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Special Issue "Identification and Roles of the Structure of DNA"

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry, Molecular Biology and Biophysics".

Deadline for manuscript submissions: closed (30 May 2014)

Special Issue Editor

Guest Editor
Prof. Dr. Youri Timsit (Website)

CNRS, Aix-Marseille Université, IGS UMR7256, FR-13288 Marseille, France
Interests: higher-order DNA structures; chirality; chromatin folding; topology; DNA unwinding; DNA self-assembly; DNA dynamics; DNA flexibility; kinking; base-pair opening

Special Issue Information

Dear Colleagues,

Since its discovery in 1953, the double helix has been mainly considered as a passive support of the genetic information. However, this current view overlooks subtle properties of DNA that possesses all the attributes to be an active player in the cell. Indeed, a complex interplay between the nucleotide sequence and its molecular environment generates DNA structures that may play critical roles in key cellular functions. From local base-pair opening to global topology, the double helix is finely tuned to solve the multiple tasks required to generate and regulate the genetic information. For example, the DNA structure may directly influence the rate of replication errors within the active site of DNA polymerases, but it can also direct chiral DNA–DNA interactions that help to locally sense the global DNA topology by type II topoisomerases. Understanding how DNA may actively contribute to generate, control and spatially organize the genetic information, requires deciphering the complex relationships between the DNA sequence, structure, dynamics and the electrostatic environment. The aim of this Special Issue is to explore these new concepts in combining experimental and theoretical studies.

Dr. Youri Timsit
Guest Editor

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed Open Access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs).

Keywords

  • Higher-order DNA structures
  • chirality
  • chromatin folding
  • topology
  • DNA unwinding
  • DNA self-assembly
  • DNA dynamics
  • DNA flexibility
  • kinking
  • base-pair opening

Published Papers (9 papers)

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Research

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Open AccessArticle What Controls DNA Looping?
Int. J. Mol. Sci. 2014, 15(9), 15090-15108; doi:10.3390/ijms150915090
Received: 11 July 2014 / Revised: 11 August 2014 / Accepted: 19 August 2014 / Published: 27 August 2014
Cited by 2 | PDF Full-text (2377 KB) | HTML Full-text | XML Full-text
Abstract
The looping of DNA provides a means of communication between sequentially distant genomic sites that operate in tandem to express, copy, and repair the information encoded in the DNA base sequence. The short loops implicated in the expression of bacterial genes suggest [...] Read more.
The looping of DNA provides a means of communication between sequentially distant genomic sites that operate in tandem to express, copy, and repair the information encoded in the DNA base sequence. The short loops implicated in the expression of bacterial genes suggest that molecular factors other than the naturally stiff double helix are involved in bringing the interacting sites into close spatial proximity. New computational techniques that take direct account of the three-dimensional structures and fluctuations of protein and DNA allow us to examine the likely means of enhancing such communication. Here, we describe the application of these approaches to the looping of a 92 base-pair DNA segment between the headpieces of the tetrameric Escherichia coli Lac repressor protein. The distortions of the double helix induced by a second protein—the nonspecific nucleoid protein HU—increase the computed likelihood of looping by several orders of magnitude over that of DNA alone. Large-scale deformations of the repressor, sequence-dependent features in the DNA loop, and deformability of the DNA operators also enhance looping, although to lesser degrees. The correspondence between the predicted looping propensities and the ease of looping derived from gene-expression and single-molecule measurements lends credence to the derived structural picture. Full article
(This article belongs to the Special Issue Identification and Roles of the Structure of DNA)
Figures

Open AccessArticle Theoretical Study of the Transpore Velocity Control of Single-Stranded DNA
Int. J. Mol. Sci. 2014, 15(8), 13817-13832; doi:10.3390/ijms150813817
Received: 10 June 2014 / Revised: 15 July 2014 / Accepted: 22 July 2014 / Published: 11 August 2014
Cited by 3 | PDF Full-text (1565 KB) | HTML Full-text | XML Full-text
Abstract
The electrokinetic transport dynamics of deoxyribonucleic acid (DNA) molecules have recently attracted significant attention in various fields of research. Our group is interested in the detailed examination of the behavior of DNA when confined in micro/nanofluidic channels. In the present study, the [...] Read more.
The electrokinetic transport dynamics of deoxyribonucleic acid (DNA) molecules have recently attracted significant attention in various fields of research. Our group is interested in the detailed examination of the behavior of DNA when confined in micro/nanofluidic channels. In the present study, the translocation mechanism of a DNA-like polymer chain in a nanofluidic channel was investigated using Langevin dynamics simulations. A coarse-grained bead-spring model was developed to simulate the dynamics of a long polymer chain passing through a rectangular cross-section nanopore embedded in a nanochannel, under the influence of a nonuniform electric field. Varying the cross-sectional area of the nanopore was found to allow optimization of the translocation process through modification of the electric field in the flow channel, since a drastic drop in the electric potential at the nanopore was induced by changing the cross-section. Furthermore, the configuration of the polymer chain in the nanopore was observed to determine its translocation velocity. The competition between the strength of the electric field and confinement in the small pore produces various transport mechanisms and the results of this study thus represent a means of optimizing the design of nanofluidic devices for single molecule detection. Full article
(This article belongs to the Special Issue Identification and Roles of the Structure of DNA)
Open AccessCommunication DNA Break Mapping Reveals Topoisomerase II Activity Genome-Wide
Int. J. Mol. Sci. 2014, 15(7), 13111-13122; doi:10.3390/ijms150713111
Received: 31 May 2014 / Revised: 9 July 2014 / Accepted: 14 July 2014 / Published: 23 July 2014
Cited by 7 | PDF Full-text (1234 KB) | HTML Full-text | XML Full-text
Abstract
Genomic DNA is under constant assault by endogenous and exogenous DNA damaging agents. DNA breakage can represent a major threat to genome integrity but can also be necessary for genome function. Here we present approaches to map DNA double-strand breaks (DSBs) and [...] Read more.
Genomic DNA is under constant assault by endogenous and exogenous DNA damaging agents. DNA breakage can represent a major threat to genome integrity but can also be necessary for genome function. Here we present approaches to map DNA double-strand breaks (DSBs) and single-strand breaks (SSBs) at the genome-wide scale by two methods called DSB- and SSB-Seq, respectively. We tested these methods in human colon cancer cells and validated the results using the Topoisomerase II (Top2)-poisoning agent etoposide (ETO). Our results show that the combination of ETO treatment with break-mapping techniques is a powerful method to elaborate the pattern of Top2 enzymatic activity across the genome. Full article
(This article belongs to the Special Issue Identification and Roles of the Structure of DNA)
Open AccessArticle Base Flip in DNA Studied by Molecular Dynamics Simulationsof Differently-Oxidized Forms of Methyl-Cytosine
Int. J. Mol. Sci. 2014, 15(7), 11799-11816; doi:10.3390/ijms150711799
Received: 30 May 2014 / Revised: 23 June 2014 / Accepted: 25 June 2014 / Published: 3 July 2014
PDF Full-text (1865 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Distortions in the DNA sequence, such as damage or mispairs, are specifically recognized and processed by DNA repair enzymes. Many repair proteins and, in particular, glycosylases flip the target base out of the DNA helix into the enzyme’s active site. Our molecular [...] Read more.
Distortions in the DNA sequence, such as damage or mispairs, are specifically recognized and processed by DNA repair enzymes. Many repair proteins and, in particular, glycosylases flip the target base out of the DNA helix into the enzyme’s active site. Our molecular dynamics simulations of DNA with intact and damaged (oxidized) methyl-cytosine show that the probability of being flipped is similar for damaged and intact methyl-cytosine. However, the accessibility of the different 5-methyl groups allows direct discrimination of the oxidized forms. Hydrogen-bonded patterns that vary between methyl-cytosine forms carrying a carbonyl oxygen atom are likely to be detected by the repair enzymes and may thus help target site recognition. Full article
(This article belongs to the Special Issue Identification and Roles of the Structure of DNA)
Figures

Open AccessArticle Comparisons of Non-Gaussian Statistical Models in DNA Methylation Analysis
Int. J. Mol. Sci. 2014, 15(6), 10835-10854; doi:10.3390/ijms150610835
Received: 24 March 2014 / Revised: 12 May 2014 / Accepted: 10 June 2014 / Published: 16 June 2014
Cited by 1 | PDF Full-text (596 KB) | HTML Full-text | XML Full-text
Abstract
As a key regulatory mechanism of gene expression, DNA methylation patterns are widely altered in many complex genetic diseases, including cancer. DNA methylation is naturally quantified by bounded support data; therefore, it is non-Gaussian distributed. In order to capture such properties, we [...] Read more.
As a key regulatory mechanism of gene expression, DNA methylation patterns are widely altered in many complex genetic diseases, including cancer. DNA methylation is naturally quantified by bounded support data; therefore, it is non-Gaussian distributed. In order to capture such properties, we introduce some non-Gaussian statistical models to perform dimension reduction on DNA methylation data. Afterwards, non-Gaussian statistical model-based unsupervised clustering strategies are applied to cluster the data. Comparisons and analysis of different dimension reduction strategies and unsupervised clustering methods are presented. Experimental results show that the non-Gaussian statistical model-based methods are superior to the conventional Gaussian distribution-based method. They are meaningful tools for DNA methylation analysis. Moreover, among several non-Gaussian methods, the one that captures the bounded nature of DNA methylation data reveals the best clustering performance. Full article
(This article belongs to the Special Issue Identification and Roles of the Structure of DNA)

Review

Jump to: Research

Open AccessReview DNA and RNA Quadruplex-Binding Proteins
Int. J. Mol. Sci. 2014, 15(10), 17493-17517; doi:10.3390/ijms151017493
Received: 20 August 2014 / Revised: 15 September 2014 / Accepted: 22 September 2014 / Published: 29 September 2014
Cited by 20 | PDF Full-text (1119 KB) | HTML Full-text | XML Full-text
Abstract
Four-stranded DNA structures were structurally characterized in vitro by NMR, X-ray and Circular Dichroism spectroscopy in detail. Among the different types of quadruplexes (i-Motifs, minor groove quadruplexes, G-quadruplexes, etc.), the best described are G-quadruplexes which are featured by Hoogsteen base-paring. Sequences [...] Read more.
Four-stranded DNA structures were structurally characterized in vitro by NMR, X-ray and Circular Dichroism spectroscopy in detail. Among the different types of quadruplexes (i-Motifs, minor groove quadruplexes, G-quadruplexes, etc.), the best described are G-quadruplexes which are featured by Hoogsteen base-paring. Sequences with the potential to form quadruplexes are widely present in genome of all organisms. They are found often in repetitive sequences such as telomeric ones, and also in promoter regions and 5' non-coding sequences. Recently, many proteins with binding affinity to G-quadruplexes have been identified. One of the initially portrayed G-rich regions, the human telomeric sequence (TTAGGG)n, is recognized by many proteins which can modulate telomerase activity. Sequences with the potential to form G-quadruplexes are often located in promoter regions of various oncogenes. The NHE III1 region of the c-MYC promoter has been shown to interact with nucleolin protein as well as other G-quadruplex-binding proteins. A number of G-rich sequences are also present in promoter region of estrogen receptor alpha. In addition to DNA quadruplexes, RNA quadruplexes, which are critical in translational regulation, have also been predicted and observed. For example, the RNA quadruplex formation in telomere-repeat-containing RNA is involved in interaction with TRF2 (telomere repeat binding factor 2) and plays key role in telomere regulation. All these fundamental examples suggest the importance of quadruplex structures in cell processes and their understanding may provide better insight into aging and disease development. Full article
(This article belongs to the Special Issue Identification and Roles of the Structure of DNA)
Open AccessReview Chromatin Structure and Dynamics in Hot Environments: Architectural Proteins and DNA Topoisomerases of Thermophilic Archaea
Int. J. Mol. Sci. 2014, 15(9), 17162-17187; doi:10.3390/ijms150917162
Received: 22 July 2014 / Revised: 19 August 2014 / Accepted: 9 September 2014 / Published: 25 September 2014
PDF Full-text (1072 KB) | HTML Full-text | XML Full-text
Abstract
In all organisms of the three living domains (Bacteria, Archaea, Eucarya) chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome [...] Read more.
In all organisms of the three living domains (Bacteria, Archaea, Eucarya) chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair). Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C), chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity. Full article
(This article belongs to the Special Issue Identification and Roles of the Structure of DNA)
Open AccessReview Making the Bend: DNA Tertiary Structure and Protein-DNA Interactions
Int. J. Mol. Sci. 2014, 15(7), 12335-12363; doi:10.3390/ijms150712335
Received: 21 May 2014 / Revised: 1 July 2014 / Accepted: 1 July 2014 / Published: 14 July 2014
Cited by 7 | PDF Full-text (1215 KB) | HTML Full-text | XML Full-text
Abstract
DNA structure functions as an overlapping code to the DNA sequence. Rapid progress in understanding the role of DNA structure in gene regulation, DNA damage recognition and genome stability has been made. The three dimensional structure of both proteins and DNA plays [...] Read more.
DNA structure functions as an overlapping code to the DNA sequence. Rapid progress in understanding the role of DNA structure in gene regulation, DNA damage recognition and genome stability has been made. The three dimensional structure of both proteins and DNA plays a crucial role for their specific interaction, and proteins can recognise the chemical signature of DNA sequence (“base readout”) as well as the intrinsic DNA structure (“shape recognition”). These recognition mechanisms do not exist in isolation but, depending on the individual interaction partners, are combined to various extents. Driving force for the interaction between protein and DNA remain the unique thermodynamics of each individual DNA-protein pair. In this review we focus on the structures and conformations adopted by DNA, both influenced by and influencing the specific interaction with the corresponding protein binding partner, as well as their underlying thermodynamics. Full article
(This article belongs to the Special Issue Identification and Roles of the Structure of DNA)
Figures

Open AccessReview The Self-Assembled Behavior of DNA Bases on the Interface
Int. J. Mol. Sci. 2014, 15(2), 1901-1914; doi:10.3390/ijms15021901
Received: 5 December 2013 / Revised: 31 December 2013 / Accepted: 7 January 2014 / Published: 27 January 2014
Cited by 6 | PDF Full-text (4287 KB) | HTML Full-text | XML Full-text
Abstract
A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA [...] Read more.
A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures. In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. From the ideal condition to a more realistic environment, the self-assembled behaviors of DNA bases are introduced. In a vacuum system, the energetic advantages will dominate the assembly formation of DNA bases, while at ambient condition, more factors such as conformational freedom and the biochemical environment will be considered. Therefore, the assemblies of DNA bases at ambient condition are different from the ones obtained under vacuum. We present the ordered nanostructures formed by DNA bases at both vacuum and ambient condition. To construct and tailor the nanostructure through the interaction between DNA bases, it is important to understand the assembly behavior and features of DNA bases and their derivatives at ambient condition. The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface. Full article
(This article belongs to the Special Issue Identification and Roles of the Structure of DNA)

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