TY - JOUR
T1 - Defect-facilitated buckling in supercoiled double-helix DNA
AU - Brahmachari, Sumitabha
AU - Dittmore, Andrew
AU - Takagi, Yasuharu
AU - Neuman, Keir C.
AU - Marko, John F.
N1 - Funding Information:
Work at NU was supported by the National Institutes of Health (NIH) [Grants No. R01-GM105847 and No. U54-CA193419 (CR-PS-OC), and a subcontract to Grant No. U54-DK107980], and by the National Science Foundation (Grants No. MCB-1022117 and No. DMR-1206868). S.B. acknowledges support from a Molecular Biophysics Training Program at NU. Work at NIH was supported in part by the Intramural Research Program of the National Heart, Lung, and Blood Institute, National Institutes of Health.
Publisher Copyright:
© 2018 American Physical Society.
PY - 2018/2/28
Y1 - 2018/2/28
N2 - 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 kBT per unpaired base. Our model predicts the coexistence of three states at the buckling and rebuckling transitions, which warrants new experiments.
AB - 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 kBT per unpaired base. Our model predicts the coexistence of three states at the buckling and rebuckling transitions, which warrants new experiments.
UR - http://www.scopus.com/inward/record.url?scp=85043482581&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85043482581&partnerID=8YFLogxK
U2 - 10.1103/PhysRevE.97.022416
DO - 10.1103/PhysRevE.97.022416
M3 - Article
C2 - 29548184
AN - SCOPUS:85043482581
SN - 2470-0045
VL - 97
JO - Physical Review E
JF - Physical Review E
IS - 2
M1 - 022416
ER -