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Showing papers on "Molecular models of DNA published in 2011"


Journal ArticleDOI
TL;DR: The structural, mechanical, and thermodynamic properties of a coarse-grained model of DNA similar to that recently introduced in a study of DNA nanotweezers are explored, resulting in an "average base" description of DNA.
Abstract: We explore in detail the structural, mechanical, and thermodynamic properties of a coarse-grained model of DNA similar to that recently introduced in a study of DNA nanotweezers [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, Phys. Rev. Lett. 134, 178101 (2010)]. Effective interactions are used to represent chain connectivity, excluded volume, base stacking, and hydrogen bonding, naturally reproducing a range of DNA behavior. The model incorporates the specificity of Watson–Crick base pairing, but otherwise neglects sequence dependence of interaction strengths, resulting in an “average base” description of DNA. We quantify the relation to experiment of the thermodynamics of single-stranded stacking, duplex hybridization, and hairpin formation, as well as structural properties such as the persistence length of single strands and duplexes, and the elastic torsional and stretching moduli of double helices. We also explore the model's representation of more complex motifs involving dangling ends, bulged bas...

424 citations


Journal ArticleDOI
TL;DR: It is shown that DNA can be used to create diverse bonds using an entirely different principle: the geometric arrangement of blunt-end stacking interactions, which may guide strategies for molecular recognition in systems beyond DNA nanostructures.
Abstract: From ligand-receptor binding to DNA hybridization, molecular recognition plays a central role in biology. Over the past several decades, chemists have successfully reproduced the exquisite specificity of biomolecular interactions. However, engineering multiple specific interactions in synthetic systems remains difficult. DNA retains its position as the best medium with which to create orthogonal, isoenergetic interactions, based on the complementarity of Watson-Crick binding. Here we show that DNA can be used to create diverse bonds using an entirely different principle: the geometric arrangement of blunt-end stacking interactions. We show that both binary codes and shape complementarity can serve as a basis for such stacking bonds, and explore their specificity, thermodynamics and binding rules. Orthogonal stacking bonds were used to connect five distinct DNA origami. This work, which demonstrates how a single attractive interaction can be developed to create diverse bonds, may guide strategies for molecular recognition in systems beyond DNA nanostructures.

349 citations


Book
23 Sep 2011
TL;DR: The basis for the selectivity of these enzymes is discussed with reference to their cleavage of cruciform loops in poly d(AT)n and of protonated polypurine/polypyrimidine structures.
Abstract: The family of zinc dependent endonucleases (Ee 30.1.30.x, herein referred to as SS nucleases, reviewed in 1) exemplified by Sl and mung bean nucleases, have been widely regarded as being specific for single stranded nucleic acids. These enzymes have recently been shown to recognize a variety of non-B structures in double stranded DNA (2-14). The basis for the selectivity of these enzymes is discussed with reference to their cleavage of cruciform loops in poly d(AT)n.d(AT)n and of protonated polypurine/polypyrimidine structures. Evidence is presented for a novel left handed form of d('IC)n.d(GA)n and for unexpectedly long range interactions between regions of different structure in plasmid DNA molecules. The existence of these interactions indicate that even the "normal" B-form of double stranded DNA has properties which are not predicted by classical theories of nucleic acid structure.

305 citations


Journal ArticleDOI
TL;DR: A brief description of main experimental features of DNA condensation inside viruses, bacteria, eukaryotes and the test tube and main theoretical approaches for the description of these systems are presented.
Abstract: DNA is stored in vivo in a highly compact, so-called condensed phase, where gene regulatory processes are governed by the intricate interplay between different states of DNA compaction. These systems often have surprising properties, which one would not predict from classical concepts of dilute solutions. The mechanistic details of DNA packing are essential for its functioning, as revealed by the recent developments coming from biochemistry, electrostatics, statistical mechanics, and molecular and cell biology. Different aspects of condensed DNA behavior are linked to each other, but the links are often hidden in the bulk of experimental and theoretical details. Here we try to condense some of these concepts and provide interconnections between the different fields. After a brief description of main experimental features of DNA condensation inside viruses, bacteria, eukaryotes and the test tube, main theoretical approaches for the description of these systems are presented. We end up with an extended discussion of the role of DNA condensation in the context of gene regulation and mention potential applications of DNA condensation in gene therapy and biotechnology.

225 citations


Journal ArticleDOI
TL;DR: An experimentally parameterized, coarse-grained model that incorporates Hoogsteen bonds is developed that reproduces many of the microscopic features of double-stranded DNA and captures the experimental melting curves for a number of short DNA hairpins, even when the open state forms complicated secondary structures.
Abstract: DNA produces a wide range of structures in addition to the canonical B-form of double-stranded DNA. Some of these structures are stabilized by Hoogsteen bonds. We developed an experimentally parameterized, coarse-grained model that incorporates such bonds. The model reproduces many of the microscopic features of double-stranded DNA and captures the experimental melting curves for a number of short DNA hairpins, even when the open state forms complicated secondary structures. We demonstrate the utility of the model by simulating the folding of a thrombin aptamer, which contains G-quartets, and strand invasion during triplex formation. Our results highlight the importance of including Hoogsteen bonding in coarse-grained models of DNA.

68 citations


Reference BookDOI
02 Sep 2011
TL;DR: The Liquid-Crystalline State of DNA in Biological Objects DNA and Biological objects DNA Reactions under conditions Causing Liquid- Crystalline Dispersions Molecular Crowding Condensation of DNA under the Effect of Chitosan in Conditions Causing molecular Crowding Activity of Nucleolytic Enzymes Under Conditions of Molecular Crowded Activity of ProteolyticEnzymes under conditions of Molecularrowding DNA
Abstract: THE LIQUID-CRYSTALLINE STATE OF DNA The Condensed State of the High-Molecular-Mass Double-Stranded DNA The DNA Condensation and Aggregation Polyphosphates as a Simplified DNA Model Models of High-Molecular-Mass DNA Condensation in Water-Polymeric Solutions Grosberg Model of High-Molecular-Mass DNA Condensation Liquid-Crystalline Phases of the Low-Molecular-Mass Double-Stranded DNA Molecules Ordering of Low-Molecular-Mass Double-Stranded DNAs Brief Concept of Types of Liquid-Crystalline Phases Liquid-Crystalline Phases of Low-Molecular-Mass Double-Stranded DNA Molecules Dispersions of Low-Molecular-Mass Double-Stranded DNA Molecules Low-Molecular-Mass Double-Stranded DNA Dispersions in Water-Polymer Solutions Formation of DNA Dispersions in PEG-Containing Solutions Circular Dichroism of Nucleic Acid Dispersions Circular Dichroism as a Method of Proof of Cholesteric Packing of Nucleic Acid Molecules in Dispersion Particles and Analysis of Their Properties Effect of Different Factors on Formation and Properties of CLCD Particles Parameter of Nucleic Acid Molecule Order in CLCD Particles Polymorphism of Liquid-Crystalline Structures Formed by (DNA-Polycation) Complexes Some Peculiarities of Interaction of DNA Molecules with Polycations Specificity of Chitosan Binding to DNA Formation of Dispersions of (DNA-Chitosan) Complexes CD Spectra of Dispersions Formed by (DNA-Chitosan) Complexes X-Ray Parameters of Phases Formed by (DNA-Chitosan) Complexes Dependence of Efficiency of CLCD Formation by (DNA-Chitosan) Complexes on Various Factors Peculiarities of Interaction of Chitosan Molecules with Nucleic Acids Attempt at a Theoretical Description of Interactions Occurring in the (DNA-Chitosan) Complexes and Resulting in the Formation of Liquid-Crystalline Dispersions with Different Optical Properties Liquid-Crystalline State of DNA Circular Molecules Phase Exclusion of Circular Molecules of Nucleic Acids Formation of Dispersions From Circular Superhelical DNA CD Spectra of Circular Superhelical DNA Dispersions Under Conditions That Modify Parameters of Their Secondary Structure Packing Density and Rearrangement of the Spatial Structure of Superhelical DNA Molecules in LCD Particles Topological Forms and Rearrangement of the Spatial Organization of Superhelical DNA Molecules in LCD Particles DNA LIQUID-CRYSTALLINE FORMS AND THEIR BIOLOGICAL ACTIVITY Liquid-Crystalline State of DNA in Biological Objects DNA and Biological Objects DNA Reactions under Conditions Causing Liquid-Crystalline Dispersions Molecular Crowding Condensation of DNA under the Effect of Chitosan in Conditions Causing Molecular Crowding Activity of Nucleolytic Enzymes Under Conditions of Molecular Crowding Activity of Proteolytic Enzymes under Conditions of Molecular Crowding DNA LIQUID-CRYSTALLINE DISPERSIONS IN NANOTECHNOLOGY AND BIOSENSORICS Nanoconstructions Based on Nucleic Acid Molecules The General Concept of Nanotechnology Biological Molecules as a Background for Nanodesign Two Strategies of Nanodesign Based on NA Molecules Biosensors Based on Nucleic Acids General Concept of Construction and Operation of Biosensors Double-Stranded DNA Molecule as Polyfunctional Biosensing Unit Content and Principle of Operation of an Optical Biosensor Based on DNA Liquid-Crystalline Dispersions DNA CLCD Particles as Sensing Units Sandwich-Type Biosensing Units Based on (DNA-Polycation) Liquid-Crystalline Dispersions DNA Nanoconstruction as a Sensing Unit (New Type of Biodetectors) Hydrogels Containing DNA NaCs as New "Film-Type Biodetectors Index

45 citations


Journal ArticleDOI
TL;DR: In this paper, the authors studied the nonlinear dynamics of DNA, for longitudinal and transverse motions, in the framework of the microscopic model of Peyrard and Bishop, which consists of two long elastic homogeneous strands connected with each other by an elastic membrane.

44 citations


Journal ArticleDOI
TL;DR: An open, planar structure of a forked DNA molecule with three duplex arms is revealed and an ion-induced conformational change is demonstrated to serve as a benchmark for DNA-protein interaction studies.
Abstract: Branched DNA structures play critical roles in DNA replication, repair, and recombination in addition to being key building blocks for DNA nanotechnology. Here we combine single-molecule multiparameter fluorescence detection and molecular dynamics simulations to give a general approach to global structure determination of branched DNA in solution. We reveal an open, planar structure of a forked DNA molecule with three duplex arms and demonstrate an ion-induced conformational change. This structure will serve as a benchmark for DNA−protein interaction studies.

36 citations


Book ChapterDOI
TL;DR: This chapter provides step-by-step instructions of how to build atomic scale models of biological and solid-state nanopore systems, use the molecular dynamics method to simulate the electric field-driven transport of ions and DNA through the nanopores, and analyze the results of such computational experiments.
Abstract: Using nanopores to sequence DNA rapidly and at a low cost has the potential to radically transform the field of genomic research. However, despite all the exciting developments in the field, sequencing DNA using a nanopore has yet to be demonstrated. Among the many problems that hinder development of the nanopore sequencing methods is the inability of current experimental techniques to visualize DNA conformations in a nanopore and directly relate the microscopic state of the system to the measured signal. We have recently shown that such tasks could be accomplished through computation. This chapter provides step-by-step instructions of how to build atomic scale models of biological and solid-state nanopore systems, use the molecular dynamics method to simulate the electric field-driven transport of ions and DNA through the nanopores, and analyze the results of such computational experiments.

33 citations


Journal ArticleDOI
TL;DR: Targeting a quantitative understanding of H1 induced DNA compaction mechanisms, the strategy is based on using small-angle x-ray microdiffraction in combination with microfluidics, which enables time-resolved access to structure formation in situ, in particular, to transient intermediate states.
Abstract: Found in all eukaryotic cells, linker histones H1 are known to bind to and rearrange nucleosomal linker DNA. In vitro, the fundamental nature of H1/DNA interactions has attracted wide interest among research communities—from biologists to physicists. Hence, H1/DNA binding processes and structural and dynamical information about these self-assemblies are of broad importance. Targeting a quantitative understanding of H1 induced DNA compaction mechanisms, our strategy is based on using small-angle x-ray microdiffraction in combination with microfluidics. The usage of microfluidic hydrodynamic focusing devices facilitates a microscale control of these self-assembly processes, which cannot be achieved using conventional bulk setups. In addition, the method enables time-resolved access to structure formation in situ, in particular, to transient intermediate states. The observed time dependent structure evolution shows that the H1/DNA interaction can be described as a two-step process: an initial unspecific bind...

17 citations


Journal ArticleDOI
TL;DR: Using Monte-Carlo simulations, the influence of (non-interacting) mobile DNA-protein-DNA bridges on the configurations of a 1000 bp piece of linear DNA is investigated, for both homogeneous DNA and DNA with an intrinsic planar bend.
Abstract: A large literature exists on modeling the influence of sequence-specific DNA-binding proteins on the shape of the DNA double helix in terms of one or a few fixed constraints. This approach is inadequate for the many proteins that bind DNA sequence independently, and that are present in very large quantities rather than as a few copies, such as the nucleoid proteins in bacterial cells. The influence of such proteins on DNA configurations is better modeled in terms of a great number of mobile constraints on the DNA. Types of constraints that mimic the influence of various known non-specifically DNA binding proteins include DNA bending, wrapping, and bridging. Using Monte-Carlo simulations, we here investigate the influence of (non-interacting) mobile DNA-protein-DNA bridges on the configurations of a 1000 bp piece of linear DNA, for both homogeneous DNA and DNA with an intrinsic planar bend. Results are compared to experimental data on the bacterial nucleoid protein H-NS that forms DNA-protein-DNA bridges. In agreement with data on H-NS, we find very strong positioning of DNA-protein-DNA bridges in the vicinity of planar bends. H-NS binds to DNA very cooperatively, but for non-interacting bridges we only find a moderate DNA-induced clustering. Finally, it has been suggested that H-NS is an important contributor to the extreme condensation of bacterial DNA into a nucleoid structure, but we find only a moderate compaction of DNA coils with increasing numbers of non-interacting bridges. Our results illustrate the importance of quantifying the various effects on DNA configurations that have been proposed for proteins that bind DNA sequence independently.

Journal ArticleDOI
TL;DR: How AFM techniques have been utilized to study DNA and DNA-protein complexes and what types of analyses have accelerated the understanding of the DNA dynamics are reviewed.
Abstract: The elucidation of structure-function relationships of biological samples has become important issue in post-genomic researches. In order to unveil the molecular mechanisms controlling gene regulations, it is essential to understand the interplay between fundamental DNA properties and the dynamics of the entire molecule. The wide range of applicability of atomic force microscopy (AFM) has allowed us to extract physicochemical properties of DNA and DNA-protein complexes, as well as to determine their topographical information. Here, we review how AFM techniques have been utilized to study DNA and DNA-protein complexes and what types of analyses have accelerated the understanding of the DNA dynamics. We begin by illustrating the application of AFM to investigate the fundamental feature of DNA molecules; topological transition of DNA, length dependent properties of DNA molecules, flexibility of double-stranded DNA, and capability of the formation of non-Watson-Crick base pairing. These properties of DNA are critical for the DNA folding and enzymatic reactions. The technical advancement in the time-resolution of AFM and sample preparation methods enabled visual analysis of DNA-protein interactions at sub-second time region. DNA tension-dependent enzymatic reaction and DNA looping dynamics by restriction enzymes were examined at a nanoscale in physiological environments. Contribution of physical properties of DNA to dynamics of nucleosomes and transition of the higher-order structure of reconstituted chromatin are also reviewed.

Journal ArticleDOI
TL;DR: It is discovered that both structural adaptations of the protein and DNA, and the subsequent correlation between them to bind, contribute to the net entropy loss associated with the complex formation.
Abstract: Protein–DNA binding is an important process responsible for the regulation of genetic activities in living organisms. The most crucial issue in this problem is how the protein recognizes the DNA and identifies its target base sequences. Water molecules present around the protein and DNA are also expected to play an important role in mediating the recognition process and controlling the structure of the complex. We have performed atomistic molecular dynamics simulations of an aqueous solution of the protein–DNA complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. The conformational fluctuations of the protein and DNA and the microscopic structure and ordering of water around them in the complex have been explored. In agreement with experimental studies, the calculations reveal conformational immobilization of the terminal segments of the protein on complexation. Importantly, it is discovered that both structural adaptations of the protein and DNA, and the subsequent correlation between them to bind, contribute to the net entropy loss associated with the complex formation. Further, it is found that water molecules around the DNA are more structured with significantly higher density and ordering than that around the protein in the complex.

11 Jul 2011
TL;DR: A graph model of DNA molecules and an abstraction of that model for efficient simulation of molecular systems powered by DNA hybridization is proposed and computer-aided design of reaction systems that consist of biological molecules may become easier than conventional designs that rely on human trial and error.
Abstract: ion of DNA Graph Structures for Efficient Enumeration and Simulation Ibuki Kawamata, Fumiaki Tanaka, Masami Hagiya Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo ibuki@is.s.u-tokyo.ac.jp, fumi95@is.s.u-tokyo.ac.jp, hagiya@is.s.u-tokyo.ac.jp Abstract— We propose a graph model of DNA molecules and an abstraction of that model for efficient simulation of molecular systems powered by DNA hybridization. In this paper, we first explain our DNA molecule model composed of graph data structures and highlight the problem of the large number of DNA structures that results. We then define an abstraction of the model, which focuses on local structures of DNA strands, and introduce reactions among the local structures. To verify the effectiveness of the abstraction, we develop simulators for the original and abstract models, and compare the number of structures generated by those simulators. Based on this research, computer-aided design of reaction systems that consist of biological molecules may become easier than conventional designs that rely on human trial and error. We propose a graph model of DNA molecules and an abstraction of that model for efficient simulation of molecular systems powered by DNA hybridization. In this paper, we first explain our DNA molecule model composed of graph data structures and highlight the problem of the large number of DNA structures that results. We then define an abstraction of the model, which focuses on local structures of DNA strands, and introduce reactions among the local structures. To verify the effectiveness of the abstraction, we develop simulators for the original and abstract models, and compare the number of structures generated by those simulators. Based on this research, computer-aided design of reaction systems that consist of biological molecules may become easier than conventional designs that rely on human trial and error.

Journal ArticleDOI
TL;DR: A new coarse-grained model of the DNA molecule has been proposed, which was elaborated on the basis of its all-atomic model analysis and has been shown to rather well reproduce the DNA structure under low and room temperatures.
Abstract: A new coarse-grained model of the DNA molecule has been proposed, which was elaborated on the basis of its all-atomic model analysis. The model has been shown to rather well reproduce the DNA structure under low and room temperatures. The Young’s and torsion moduli calculated using the coarse-grained model are in close agreement with experimental data and the theoretical results of other authors. The model can be used for DNA fragments of several hundreds base pairs for rather long time scales (of the order of μs) and for simulating their interactions with other structures.

Patent
17 Oct 2011
TL;DR: In this article, a dynamic noise adaptation (DNA) model characterizes a speech input reflecting effects of background noise and a null noise DNA model characterises the speech input based on reflecting a null-noise mismatch condition.
Abstract: A speech processing method and arrangement are described. A dynamic noise adaptation (DNA) model characterizes a speech input reflecting effects of background noise. A null noise DNA model characterizes the speech input based on reflecting a null noise mismatch condition. A DNA interaction model performs Bayesian model selection and re-weighting of the DNA model and the null noise DNA model to realize a modified DNA model characterizing the speech input for automatic speech recognition and compensating for noise to a varying degree depending on relative probabilities of the DNA model and the null noise DNA model.

Journal ArticleDOI
TL;DR: By analysing available crystallographic data and simulating a DNA triangle, it is shown that the double helix geometry, sequence‐specific cytosine–phosphate interactions and divalent cations are in fact responsible for the precise spatial assembly of DNA.
Abstract: DNA self-assembly has crucial implications in reading out the genetic information in the cell and in nanotechnological applications. In a recent paper, self-assembled DNA crystals displaying spectacular triangular motifs have been described (Zheng et al., 2009). The authors claimed that their data demonstrate the possibility to rationally design well-ordered macromolecular 3D DNA lattice with precise spatial control using sticky ends. However, the authors did not recognize the fundamental features that control DNA self-assembly in the lateral direction. By analysing available crystallographic data and simulating a DNA triangle, we show that the double helix geometry, sequence-specific cytosine–phosphate interactions and divalent cations are in fact responsible for the precise spatial assembly of DNA.

Journal Article
TL;DR: In this paper, the authors compare DNA flexibility at the base pair step level modelled using an implicit solvent model to that previously determined from explicit solvent simulations and database analysis and find that the DNA is considerably more flexible when the approximate model is used.
Abstract: DNA flexibility controls packaging, looping and in some cases sequence specific protein binding. Molecular dynamics simulations carried out with a computationally efficient implicit solvent model are potentially a powerful tool for studying larger DNA molecules than can be currently simulated when water and counterions are represented explicitly. In this work we compare DNA flexibility at the base pair step level modelled using an implicit solvent model to that previously determined from explicit solvent simulations and database analysis. Although much of the sequence dependent behaviour is preserved in implicit solvent, the DNA is considerably more flexible when the approximate model is used. In addition we test the ability of the implicit solvent to model stress induced DNA disruptions by simulating a series of DNA minicircle topoisomers which vary in size and superhelical density. When compared with previously run explicit solvent simulations, we find that while the levels of DNA denaturation are similar using both computational methodologies, the specific structural form of the disruptions is different.

Journal ArticleDOI
TL;DR: This paper reviews different mechanical models of double DNA and considers multi-pendulum models appropriate for experimental testing of visco-elastic properties of DNA, which point to existence of independent eigen multi-frequency signals in double DNA chains.
Abstract: In this paper, we review different mechanical models of double DNA (polymer models, elastic rod model, network model, torsional springs model, soliton-existence supporting models) emphasising specifities of each model. We especially considered the DNA model of Kovaleva and Manevich (2005), and Kovaleva et al. (2007). On a basis of this model, we made double DNA helical models with ideally elastic, visco-elastic, hereditary properties and fractional order model and named them multi-pendulum/multi-chain models. For each of these models, we made systems of corresponding differential equations or integro-differential equations or differential fractional order equations. Our results point to existence of independent eigen multi-frequency signals in double DNA chains with subsets of the eigen frequencies as well as set of one eigen frequency normal modes. For some of these multi-pendulum models, we calculate transfer of energy trough the double DNA chains. We consider multi-pendulum models appropriate for experimental testing of visco-elastic properties of DNA.

Book ChapterDOI
01 Jan 2011
TL;DR: This paper shows that triple-stranded DNA structure model can be used for solving the traveling salesman problem and can be solved with plans to optimize the combination of some of the NP problem.
Abstract: Traveling salesman problem is the NP problem of graph theory. The superior solution for traveling salesman problem is the Hamilton ring that finds out to have minimum power in the graph. The triple-stranded DNA computing model has a low rate of wrong solutions. Because the pool of data generated, there are the double helix structure of DNA chain, and the stability of the double-stranded DNA than single strand of DNA stability. The use of triple-stranded DNA model, can be solved with plans to optimize the combination of some of the NP problem. In this paper we show that triple-stranded DNA structure model can be used for solving the traveling salesman problem.

Posted Content
TL;DR: In this paper, a fabrication scheme of DNA nanostructures with non-complementary and/or geometrically incompatible DNA oligonucleotides was presented, which contradicts conventional DNA structure creation rules.
Abstract: Fabrication of DNA nanostructures primarily follows two fundamental rules. First, DNA oligonucleotides mutually combine by Watson-Crick base pairing rules between complementary base sequences. Second, the geometrical compatibility of the DNA oligonucleotide must match for lattices to form. Here we present a fabrication scheme of DNA nanostructures with non-complementary and/or geometrically incompatible DNA oligonucleotides, which contradicts conventional DNA structure creation rules. Quantitative analyses of DNA lattice sizes were carried out to verify the unfavorable binding occurrences which correspond to errors in algorithmic self-assembly. Further studies of these types of bindings may shed more light on the exact mechanisms at work in the self-assembly of DNA nanostructures.

Journal ArticleDOI
TL;DR: In this paper, a method of process DNA-based process management for significant model project is proposed to solve the problem of "two command line" existing in the major model project management at present, and the two-level structure of the process DNA double-strand is analyzed.
Abstract: To solve the problem of “two command line” existing in the significant model project management at present, this paper proposes a method of process DNA-based process management for significant model project. First, the technology process and management process of significant model project are analyzed. Second, the process DNA double-strand of significant model project is constructed employing the elements of technology and management as building blocks; and also, the two-level structure of the process DNA double-strand is analyzed. Third, the process DNA model of significant model project is established and the related formal definitions are given.


Posted Content
TL;DR: In this paper, the authors model the annealing-melting properties of DNA origamis and show that cooperativity between staples is critical to quantitatively explain the folding process.
Abstract: DNA based nanostructures built on a long single stranded DNA scaffold, known as DNA origamis, offer the possibility to organize various molecules at the nanometer scale in one pot experiments. The folding of the scaffold is guaranteed by the presence of short, single stranded DNA sequences (staples), that hold together separate regions of the scaffold. In this paper, we modelize the annealing-melting properties of these DNA constructions. The model captures important features such as the hysteresis between melting and annealing, as well as the dependence upon the topology of the scaffold. We show that cooperativity between staples is critical to quantitatively explain the folding process of DNA origamis.