ◽  
Self Assembling ◽  
Wide Range

Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use ofpeptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study ofbiological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries ofexisting disciplines. Many self-assembling systems are rangefrom bi- andtri-block copolymers to DNA structures as well as simple and complex proteins andpeptides. The ultimate goal is to harness molecular self-assembly such that design andcontrol ofbottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes oflife and non-life science applications. Such aspirations can be achievedthrough understanding thefundamental principles behind the selforganisation and self-synthesis processes exhibited by biological systems.

scholarly journals Co-self-assembly of multiple DNA origami nanostructures in a single pot

2021 ◽  
Author(s):  
Joshua A. Johnson ◽  
Vasiliki Kolliopoulos ◽  
Carlos E. Castro
Keyword(s):  
Self Assembly ◽  
Dna Origami ◽  
Folding Pathways

We demonstrate co-self-assembly of two distinct DNA origami structures with a common scaffold strand through programmable bifurcation of folding pathways.

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.

Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates

2009 ◽  
Vol 5 (1) ◽  
pp. 61-66 ◽  
Author(s):  
Hareem T. Maune ◽  
Si-ping Han ◽  
Robert D. Barish ◽  
Marc Bockrath ◽  
William A. Goddard III ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Self Assembly ◽  
Dna Origami ◽  
Two Dimensional

scholarly journals Thermodynamic Model for B-Z Transition of DNA Induced by Z-DNA Binding Proteins

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2748 ◽  
Author(s):  
Ae-Ree Lee ◽  
Na-Hyun Kim ◽  
Yeo-Jin Seo ◽  
Seo-Ree Choi ◽  
Joon-Hwa Lee
Keyword(s):  
Dna Binding ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Multiple Sequence ◽  
Left Handed ◽  
Transition Mechanism ◽  
Dna Strands ◽  
Z Dna

Z-DNA is stabilized by various Z-DNA binding proteins (ZBPs) that play important roles in RNA editing, innate immune response, and viral infection. In this review, the structural and dynamics of various ZBPs complexed with Z-DNA are summarized to better understand the mechanisms by which ZBPs selectively recognize d(CG)-repeat DNA sequences in genomic DNA and efficiently convert them to left-handed Z-DNA to achieve their biological function. The intermolecular interaction of ZBPs with Z-DNA strands is mediated through a single continuous recognition surface which consists of an α3 helix and a β-hairpin. In the ZBP-Z-DNA complexes, three identical, conserved residues (N173, Y177, and W195 in the Zα domain of human ADAR1) play central roles in the interaction with Z-DNA. ZBPs convert a 6-base DNA pair to a Z-form helix via the B-Z transition mechanism in which the ZBP first binds to B-DNA and then shifts the equilibrium from B-DNA to Z-DNA, a conformation that is then selectively stabilized by the additional binding of a second ZBP molecule. During B-Z transition, ZBPs selectively recognize the alternating d(CG)n sequence and convert it to a Z-form helix in long genomic DNA through multiple sequence discrimination steps. In addition, the intermediate complex formed by ZBPs and B-DNA, which is modulated by varying conditions, determines the degree of B-Z transition.

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