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Hyperplectonemes: A Higher Order Compact and Dynamic DNA Self-Organization

https://doi.org/10.1021/acs.nanolett.6b05294

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Supercoiling-dependent Site-specific Binding of HU to Naked Mu DNA

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Polyelectrolyte Theory

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DNA condensation with polyamines

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Use of site-specific recombination as a probe of DNA structure and metabolism in vivo

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Modeling superhelical DNA: recent analytical and dynamic approaches

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Four-Dimensional Imaging of E. coli Nucleoid Organization and Dynamics in Living Cells

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Bacterial chromatin

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DNA condensation by poly-l-lysine at the single molecule level: Role of DNA concentration and polymer length

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General purpose molecular dynamics simulations fully implemented on graphics processing units

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A Systematic In Vitro Study of Nucleoprotein Complexes Formed by Bacterial Nucleoid-Associated Proteins Revealing Novel Types of DNA Organization

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Structure of plectonemically supercoiled DNA

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Toward an Effective Control of DNA’s Submolecular Conformation on a Surface

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Highly Effective Compaction of Long Duplex DNA Induced by Polyethylene Glycol with Pendant Amino Groups

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Numerical Study of Linear and Circular Model DNA Chains Confined in a Slit: Metric and Topological Properties

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Molecular Dynamics Simulation of Supercoiled DNA Rings

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Influence of DNA Binding Dyes on Bare DNA Structure Studied with Atomic Force Microscopy

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Compact form of DNA induced by spermidine

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Structural diversity of supercoiled DNA

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Bacterial nucleoid-associated proteins, nucleoid structure and gene expression

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Quantifying supercoiling-induced denaturation bubbles in DNA

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FIS modulates growth phase‐dependent topological transitions of DNA in Escherichia coli

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DNA supercoiling contributes to disconnect σS accumulation from σS‐dependent transcription in Escherichia coli

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Multiscaling in a long semiflexible polymer chain in two dimensions

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Chromosomes in living Escherichia coli cells are segregated into domains of supercoiling.

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Atomic force microscopy of long DNA: imaging in air and under water.

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Surface-directed DNA condensation in the absence of soluble multivalent cations

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H-NS mediated compaction of DNA visualised by atomic force microscopy

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An architectural role of the Escherichia coli chromatin protein FIS in organising DNA

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The nucleoid-associated proteins H-NS and FIS modulate the DNA supercoiling response of the pel genes, the major virulence factors in the plant pathogen bacterium Dickeya dadantii

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Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes

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Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling

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Polymer Physics

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Topological domain structure of the Escherichia coli chromosome

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Conformation of Circular DNA in Two Dimensions

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Supercoiling Induces Denaturation Bubbles in Circular DNA

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Conformation of Ring Polymers in 2D Constrained Environments

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Scaling Exponents and Probability Distributions of DNA End-to-End Distance

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DNA structure and function

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Immobilization and condensation of DNA with 3‐aminopropyltriethoxysilane studied by atomic force microscopy

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Organization of supercoil domains and their reorganization by transcription

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Bacterial Chromosome Dynamics

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Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria

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High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

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Changes in the linking number of supercoiled DNA accompany growth transitions in Escherichia coli

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Growth Phase-Dependent Variation in Protein Composition of the Escherichia coli Nucleoid

inferredcites →https://doi.org/10.1146/annurev.bb.23.060194.003141openalex-snapshot

Conformational and Thermodynamic Properties of Supercoiled DNA

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DNA Trace: A Comprehensive Software for Polymer Image Processing

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Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli

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Transposable Prophage Mu Is Organized as a Stable Chromosomal Domain of E. coli

inferredcites →https://doi.org/10.1371/journal.pone.0019172openalex-snapshot

Proteomic Analyses of Nucleoid-Associated Proteins in Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus aureus

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Real-Time Monitoring of Protein Conformational Changes Using a Nano-Mechanical Sensor

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Long-Term Experimental Evolution in Escherichia coli. XII. DNA Topology as a Key Target of Selection

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Gwyddion: an open-source software for SPM data analysis

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