Extreme bendability of DNA double helix due to bending asymmetry

Salari, Hadi; Eslami-Mossallam, Behrouz; Naderi, Sirvan; Ejtehadi, Mohammad Reza

doi:10.1063/1.4929994

Cited by 15 publications

(15 citation statements)

References 45 publications

(140 reference statements)

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“…To address these issues we have recently applied a mesoscopic Hamiltonian model, which treats the dsDNA at the level of the base pair [26,27], to the analysis of the looping probabilities in short molecules: the obtained J-factors fit the order of magnitude of the experimental data and reproduce the observed trend as a function of the fragment size [28]. Importantly, radial fluctuations between the pair mates and large bending angles between adjacent base pairs have been incorporated in the computational method thus allowing for the formation of kinks which locally unstack the helix [29][30][31][32], enhance the cyclization efficiency and may reduce the persistence length [23,[33][34][35].…”

Section: Analysis Of Looping Probability Induced By T4 Ligase Enzymesmentioning

confidence: 99%

End-to-end distance and contour length distribution functions of DNA helices

Zoli

2018

The Journal of Chemical Physics

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I present a computational method to evaluate the end-to-end and the contour length distribution functions of short DNA molecules described by a mesoscopic Hamiltonian. The method generates a large statistical ensemble of possible configurations for each dimer in the sequence, selects the global equilibrium twist conformation for the molecule, and determines the average base pair distances along the molecule backbone. Integrating over the base pair radial and angular fluctuations, I derive the room temperature distribution functions as a function of the sequence length. The obtained values for the most probable end-to-end distance and contour length distance, providing a measure of the global molecule size, are used to examine the DNA flexibility at short length scales. It is found that, also in molecules with less than ∼60 base pairs, coiled configurations maintain a large statistical weight and, consistently, the persistence lengths may be much smaller than in kilo-base DNA.

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Section: Analysis Of Looping Probability Induced By T4 Ligase Enzymesmentioning

confidence: 99%

End-to-end distance and contour length distribution functions of DNA helices

Zoli

2018

The Journal of Chemical Physics

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“…The transition point from the harmonic to the linear bending regime occurs at the beginning of the convex hull segment -this point plays a special role in the new theory. These general considerations are expected to hold for any polymer with an effective bending energy that has a distinct non-convex region, regardless of its origin 20,24 . For generic "sequence-averaged" double-stranded DNA considered here, we conclude that the effective bending deformation energy becomes non-convex for strong bends greater than ∼ 2 • /bp, which corresponds to circular loops shorter than ∼ 160 bp.…”

Section: Discussionmentioning

confidence: 99%

Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment

2019

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The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As the bending deformation increases beyond a certain (polymer-specific) point, the change in the convexity properties of the effective bending energy of the polymer makes the harmonic deformation energetically unfavorable: in this strong bending regime the energy of the polymer varies linearly with the average bending angle as the system follows the convex hull of the deformation energy function. For double-stranded DNA, the effective bending deformation energy becomes non-convex for bends greater than ∼ 2 • per base-pair, equivalent to the curvature of a closed circular loop of ∼ 160 base pairs. A simple equation is derived for the polymer loop energy that covers both the weak and strong bending regimes. The theory shows quantitative agreement with recent DNA cyclization experiments on short DNA fragments, while maintaining the expected agreement with experiment in the weak bending regime. Counterintuitively, cyclization probability (j-factor) of very short DNA loops is predicted to increase with decreasing loop length; the j-factor reaches its minimum for loops of ≃ 45 base pairs. Atomistic simulations reveal that the attractive component of the short-range Lennard-Jones interaction between the backbone atoms can explain the underlying non-convexity of the DNA effective bending energy, leading to the linear bending regime. Applicability of the theory to protein-DNA complexes, including the nucleosome, is discussed.

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“…The stiffness of the spring ( K ) and undeformed spring lengths ( r 0, j ) have to be chosen carefully to cover the entire range of the end-to-end distance while allowing the histograms to be overlapped significantly. Once a full set of histograms are constructed, the unbiased probability distribution can be found using the weighted histogram analysis method (WHAM) [34, 28, 40]. Specifically, the unnormalized radial probability density in the i -th bin ( p i ) is given by…”

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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Extreme bendability of DNA double helix due to bending asymmetry

Cited by 15 publications

References 45 publications

End-to-end distance and contour length distribution functions of DNA helices

End-to-end distance and contour length distribution functions of DNA helices

Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment

Single-molecule fluorescence studies on DNA looping

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