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. 2010 Nov 3;99(9):2987-94.
doi: 10.1016/j.bpj.2010.08.021.

Effect of spontaneous twist on DNA minicircles

Shlomi Medalion  1 , David A Kessler, Yitzhak Rabin
Affiliations

Effect of spontaneous twist on DNA minicircles

Shlomi Medalion et al. Biophys J. .

Abstract

Monte Carlo simulations are used to study the effect of spontaneous (intrinsic) twist on the conformation of topologically equilibrated minicircles of dsDNA. The twist, writhe, and radius of gyration distributions and their moments are calculated for different spontaneous twist angles and DNA lengths. The average writhe and twist deviate in an oscillatory fashion (with the period of the double helix) from their spontaneous values, as one spans the range between two neighboring integer values of intrinsic twist. Such deviations vanish in the limit of long DNA plasmids.

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Figures

Figure 1
Figure 1
(Color online) A dsDNA plasmid of length N = 180 bp (lp = 50 nm and l3 = 74 nm). (a) 〈Tw〉 vs. ω˜3(0) in the range 0.595–0.627 rad (the vertical violet dashed line corresponds to Tw(0) = 17.5). (b) P(Tw) for ω˜3(0)=0.608 (red circles), ω˜3(0)=0.610 (blue squares), and ω˜3(0)=0.612 (brown asterisks). Solid lines are guides to the eye.
Figure 2
Figure 2
(Color online) N = 180 bp with dsDNA parameters (l˜p=50nm and l˜3=74nm): 〈ΔTw〉 (red circles), 〈ΔLk〉 (green diamonds), and 〈Wr〉 (blue squares) for ω˜3(0)s in the range 0.595–0.627 rad (vertical dashed line is the ω˜3(0) corresponding to Tw(0) = 17.5). Solid lines are guides to the eye.
Figure 3
Figure 3
(Color online) The variance of P(Wr) in the absence of spontaneous twist as a function of chain length (violet points). The value lp is 50 nm, and l3 is 74 nm as in the case of dsDNA. (Red dashed line) Linear fit to the variance in the long chain limit.
Figure 4
Figure 4
(Color online) Plot of 〈|Wr|〉max as a function of N (using WLC simulations and the factorization approximation described in the Supporting Material, with lp = 50 nm and l3 = 74 nm). Solid lines are guides to the eye.
Figure 5
Figure 5
(Color online) P(Wr) for different twist rigidities: l˜3/l˜p=1.48 (green asterisks), 2 (blue squares), and 3, (red circles), where lp = 50 nm. (a) N = 251 bp (Tw(0) = 24.019). Even though the distributions for the above three cases are nearly indistinguishable, a small satellite peak can be observed for l˜3/l˜p=3 (an amplified image of one of the satellite peaks is shown in the inset). (b) N = 256 bp (Tw(0) = 24.49). Progressive splitting of the central peak into two distinct peaks with increasing l˜3/l˜p is clearly observed. Solid lines are guides to the eye.
Figure 6
Figure 6
(Color online) Effect of spontaneous twist on Rgrms of DNA minicircles (lp = 50 nm and l3 = 74 nm). (a) Constant length (N = 180 bp) with ω˜3(0) varying in the range 0.595–0.626 rad (violet circles). (b) Constant ω˜3(0) with N varying in the range 237–258 bp (violet circles). In both graphs, the ω˜3(0)=0 case is shown by blue asterisks. Solid lines are guides to the eye.
Figure 7
Figure 7
(Color online) P(Rg) for Np = 150 bp and different twist rigidities l˜3/l˜p=1.48 (green asterisks), l˜3/l˜p=2 (blue squares), and l˜3/l˜p=3 (red circles). (a) N = 251 bp (Tw(0) = 24.0191). Solid lines are guides to the eye. (Inset) Magnified view of the new peak at Rg≃32. (b) N = 256 bp (Tw(0) = 24.497).
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