Qian Wang1, Rossitza N. Irobalieva2,#, Wah Chiu2,3,4, Michael F. Schmid2,3, Jonathan M. Fogg3,4,5, Lynn. Zechiedrich2,3,4,5, and B. Montgomery Pettitt1,2*.
Influence of DNA Sequence on the Structure of Minicircles under Torsional Stress Qian Wang1, Rossitza N. Irobalieva2,#, Wah Chiu2,3,4, Michael F. Schmid2,3, Jonathan M. Fogg3,4,5, Lynn Zechiedrich2,3,4,5, and B. Montgomery Pettitt1,2*
1
Department of Biochemistry and Molecular Biology,
Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555 USA
2
Graduate Program in Structural and Computational Biology and Molecular Biophysics
3
Verna and Marrs McLean Department of Biochemistry and Molecular Biology
4
Department of Molecular Virology and Microbiology
5
Department of Pharmacology
Baylor College of Medicine Houston, TX, 77030 USA
#
Current Address, Universität Zürich, 8057 Zurich, Switzerland
SUPPLEMENTARY INFORMATION
Calculating writhe We calculated writhe (Wr) according to previous references (1,2).
Base pair opening In the coarse-grained simulation, base pair opening (hydrogen-bond breaking) was defined as the distance between the complementary bases in a Watson-Crick base pair larger than 1.0 σ (σ = 8.52Å). This choice follows our previous work (3).
Contact between non-complementary base pairs For two base pairs i and j ( i j 20 ), a contact is defined when the distance between any “backbone bead” in one base pair and any “backbone bead” in another base pair is less than 3σ (σ = 8.52Å). The fraction of the contact formations, C, is defined by the number of base pairs forming at least one contact with other base pairs normalized by the total number of base pairs (in this case 336).
Number of bend locations on a circle, Nv Nv describes how many bends a DNA circle has. For any base pair index, i, if the angle between the vector from the backbone bead of bp i to the backbone bead of bp i+30 and the vector from the backbone bead of bp i to the backbone bead of bp i-30 is less than 67.6 degrees (reasonable variations of these values will not change the main conclusion qualitatively), it is counted as bent. A bend location can be base pair opening, kinking, or strong bending due to mechanical correlations. The cause of the bends are not distinguished when calculating Nv.
Bend location correlation coefficient (BCC) BCC between base pair i and j was calculated by BCC
Cov( I i , I j )
i j
Ii = 1 when bp i is one of the bending locations and Ii = 0 when not. Cov represents the covariance and σ represents the standard deviation.
Figure S1. The root-mean-square deviation of the minicircle topoisomer Lk = 26 (ΔLk = -6) over 240 trajectories simulated without constraints. The RMSD for a single trajectory from that set inside the red circle is shown in the inset figure
Figure S2. The probability distribution of the radius of gyration (Rg) of the relaxed (Lk = 32, ΔLk = 0) DNA minicircle topoisomer. Rg is the average mass weighted root mean square deviation of the coordinates. Representative structures are shown straight-on (top) and rotated 90°(bottom).
Figure S3. The distribution of the radius of gyration (Rg) of the ΔLk = +1 minicircle topoisomer. A representative structure from the left side of the distribution is shown.
Figure S4. Twist of minicircles as a function of Lk. The error bars in all cases are smaller than the size of the symbol.
Figure S5. Approximate (3) free energy per base pair in the 336 bp minicircle for Lk = 32 without sliding averaging. The energy unit is kcal/mol/bp. The prediction shows that the thermodynamically least stable position is near bp 293. The absolute value of the free energy is sensitive to the length of the minicircle as well as the parameters used in the model (3).
Figure S6. Isosurface of experimental electron density map of a DNA minicircle at ΔLk = -2 with different thresholds: (A) 0, (B) 0.27, (C) 0.37 and (D) 0.47. The parameter unit is s, the standard deviation of the density at all grid points in the tomogram.
1. 2. 3.
Klenin, K. and Langowski, J. (2000) Computation of writhe in modeling of supercoiled DNA. Biopolymers, 54, 307-317. Levitt, M. (1983) Protein folding by restrained energy minimization and molecular-dynamics. J. Mol. Biol., 170, 723-764. Wang, Q. and Pettitt, B.M. (2014) Modeling DNA thermodynamics under torsional stress. Biophys. J., 106, 1182-1193.
