Table 2. Collective Variables (CVs) Biased in the RECT Simulations.

simulation	residues with biases	CVs biased in each of the residuesa	additional biased CVsb	penaltyc
1KF1 A	T11, T12, A13	α, β, γ, ε, ζ, χ, pucker, base-coor.
1KF1 B	T11, T12, A13	α, β, γ, ε, ζ, χ, pucker, base-coor.		zg
1KF1 C	T11, T12, A13	α, β, γ, ε, ζ, χ, pucker, base-coor.	dist G9(H22)-T11(O4)
1KF1 D	T11, T12, A13	α, β, γ, ε, ζ, χ, pucker, base-coor.	dist G9(H22)-T11(O4)	zg
2GKU A	T6, T7, A8	α, β, γ, ε, ζ, χ, pucker, base-coor.
2MBJ A	T13, T14, A15	α, β, γ, ε, ζ, χ, pucker, base-coor.
2MBJ B	T13, T14, A15	α, β, γ, ε, ζ, χ, pucker, base-coor.	dist. G11-T14

^aα, β, γ, ε, ζ, and χ = dihedral angles; pucker = x-axis component of pucker; “base-coor.’’ = nucleobase coordination number i.e. number of nucleobases in proximity of the corresponding nucleobase (each nucleobase is approximated by its center of mass), computed using , where r₀ = 4Å.

^bdist = distance; measured either between selected atoms (in parentheses) or nucleobases’ centers of mass.

^czg = flat-well potential function applied on ζ(G10) and γ(T11) (Figures S2 and S3).