Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2021 Mar 21;49(7):3651–3660. doi: 10.1093/nar/gkab153

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

PMC Copyright notice

Figure 5. — Kinetics of the B–Z transition induced by supercoiling and molecular picture for the transition. Rate constants and equilibrium constants of the B–Z transition of (A) (TG)₁₁ and (B) (CG)₁₁ are shown for various temperatures (in Kelvin). Figure conventions are the same as in Figure 4. (C) ln k-versus-1/T graphs for (TG)₁₁ (: circle, : cross) and for (CG)₁₁ (: square, : plus) at 100 mM NaCl. Lines are linear fits to data based on the Arrhenius equation. (D) Schematic free energy landscapes of (CG)₁₁ (left) and (TG)₁₁ (right) molecules in the absence (blue curve) or presence (red curve) of σ_m. The abscissa of the plot is E_FRET and the ordinate represents the free energy () of the system. In each double-well potential, the left and right minima correspond to Z- and B-DNA states, respectively. The tension to DNA is 1.4 pN. (E) Molecular picture for the B–Z transition based on the interplay of Z-DNA, L-DNA, plectonemes and twisted B-DNA together with configurational states of CG and TG molecules under various mechanical conditions. The B-form DNA (red Core with middle E_FRET) in the absence of torsional stress (far left) undergoes the transition to the Z-form DNA (blue Core with low E_FRET) at sufficiently high negative torsion (far right) through various conformational states (middle) depending on type of sequence and mechanical conditions. The Z-form in TG molecules is preceded by other conformations depending on applied tension and torsion, and can compete with them beyond the tension threshold (f > f_c ∼ 0.3 pN) and a certain negative torsion while the Z-form in CG molecules can form at small negative torsion over the entire range of tension applied. High force (f > f_c) favors DNA bubble over plectonemes while low force (f < f_c) does the opposite in unwound DNA. In the middle panel, the red and blue Cores represent the B- and Z-forms, respectively. The red-blue Core represents the Core alternating between B- and Z-forms by trading turns with the rest of the molecules. The cartoon displays a denaturation bubble (separated strands) and plectonemes (DNA gyre), respectively. ‘: -’ implies additional unwinding of DNA and f_c indicates the critical tension for DNA buckling.

Inline graphic — Kinetics of the B–Z transition induced by supercoiling and molecular picture for the transition. Rate constants and equilibrium constants of the B–Z transition of (A) (TG)₁₁ and (B) (CG)₁₁ are shown for various temperatures (in Kelvin). Figure conventions are the same as in Figure 4. (C) ln k-versus-1/T graphs for (TG)₁₁ (: circle, : cross) and for (CG)₁₁ (: square, : plus) at 100 mM NaCl. Lines are linear fits to data based on the Arrhenius equation. (D) Schematic free energy landscapes of (CG)₁₁ (left) and (TG)₁₁ (right) molecules in the absence (blue curve) or presence (red curve) of σ_m. The abscissa of the plot is E_FRET and the ordinate represents the free energy () of the system. In each double-well potential, the left and right minima correspond to Z- and B-DNA states, respectively. The tension to DNA is 1.4 pN. (E) Molecular picture for the B–Z transition based on the interplay of Z-DNA, L-DNA, plectonemes and twisted B-DNA together with configurational states of CG and TG molecules under various mechanical conditions. The B-form DNA (red Core with middle E_FRET) in the absence of torsional stress (far left) undergoes the transition to the Z-form DNA (blue Core with low E_FRET) at sufficiently high negative torsion (far right) through various conformational states (middle) depending on type of sequence and mechanical conditions. The Z-form in TG molecules is preceded by other conformations depending on applied tension and torsion, and can compete with them beyond the tension threshold (f > f_c ∼ 0.3 pN) and a certain negative torsion while the Z-form in CG molecules can form at small negative torsion over the entire range of tension applied. High force (f > f_c) favors DNA bubble over plectonemes while low force (f < f_c) does the opposite in unwound DNA. In the middle panel, the red and blue Cores represent the B- and Z-forms, respectively. The red-blue Core represents the Core alternating between B- and Z-forms by trading turns with the rest of the molecules. The cartoon displays a denaturation bubble (separated strands) and plectonemes (DNA gyre), respectively. ‘: -’ implies additional unwinding of DNA and f_c indicates the critical tension for DNA buckling.