Fullerene Cluster Assisted Self-Assembly of Short DNA Strands into Semiconducting Nanowires

2017 ◽  
Vol 23 (62) ◽  
pp. 15759-15765 ◽  
Author(s):  
Sandeepa Kulala Vittala ◽  
Sajena Kanangat Saraswathi ◽  
Joshy Joseph
Keyword(s):  
Self Assembly ◽  
Semiconducting Nanowires ◽  
Dna Strands

scholarly journals Controlling Matter at the Molecular Scale with DNA Circuits

2019 ◽  
Vol 21 (1) ◽  
pp. 469-493 ◽  
Author(s):  
Dominic Scalise ◽  
Rebecca Schulman
Keyword(s):  
Self Assembly ◽  
Dna Computing ◽  
Chemical Information ◽  
Dna Nanostructures ◽  
Program Complex ◽  
Responsive Materials ◽  
Dna Crystals ◽  
Dna Strands ◽  
Particle Assemblies ◽  
Specific Sequences

In recent years, a diverse set of mechanisms have been developed that allow DNA strands with specific sequences to sense information in their environment and to control material assembly, disassembly, and reconfiguration. These sequences could serve as the inputs and outputs for DNA computing circuits, enabling DNA circuits to act as chemical information processors to program complex behavior in chemical and material systems. This review describes processes that can be sensed and controlled within such a paradigm. Specifically, there are interfaces that can release strands of DNA in response to chemical signals, wavelengths of light, pH, or electrical signals, as well as DNA strands that can direct the self-assembly and dynamic reconfiguration of DNA nanostructures, regulate particle assemblies, control encapsulation, and manipulate materials including DNA crystals, hydrogels, and vesicles. These interfaces have the potential to enable chemical circuits to exert algorithmic control over responsive materials, which may ultimately lead to the development of materials that grow, heal, and interact dynamically with their environments.

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.

Topographic Comparison of G-Wire DNA Imaged by Hydration Scanning Tunneling and Atomic Force Microscopy as a Function of Humidity

1998 ◽  
Vol 4 (S2) ◽  
pp. 302-303
Author(s):  
D. Janigian ◽  
E. Morales ◽  
T. Muir ◽  
B. Garcia ◽  
J. Vesenka
Keyword(s):  
Relative Humidity ◽  
Self Assembly ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Force Microscopy ◽  
Atomic Force ◽  
Wide Range ◽  
Dna Strands ◽  
Humidity Dependence ◽  
Better Than

The tendency of poly-G oligonucleotides to undergo self-assembly into helical nucleic acid tetramers have been termed G-quartets. Also known as G-wires, these structures retain their crystallographic determined dimensions better than duplex DNA when imaged with the atomic force microscope (AFM). Relative humidity has been known to affect both the resolution and measured height DNA strands on mica. The results below aim to develop a model that can be used to define the mechanical properties of G-wires by scanning probe microscopy investigations. G-wires were examined under a wide range of relative humidity to determine their tolerance to shear forces under the AFM, and to establish imaging conditions for hydration scanning tunneling microscopy (HSTM).The relative humidity dependence of G-wires were taken with 125 μm long, 20 μm wide silicon nitride cantilevers in contact AFM mode (spring constant ∼ 0.4 N/m) (Fig. 1).

scholarly journals Review of the Electrical Characterization of Metallic Nanowires on DNA Templates

2018 ◽  
Vol 19 (10) ◽  
pp. 3019 ◽  
Author(s):  
Türkan Bayrak ◽  
Nagesh Jagtap ◽  
Artur Erbe
Keyword(s):  
Electronic Properties ◽  
Self Assembly ◽  
Dna Nanotechnology ◽  
Electrical Characterization ◽  
Dna Nanostructures ◽  
Metallic Nanowires ◽  
Electronic Circuits ◽  
Electrically Conducting ◽  
Dna Strands

The use of self-assembly techniques may open new possibilities in scaling down electronic circuits to their ultimate limits. Deoxyribonucleic acid (DNA) nanotechnology has already demonstrated that it can provide valuable tools for the creation of nanostructures of arbitrary shape, therefore presenting an ideal platform for the development of nanoelectronic circuits. So far, however, the electronic properties of DNA nanostructures are mostly insulating, thus limiting the use of the nanostructures in electronic circuits. Therefore, methods have been investigated that use the DNA nanostructures as templates for the deposition of electrically conducting materials along the DNA strands. The most simple such structure is given by metallic nanowires formed by deposition of metals along the DNA nanostructures. Here, we review the fabrication and the characterization of the electronic properties of nanowires, which were created using these methods.

scholarly journals DNA–melamine hybrid molecules: from self-assembly to nanostructures

2015 ◽  
Vol 6 ◽  
pp. 1432-1438 ◽  
Author(s):  
Rina Kumari ◽  
Shib Shankar Banerjee ◽  
Anil K Bhowmick ◽  
Prolay Das
Keyword(s):  
Self Assembly ◽  
Coupling Reaction ◽  
Building Blocks ◽  
The Self ◽  
Organic Hybrid ◽  
Molecular Building Blocks ◽  
Cross Coupling Reaction ◽  
Linear Chains ◽  
Hybrid Molecules ◽  
Dna Strands

Single-stranded DNA–melamine hybrid molecular building blocks were synthesized using a phosphoramidation cross-coupling reaction with a zero linker approach. The self-assembly of the DNA–organic hybrid molecules was achieved by DNA hybridization. Following self-assembly, two distinct types of nanostructures in the form of linear chains and network arrays were observed. The morphology of the self-assembled nanostructures was found to depend on the number of DNA strands that were attached to a single melamine molecule.

scholarly journals State Complexity of Overlap Assembly

2020 ◽  
pp. 1-20
Author(s):  
Janusz A. Brzozowski ◽  
Lila Kari ◽  
Bai Li ◽  
Marek Szykuła
Keyword(s):  
Self Assembly ◽  
Binary Operation ◽  
The State ◽  
Regular Languages ◽  
Deterministic Finite Automaton ◽  
State Complexity ◽  
Dna Strands ◽  
Unary Languages ◽  
Number Formula ◽  
Dna Strand

The state complexity of a regular language [Formula: see text] is the number [Formula: see text] of states in a minimal deterministic finite automaton (DFA) accepting [Formula: see text]. The state complexity of a regularity-preserving binary operation on regular languages is defined as the maximal state complexity of the result of the operation where the two operands range over all languages of state complexities [Formula: see text] and [Formula: see text], respectively. We determine, for [Formula: see text], [Formula: see text], the exact value of the state complexity of the binary operation overlap assembly on regular languages. This operation was introduced by Csuhaj-Varjú, Petre, and Vaszil to model the process of self-assembly of two linear DNA strands into a longer DNA strand, provided that their ends “overlap”. We prove that the state complexity of the overlap assembly of languages [Formula: see text] and [Formula: see text], where [Formula: see text] and [Formula: see text], is at most [Formula: see text]. Moreover, for [Formula: see text] and [Formula: see text] there exist languages [Formula: see text] and [Formula: see text] over an alphabet of size [Formula: see text] whose overlap assembly meets the upper bound and this bound cannot be met with smaller alphabets. Finally, we prove that [Formula: see text] is the state complexity of the overlap assembly in the case of unary languages and that there are binary languages whose overlap assembly has exponential state complexity at least [Formula: see text].

Basic: Bio-Inspired Assembly of Semiconductor Integrated Circuits

2000 ◽  
Vol 636 ◽  
Author(s):  
R. Bashir ◽  
S. Lee ◽  
D. Guo ◽  
M. Pingle ◽  
D. Bergstrom ◽  
...  
Keyword(s):  
Integrated Circuits ◽  
Self Assembly ◽  
Silicon Layer ◽  
Silicon On Insulator ◽  
General Idea ◽  
Main Theme ◽  
Biologically Inspired ◽  
Silicon Devices ◽  
Dna Strands ◽  
Soi Substrates

AbstractIn the recent years, biologically-inspired self-assembly of artificial structures, some with useful optical properties, has been demonstrated. However, to date there has been no demonstration of self-assembly of useful electronic devices for the construction of complex systems. In this paper, a new process called BASIC (Bio-Inspired Assembly of Semiconductor Integrated Circuits) is proposed. The main theme is to use the mutual binding (hybridization) and specificity of DNA strands (oligonucleotides) for the assembly of useful silicon devices on silicon or other substrate. These devices need to be ‘released’ from their host substrate into a liquid medium where they can be functionalized with single stranded DNA. Silicon-on-insulator (SOI) substrates, which naturally lend themselves for such application, due to the presence of an oxide layer underlying the silicon layer, are used. These devices can vary in size and have a thin gold layer on one surface. This approach can be used to assemble micro and nano-scale devices and circuits and can also be a powerful technique for heterogeneous integration of materials (e.g. Si on Glass or polymer). The general idea of the BASIC process can also be extended to be used with any antibody/antigen complex. Preliminary results regarding the fabrication and release of the device islands will be presented. In addition, surface AFM characterization of the gold surfaces, prior to attachment of bio-molecules, is also presented.

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.

Hydrogen-bond self-assembly of DNA-base analogues — Experimental results

2009 ◽  
Vol 87 (5) ◽  
pp. 627-639 ◽  
Author(s):  
Felaniaina Rakotondradany ◽  
Hanadi Sleiman ◽  
M. A. Whitehead
Keyword(s):  
Hydrogen Bond ◽  
Self Assembly ◽  
Cyanuric Acid ◽  
Experimental Studies ◽  
Acid Complex ◽  
Hybridization Probes ◽  
Dna Strands ◽  
Artificial Dna ◽  
Self Association ◽  
Hydrogen Bonded

A novel biomimetic DNA analogue with fluorescence has been synthesized to generate functional supramolecular architectures. Experimental studies show that triaminopyrimidine nucleoside (2) undergoes a sterically controlled self-assembly into hydrogen-bonded linear tapes and hexameric rosettes. Self-association of the hydrogen-bonded triaminopyrimidine–cyanuric acid complex into elongated, rodlike nanostructures was shown by dynamic light scattering and transmission electron microscopy, suggesting hierarchical formation of higher-order, π-stacked assemblies. The hydrogen-bond self-assembly of the DNA analogue decreased the fluorescence of the nucleosides. This guest-induced fluorescence quenching can be used to develop DNA-hybridization probes. MM+ molecular modelling and semi-empirical molecular orbital PM3 calculations (1) predicted the incorporation of triaminopyrimidine nucleoside into new types of artificial DNA strands and triplex formation with natural, complementary DNA strands containing thymine (1).

Sign in / Sign up

Export Citation Format

Share Document