Utilization of Computer Science for Construction and Characterization of DNA nano-Structures (original) (raw)

Design Approaches and Computational Tools for DNA Nanostructures

IEEE Open Journal of Nanotechnology

Designing a structure in nanoscale with desired shape and properties has been enabled by structural DNA nanotechnology. Design strategies in this research field have evolved to interpret various aspects of increasingly more complex nanoscale assembly and to realize molecular-level functionality by exploring static to dynamic characteristics of the target structure. Computational tools have naturally been of significant interest as they are essential to achieve a fine control over both shape and physicochemical properties of the structure. Here, we review the basic design principles of structural DNA nanotechnology together with its computational analysis and design tools.

DNA closed nanostructures: a structural and Monte Carlo simulation study

The Journal of …, 2008

DNA nanoconstructs are obtained in solution by using six unique 42-mer DNA oligonucleotides, whose sequences have been designed to form a pseudohexagonal structure. The required flexibility is provided by the insertion of two non-base-paired thymines in the middle of each sequence that work as flexible hinges and constitute the corners of the nanostructure when formed. We show that hexagonally shaped nanostructures of about 7 nm diameter and their corresponding linear open constructs are formed by self-assembly of the specifically designed linear oligonucleotides. The structural and dynamical characterization of the nanostructure is obtained in situ for the first time by using dynamic light scattering (DLS), a noninvasive method that provides a fast dynamic and structural analysis and allows the characterization of the different synthetic DNA nanoconstructs in solution. A validation of the LS results is obtained through Monte Carlo (MC) simulations and atomic force microscopy (AFM). In particular, a mesoscale molecular model for DNA, developed by Knotts et al., is exploited to perform MC simulations and to obtain information about the conformations as well as the conformational flexibilities of these nanostructures, while AFM provides a very detailed particle analysis that yields an estimation of the particle size and size distribution. The structural features obtained by MC and AFM are in good agreement with DLS, showing that DLS is a fast and reliable tool for characterization of DNA nanostructures in solution.

Mastering the complexity of DNA nanostructures

Trends in Biotechnology, 2006

The self-assembly of oligodeoxynucleotides is a versatile and powerful tool for the construction of objects in the nanoscale. The strictly information-driven pairing of DNA fragments can be used to rationally design and build nanostructures with planned topologies and geometries. Taking advantage of the steadily expanding library of well-characterized DNA motifs, several examples of structures with different dimensionalities have appeared in the literature in the past few years, laying the foundations for a promising DNA-mediated, bottom-up approach to nanotechnology. This article focuses on recent developments in this area of research and proposes a classification of DNA nanostructures based on topological considerations in addition to describing strategies for tackling the inherent complexities of such an endeavor.

Rational Design of DNA Nanoarchitectures

Angewandte Chemie International Edition, 2006

DNA has many physical and chemical properties that make it a powerful material for molecular constructions at the nanometer length scale. In particular, its ability to form duplexes and other secondary structures through predictable nucleotide-sequencedirected hybridization allows for the design of programmable structural motifs which can self-assemble to form large supramolecular arrays, scaffolds, and even mechanical and logical nanodevices. Despite the large variety of structural motifs used as building blocks in the programmed assembly of supramolecular DNA nanoarchitectures, the various modules share underlying principles in terms of the design of their hierarchical configuration and the implemented nucleotide sequences. This Review is intended to provide an overview of this fascinating and rapidly growing field of research from the structural design point of view. From the Contents 1. Introduction 1857 2. General Considerations of DNA-Sequence Design 1858 3. One-Dimensional DNA Strands for Assembly and Immobilization of Non-Nucleic Acid Compounds 1859 4. Design and Assembly of DNA Motifs 1860 5. Three-Dimensional Structures from DNA 1866 6. Applications of DNA Nanoarchitectures 1868 7. Conclusions and Perspectives 1872 DNA Nanoarchitectures Angewandte Chemie Udo Feldkamp is a research assistant at the University of Dortmund (Germany). He was born in Duisburg and studied Computer Science in Kaiserslautern and Dortmund, where he also completed his PhD thesis on computer-aided DNA sequence design under the supervision of Prof. Wolfgang Banzhaf. His research still focuses on DNA-based nanotechnology and DNA computing, but he is also interested in other fields of bioinformatics and in computational intelligence. Christof M. Niemeyer has been Professor of Chemistry (chair of Biological and Chemical Microstructuring) at the University of Dortmund (Germany) since 2002. He studied chemistry at the University of Marburg and completed his PhD on organometallic chemistry at the Max-Planck-Institut für Kohlenforschung in Mülheim/Ruhr with Prof. Manfred T. Reetz. He then did postdoctoral research at the Center for Advanced Biotechnology in Boston (USA) with Prof. Charles R. Cantor, and received his habilitation at the University of Bremen. He is interested in semisynthetic DNA-protein and nanoparticle-conjugates as well as their applications in life sciences, catalysis, and molecular nanotechnology.

DNAjig: A New Approach for Building DNA Nanostructures

2009

DNA self-assembly is an emerging technique in DNA nanotechnology that holds promise for high impact applications such as in the synthesis of DNA-based nanodevices in medicine, robotics and electronics. Recent advancements in technologies and ideas have spurred new growth in the area. The most significant challenge faced by designers in the field is the lack of algorithmic and software options to aid in the design process, and as a result the scope of synthesis has been restricted to modeling a limited set of shapes in 2D. In this paper, we propose a new design methodology called DNAjig to build DNA nanostructures. The highlights of this method are as follows: i) The construction procedure is based on a novel application of space-filling curves to model the shape of an arbitrary user-specified 2D or 3D object. ii) The method results in a simple, yet recursively constructable design layout that is inherently interlocked. iii) Almost all steps within the proposed design procedure can be automated and we present algorithms and a base-version implementation for the same. Wetlab validation showing the results of self-assembly of our first batch of computer generated 2D models is presented.

CATANA: an online modelling environment for proteins and nucleic acid nanostructures

Nucleic Acids Research

In the last decade, significant advances have been made towards the rational design of proteins, DNA, and other organic nanostructures. The emerging possibility to precisely engineer molecular structures resulted in a wide range of new applications in fields such as biotechnology or medicine. The complexity and size of the artificial molecular systems as well as the number of interactions are greatly increasing and are manifesting the need for computational design support. In addition, a new generation of AI-based structure prediction tools provides researchers with completely new possibilities to generate recombinant proteins and functionalized DNA nanostructures. In this study, we present Catana, a web-based modelling environment suited for proteins and DNA nanostructures. User-friendly features were developed to create and modify recombinant fusion proteins, predict protein structures based on the amino acid sequence, and manipulate DNA origami structures. Moreover, Catana was jo...

Extending the Repertoire of Structures in DNA Nanotechnology

American Journal of Nanotechnology, 2015

DNA nanotechnology remains an active area of research and advances have been reviewed recently. DNA nanotechnology seeks to deploy molecules at an atomic level and on a small molecule scale. Other techniques in biophysics and biochemistry do not need to address the issue of the true structure of the nucleic acids at an atomic level but, rather, at a macro-atomic level such as in genetics and in immunology, for example. Accordingly, DNA nanotechnology is perhaps uniquely dependent upon exact clarity in the secondary and tertiary structures of the nucleic acids, as well as that can ever be achieved. Challenges include expanding the use of DNA in medicine, and the construction of detectors with higher sensitivity for biological and chemical settings. Though increasingly complex architectures have been constructed, novel approaches to a greater rôle in biological computation and data storage remain important goals. Here a repertoire of structures for DNA at an atomic level is described which offers a new conjecture with which to move forward. The DNA double helix model faces many problems which have become apparent in the 62 years of research in molecular biology that have elapsed since it was formulated by Watson and Crick in 1953. Experimental evidence is set out seeking to show that the only truly side-by-side alternative, the paranemic model, accounts better for the wide range of phenomena otherwise inexplicable with the double helix model. This paranemic model can engage in a repertoire of structural options denied to the DNA double helix model. Without the requirement to postulate unwinding of the DNA strands, the nucleotide base sequence is immediately accessible to complementary DNA sequences to promote rapid detection of specific molecules in biological and medical settings. Rapid switching between Watson-Crick and Hoogsteen base pairing and four-stranded structures can allow greater complexity in the construction of molecular switches and digital programming.

Overview of New Structures for DNA-Based Nanofabrication and Computation

2000

Summary This paper presents an overview of recent experimental progress by the Duke DNA NanoTech Group in our efforts to utilize novel DNA nanostructures for computational self-assembly as well as for templates in the fabrication of functional nano-patterned materials. We have prototyped a new DNA tile type known as the 4x4 (a cross-like structure composed of four four-arm junctions) upon

Design Optimization for DNA Nanostructures

American Journal of Undergraduate Research, 2011

This paper is concerned with minimizing the cost of self-assembling DNA nanostructures. We first demonstrate that the octet truss provides an accurate geometric framework for current branched junction molecule assembly. We then develop a method of differentiating among junction molecules, the basic building blocks of the nanostructures themselves, within this structure. We use this approach to find the minimum number of junction molecules necessary to construct all of the platonic and archimedean solids naturally occurring within the octet truss.

DNA by Design: De novo Computational Framework for DNA Sequence Design and Nanotechnology

Journal of self-assembly and molecular electronics, 2022

Chemical analysis of metalized DNA has made it quite clear that traditional models of DNA thermodynamics are insufficient to predict and control self-assembly in the context of orthogonally-paired nucleotides. Recently, there has been an increase in reports of Watson-Crick assembly of DNA wires and nanostructures [1-4]. The ability to add or remove pairing rules between nucleobases toward non-Watson-Crick, or orthogonal, self-assembly alters the fundamental language of DNA assembly: this change in behavior necessitates an accompanying shift in computational design. We begin by