Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics
Fig 2
Distribution of backbone (ε-ζ) values and 5’ sugar behavior in MD snapshots.
Top panels: the frequencies (N) of (ε-ζ) values were extracted from P-MDs (left panel, blue line) and C-MDs (right panels, red line) snapshots. The BI and BII regions are indicated, in accordance with the analysis presented in the main text. The hashed regions correspond to the distribution of ε/ζ:trans/trans, the categorization of which is ambiguous with regard to BI or BII. Bottom panels: pseudorotation phase angle (P) of the 5’ sugar puckers as a function of (ε-ζ) values (°), extracted from P-MDs (left panel) and C-MDs (right panel). The sugar ring conformations were in north (pseudorotation phase angle 0 to 50°), east (50 to 120°) or south (120 to 220°). The (ε-ζ) region assigned to BII does not contain 5’ north sugars. The color gradient is indicative of the density, with the highest densities in yellow. The vertical lines indicate the (ε-ζ) values used here to separate BI from BII in P- (blue lines) and C-MDs (red lines).