Figure 4.

the effect of 5-hydroxymethylcytosine on the DDD is amplified by cNMs. (A) The DDD is depicted with the backbone in orange and bases in gray. The two 5hmC modifications are colored based on atom type (O, red; C, green; and H, white). The sets of DOFs chosen for the 5hmC modification are shown on the right. Curved arrows indicate free torsional sampling, while the black crosses indicate fixed χ-torsion on rotations around corresponding bonds (χ1, C5-C5M; χ2, C5M-OH). ¹¹¹T: Full sampling of all torsion angles; ⁰⁰¹T: Fixed torsion angles in 5hmC; ⁰⁰⁰T: Fixed torsion angles in 5hmC and relative orientation between 5hmC and G. (B) Distributions of the shear, stretch, and propeller are shown for the three different test cases. Each column compares simulations without modification (control) in green against test cases ¹¹¹T, ⁰⁰¹T, and ⁰⁰⁰T in orange. The shear is shown for basepair 10 and the stretch and propeller are shown for basepair 8. To see this figure in color, go online.