Biophysics of protein–DNA interactions and chromosome organization

Marko, John F.

doi:10.1016/j.physa.2014.07.045

Cited by 55 publications

(83 citation statements)

References 133 publications

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“…At low HU concentration, the bending rigidity of the DNA always is reduced irrespective of whether the HUinduced°exible hinges result in rigid bends. 14,16,18 At higher HU concentration, the spontaneous formation of HU¯laments due to DNA allostery creates large°exible hinges 4 ; however, their e®ectiveness is limited by the repulsive HU-HU electrostatic interaction. Electrostatic interactions increase the rigidity of the¯laments, which consequently increase the sti®ness of the DNA.…”

Section: Discussionmentioning

confidence: 99%

“…13) to incorporate the e®ects of DNA bending or sti®ening proteins. [14][15][16] Through transfer matrix calculations, they provided the exact results of DNA end-to-end distributions and force-extension curves as a function of bending proteins concentration. They particularly showed that both thermally-induced and protein-induced local DNA inhomogeneities could facilitate the cyclization of short DNA molecules.…”

Section: Introductionmentioning

confidence: 99%

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A stochastic reaction-diffusion model for protein aggregation on DNA

Voulgarakis

2017

Int. J. Mod. Phys. C

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Vital functions of DNA, such as transcription and packaging, depend on the proper clustering of proteins on the double strand. The present study investigates how the interplay between DNA allostery and electrostatic interactions a®ects protein clustering. The statistical analysis of a simple but transparent computational model reveals two major consequences of this interplay. First, depending on the protein and salt concentration, protein¯laments exhibit a bimodal DNA sti®ening and softening behavior. Second, within a certain domain of the control parameters, electrostatic interactions can cause energetic frustration that forces proteins to assemble in rigid spiral con¯gurations. Such spiral¯laments might trigger both positive and negative supercoiling, which can ultimately promote gene compaction and regulate the promoter. It has been experimentally shown that bacterial histone-like proteins assemble in similar spiral patterns and/or exhibit the same bimodal behavior. The proposed model can, thus, provide computational insights into the physical mechanisms used by proteins to control the mechanical properties of the DNA.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A stochastic reaction-diffusion model for protein aggregation on DNA

Voulgarakis

2017

Int. J. Mod. Phys. C

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“…Although supercoiled DNA has been extensively studied theoretically (10)(11)(12)(13)(14)(15)(16)(17)(18) as well as experimentally (19)(20)(21)(22)(23)(24)(25)(26), both simulation and experimental studies that directly investigate the large-scale organization of supercoiled DNA are typically limited to supercoiling densities up to the average supercoiling density in E. coli (s~À0.06). However, the topological state of the bacterial chromosome is highly dynamic (27), and both DNA gyrase and RNA polymerase are capable of generating negative supercoiling densities far in excess of average supercoiling levels (28)(29)(30).…”

Section: Introductionmentioning

confidence: 99%

“…Despite decades of theoretical and computational investigation on supercoiled DNA (10)(11)(12)(13)(14)(15)(16)(17)(18)(34)(35)(36), the behavior of supercoiled DNA rings in free solution at the length scale of topological domains in bacteria with supercoiling <s~À0.07 has remained underexplored. However, these larger linking deficits represent an important biological regime, because DNA gyrase is capable of generating supercoiling densities up to s~À0.12, and RNA polymerase has been observed to generate similar or greater linking deficits (28)(29)(30).…”

Section: Introductionmentioning

confidence: 99%

Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation

Krajina

Spakowitz

2016

Biophysical Journal

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Topological constraints, such as those associated with DNA supercoiling, play an integral role in genomic regulation and organization in living systems. However, physical understanding of the principles that underlie DNA organization at biologically relevant length scales remains a formidable challenge. We develop a coarse-grained simulation approach for predicting equilibrium conformations of supercoiled DNA. Our methodology enables the study of supercoiled DNA molecules at greater length scales and supercoiling densities than previously explored by simulation. With this approach, we study the conformational transitions that arise due to supercoiling across the full range of supercoiling densities that are commonly explored by living systems. Simulations of ring DNA molecules with lengths at the scale of topological domains in the Escherichia coli chromosome (~10 kilobases) reveal large-scale conformational transitions elicited by supercoiling. The conformational transitions result in three supercoiling conformational regimes that are governed by a competition among chiral coils, extended plectonemes, and branched hyper-supercoils. These results capture the nonmonotonic relationship of size versus degree of supercoiling observed in experimental sedimentation studies of supercoiled DNA, and our results provide a physical explanation of the conformational transitions underlying this behavior. The length scales and supercoiling regimes investigated here coincide with those relevant to transcription-coupled remodeling of supercoiled topological domains, and we discuss possible implications of these findings in terms of the interplay between transcription and topology in bacterial chromosome organization.

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“…L p has been measured using different methods in various conditions. The values can vary widely [32], but the consensus value for modeling purpose is around 50 nm [33]. …”

Section: Theorymentioning

confidence: 99%

Single-molecule fluorescence studies on DNA looping

Jeong

Kim

2016

Methods

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Structure and dynamics of DNA impact how the genetic code is processed and maintained. In addition to its biological importance, DNA has been utilized as building blocks of various nanomachines and nanostructures. Thus, understanding the physical properties of DNA is of fundamental importance to basic sciences and engineering applications. DNA can undergo various physical changes. Among them, DNA looping is unique in that it can bring two distal sites together, and thus can be used to mediate interactions over long distances. In this paper, we introduce a FRET-based experimental tool to study DNA looping at the single molecule level. We explain the connection between experimental measurables and a theoretical concept known as the J factor with the intent of raising awareness of subtle theoretical details that should be considered when drawing conclusions. We also explore DNA looping-assisted protein diffusion mechanism called intersegmental transfer using protein induced fluorescence enhancement (PIFE). We present some preliminary results and future outlooks.

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Biophysics of protein–DNA interactions and chromosome organization

Cited by 55 publications

References 133 publications

A stochastic reaction-diffusion model for protein aggregation on DNA

A stochastic reaction-diffusion model for protein aggregation on DNA

Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation

Single-molecule fluorescence studies on DNA looping

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