Nucleation of Multiple Buckled Structures in Intertwined DNA Double Helices

Brahmachari, Sumitabha; Gunn, Kathryn H.; Giuntoli, Rebecca D.; Mondragón, Alfonso; Marko, John F.

doi:10.1103/physrevlett.119.188103

Cited by 8 publications

(11 citation statements)

References 33 publications

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“…[34]. DNA braids have the same geometry as plectonemes, however experimentally studied braids [40–42] are force extended, while plectonemes are buckled structures that do not have force-extension energy [Appendix A].…”

Section: Supercoiled Defect-free Dnamentioning

confidence: 99%

Defect-facilitated buckling in supercoiled double-helix DNA

et al. 2018

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We present a statistical-mechanical model for stretched twisted double-helix DNA, where thermal fluctuations are treated explicitly from a Hamiltonian without using any scaling hypotheses. Our model applied to defect-free supercoiled DNA describes the coexistence of multiple plectoneme domains in long DNA molecules at physiological salt concentrations (≈0.1M Na^{+}) and stretching forces (≈1pN). We find a higher (lower) number of domains at lower (higher) ionic strengths and stretching forces, in accord with experimental observations. We use our model to study the effect of an immobile point defect on the DNA contour that allows a localized kink. The degree of the kink is controlled by the defect size, such that a larger defect further reduces the bending energy of the defect-facilitated kinked end loop. We find that a defect can spatially pin a plectoneme domain via nucleation of a kinked end loop, in accord with experiments and simulations. Our model explains previously reported magnetic tweezer experiments [A. Dittmore et al., Phys. Rev. Lett. 119, 147801 (2017)PRLTAO0031-900710.1103/PhysRevLett.119.147801] showing two buckling signatures: buckling and "rebuckling" in supercoiled DNA with a base-unpaired region. Comparing with experiments, we find that under 1 pN force, a kinked end loop nucleated at a base-mismatched site reduces the bending energy by ≈0.7 k_{B}T per unpaired base. Our model predicts the coexistence of three states at the buckling and rebuckling transitions, which warrants new experiments.

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Section: Supercoiled Defect-free Dnamentioning

confidence: 99%

Defect-facilitated buckling in supercoiled double-helix DNA

et al. 2018

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“…[34]. DNA braids have the same geometry as plectonemes, however experimentally studied braids [40][41][42] are force extended, while plectonemes are buckled structures that do not have force-extension energy [Appendix A].…”

Section: Thermal Fluctuationsmentioning

confidence: 99%

Defect-Facilitated Buckling in Supercoiled Double-Helix DNA

Brahmachari¹,

Dittmore

Takagi

et al. 2018

Preprint

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We present a statistical-mechanical model for stretched twisted double-helix DNA, where thermal fluctuations are treated explicitly from a Hamiltonian without using any scaling hypotheses. Our model applied to defect-free supercoiled DNA describes coexistence of multiple plectoneme domains in long DNA molecules at physiological salt concentrations (≈ 0.1 M Na + ) and stretching forces (≈ 1 pN). We find higher (lower) number of domains at lower (higher) ionic strengths and stretching forces, in accord with experimental observations. We use our model to study the effect of an immobile point defect on the DNA contour that allows a localized kink. The degree of the kink is controlled by the defect size, such that a larger defect further reduces the bending energy of the defect-facilitated kinked end loop. We find that a defect can spatially pin a plectoneme domain via nucleation of a kinked end loop, in accord with experiments and simulations. Our model explains previously-reported magnetic tweezer experiments [1] showing two buckling signatures: buckling and 'rebuckling' in supercoiled DNA with a base-unpaired region. Comparing with experiments, we find that under 1 pN force, a kinked end loop nucleated at a base-mismatched site reduces the bending energy by ≈ 0.7 kBT per unpaired base. Our model predicts coexistence of three states at the buckling and rebuckling transitions that warrants new experiments.

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“…On theoretical grounds it has been predicted that highly twisted braids should tend to form smaller plectonemic domains than supercoiled single DNAs due to the greater bulk (cross-sectional area) of braided DNAs [24]. Our experimental reports of the buckling dynamics of braid shave indirectly observed the effects of multiple small domains [31]. Future experiments using fluorescence visualization of braid supercoiling would be desirable to allow direct observation of the size and dynamics of braid-plectoneme domains.…”

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confidence: 69%

“…The torque increased with Ca until reached a plateau of ~58 pNꞏnm at Ca=52.For the widest intertether braid (d/L=0.54) held by an 8.03 pN force, the torque increased from 0 to a peak of 76 pNꞏnm when the catenation was increased from 0 to Ca=30 or =0.53(Figure 2d). At 2 pN force and Ca=20, the torques were 31, 21 and 15 pNꞏnm in braids of large (0.54 L), mid (0.31 L) and small (0.26 L) intertether distances, respectively(Figure 2b).Theoretical calculations generating the extension-catenation curves(Figures 3d and 4d)were carried out based on a statistical-mechanical model for braids (SeeSupplementary Material)[24,31]. The torques from the model(Figures 3e and 4e)were obtained from the derivative of the free energy as a function of catenation.…”

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Measurement of the torque in braided DNAs using a thermodynamic Maxwell relation

Xiao

Brahmachari

Liu

et al. 2020

Preprint

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Braided DNAs are significant structural intermediates in cellular processes, yet little has been experimentally demonstrated about their higher-order structure and twisting torques. We use magnetic tweezers to measure braid extensions at forces ranging from 0.3 to 8 piconewtons, and then apply a thermodynamic Maxwell relation to calculate the torque. Experimentally inferred torques in unbuckled braids take on values up to 76 pNꞏnm, which depends on force, and inter-tether distance. As predicted using a statistical mechanical model, the twist modulus of the braids increases with catenation prior to buckling or formation of plectoneme, and is comparable to that of single DNA.

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Nucleation of Multiple Buckled Structures in Intertwined DNA Double Helices

Cited by 8 publications

References 33 publications

Defect-facilitated buckling in supercoiled double-helix DNA

Defect-facilitated buckling in supercoiled double-helix DNA

Defect-Facilitated Buckling in Supercoiled Double-Helix DNA

Measurement of the torque in braided DNAs using a thermodynamic Maxwell relation

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