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

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.

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Controlling Matter at the Molecular Scale with DNA Circuits

Annual Review of Biomedical Engineering ◽

10.1146/annurev-bioeng-060418-052357 ◽

2019 ◽

Vol 21 (1) ◽

pp. 469-493 ◽

Cited By ~ 11

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.

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Automated exploration of DNA-based structure self-assembly networks

Royal Society Open Science ◽

10.1098/rsos.210848 ◽

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.

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

Beilstein Journal of Nanotechnology ◽

10.3762/bjnano.6.148 ◽

2015 ◽

Vol 6 ◽

pp. 1432-1438 ◽

Cited By ~ 3

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.

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Operation of Queue and Stack by DNA Tiles

E3S Web of Conferences ◽

10.1051/e3sconf/202021803051 ◽

2020 ◽

Vol 218 ◽

pp. 03051

Author(s):

Xinxin Zhang ◽

Nan Zhao ◽

Jing Yang

Keyword(s):

Self Assembly ◽

Dna Computing ◽

Active Material ◽

Software Systems ◽

Experimental Conditions ◽

Free System ◽

Insertion And Deletion ◽

Dna Tiles ◽

Dna Strands ◽

First In First Out

DNA is used as self-nanomaterials to assemble into specific structures. DNA tile provides a new idea for the application of DNA tile in the field of computing. Recent years, Queue and Stack are important linear data structures which are used in various software systems widely. The implementation of DNA based queue and stack has been studied continuously for many years. In the traditional DNA computing, queue and stack are mostly realized by DNA strands displacement, restriction endonuclease and ligase were used. However, as an active material, it has a high requirement for enzyme experimental conditions. The purpose of this paper is to implement queue and stack structures using non-enzyme systems. The rule of Queue is characterized by FIFO (first in first out), which allows for insertion at one end of the list and deletion at the other. The rule of Stack is characterized by FILO(first in last out), which allows for insertion and deletion at one end of the list. We are aimed to implement Queue and Stack using self-assembly and disassembly via DNA Tiles. No enzymes are needed for the whole experiment. As an enzyme-free system, it provides a new method to implement stack and queue.

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SELF-RECOGNITION OF DNA FROM LIFE PROCESSES TO DNA COMPUTATION

Biophysical Reviews and Letters ◽

10.1142/s1793048007000490 ◽

2007 ◽

Vol 02 (02) ◽

pp. 123-137 ◽

Cited By ~ 4

Author(s):

WEI DA NG ◽

CHEE KEONG BENJAMIN WONG

Keyword(s):

Nucleic Acid ◽

Self Assembly ◽

Dna Computing ◽

Dna Nanotechnology ◽

Computing Technology ◽

Dna Computation ◽

Dna Codes ◽

Self Recognition ◽

Dna Strands ◽

Adenine Thymine

Ever since the first appearance of deoxyribose nucleic acid (DNA) in 1953, it has fascinated multitudes with its simplicity. With a modest syllabus of four nucleotides (adenine, thymine, cytosine and guanine), it codes for the complexity of life around us. In this paper, we investigate how the structure of DNA codes for life processes and how we can take advantage of its minuscule size, mechanism of self-recognition and self-assembly for "bottom-up" nanotechnology. High hopes are also placed on miniaturizing present computing technology using DNA computing based on two fundamental features; massive parallelism of DNA strands and Watson–Crick complementarity. Advances in DNA-based computation and algorithmic assembly are then used to complement researches in DNA nanotechnology.

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Factors Affecting Molecular Self-Assembly and Its Mechanism

Scientific Research Journal ◽

10.24191/srj.v9i1.5385 ◽

2012 ◽

Vol 9 (1) ◽

pp. 43 ◽

Cited By ~ 1

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.

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A Bottom-Up Approach to Solution-Processed, Atomically Precise Graphitic Cylinders on Surfaces

10.26434/chemrxiv.7158959 ◽

2018 ◽

Author(s):

Erik Leonhardt ◽

Jeff M. Van Raden ◽

David Miller ◽

Lev N. Zakharov ◽

Benjamin Aleman ◽

...

Keyword(s):

Self Assembly ◽

Carbon Nanostructures ◽

Carbon Nanomaterials ◽

Circle Packing ◽

Pyrolytic Graphite ◽

Building Blocks ◽

Bottom Up ◽

Casting Technique ◽

New Class ◽

Solution Casting Technique

Extended carbon nanostructures, such as carbon nanotubes (CNTs), exhibit remarkable properties but are difficult to synthesize uniformly. Herein, we present a new class of carbon nanomaterials constructed via the bottom-up self-assembly of cylindrical, atomically-precise small molecules. Guided by supramolecular design principles and circle packing theory, we have designed and synthesized a fluorinated nanohoop that, in the solid-state, self-assembles into nanotube-like arrays with channel diameters of precisely 1.63 nm. A mild solution-casting technique is then used to construct vertical “forests” of these arrays on a highly-ordered pyrolytic graphite (HOPG) surface through epitaxial growth. Furthermore, we show that a basic property of nanohoops, fluorescence, is readily transferred to the bulk phase, implying that the properties of these materials can be directly altered via precise functionalization of their nanohoop building blocks. The strategy presented is expected to have broader applications in the development of new graphitic nanomaterials with π-rich cavities reminiscent of CNTs.

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Reversible microscale assembly of nanoparticles driven by the phase transition of a thermotropic liquid crystal

10.26434/chemrxiv.5691169 ◽

2017 ◽

Author(s):

Niamh Mac Fhionnlaoich ◽

Stephen Schrettl ◽

Nicholas B. Tito ◽

Ye Yang ◽

Malavika Nair ◽

...

Keyword(s):

Phase Transition ◽

Liquid Crystal ◽

Self Assembly ◽

Nematic Phase ◽

Hierarchical Control ◽

Building Blocks ◽

Model System ◽

Microscopic Level ◽

Reversible Process ◽

Thermotropic Liquid Crystal

The arrangement of nanoscale building blocks into patterns with microscale periodicity is challenging to achieve via self-assembly processes. Here, we report on the phase transition-driven collective assembly of gold nanoparticles in a thermotropic liquid crystal. A temperature-induced transition from the isotropic to the nematic phase leads to the assembly of individual nanometre-sized particles into arrays of micrometre-sized aggregates, whose size and characteristic spacing can be tuned by varying the cooling rate. This fully reversible process offers hierarchical control over structural order on the molecular, nanoscopic, and microscopic level and is an interesting model system for the programmable patterning of nanocomposites with access to micrometre-sized periodicities.

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Synthesis and Self-assembly of Amphiphilic Precision Glycomacromolecules

Polymer Chemistry ◽

10.1039/d1py00422k ◽

2021 ◽

Author(s):

Alexander Banger ◽

Julian Sindram ◽

Marius Otten ◽

Jessica Kania ◽

Alexander Strzelczyk ◽

...

Keyword(s):

Self Assembly ◽

Solid Phase ◽

Building Blocks ◽

Polymer Synthesis

We present the synthesis of so called amphiphilic glycomacromolecules (APGs) by using solid-phase polymer synthesis. Based on tailor made building blocks, monosdisperse APGs with varying compositions are synthesized, introducing carbohydrate...

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