Structures and axis-curves for ideal dsDNA and dsRNA.

<p>Left: DNA. Right: dsRNA. The length of the helices is 50 base-pairs. The red lines are the corresponding axis-curves, forming a spiral. Blue numbers are the vertical length of the axis-curve spirals and red numbers are the diameter of the spirals. The axis curve for dsRNA is more “springy” than DNA.</p

Summary and statistics of the curated base-pair step parameter sets.

1<p>For removing A-DNA conformation. Only for DNA parameter sets.</p>2<p>First value is the mean of that parameter; second value in the parenthesis is the corresponding standard deviation.</p

Normalized population distributions of the base-pair step parameters.

<p>Black: DNA. Red: RNA. Solid lines: default dataset (2.8 Å resolution cutoff, excluding protein-binding models). Dashed lines: 2.8_all dataset (2.8 Å resolution cutoff, including protein-binding models). Dotted lines: 2.0_noprot dataset (2.0 Å resolution cutoff, excluding protein-binding models). The inset illustrates the geometrical definition of each base-pair step parameter.</p

Validation of the link calculations.

<p>(A) Plot of calculated link vs. bead rotation in DNA simulation with 7 pN stretching force and no link constraint. The red line is the function y = x. The link is folded into the range of 0 to 1 turn for better comparison. RMSD of the calculated link is 5.7°. (B) Plot of Fuller writhe vs. exact writhe in DNA simulation with 0.1 pN stretching force and no link constraint. The separation of two turns between parallel traces demonstrates that Fuller writhe is only correct modulo 4π in this criteria. (C) RMSD for Fuller writhe at different stretching forces with no link constraint. Black: DNA; Red: dsRNA. (D) RMSD for Fuller writhe at different link constraints in simulations at 7 pN stretching force.</p

The base-pair level model and the twist and writhe calculation.

<p>(A) Illustration of the base-pair level model and ribbon model abstraction. Black dots and vectors: centers of base-pairs and the axis curve; red vectors: original ribbon vectors; blue vectors: reference ribbon vectors. See the main text for definition of <i>α</i> and <i>β</i>. (B) Conversion from an open curve to a closed curve for writhe calculation. (C) Twist for a straight line segment. (D) Effect of using reference ribbon vectors in the middle of a helix. The corresponding <i>α</i>, <i>β</i>, <i>T</i>, <i>Tw_ref</i> and <i>Tw</i> are given. The original ribbon (red) is perfectly straight with zero twist. Using reference ribbon vectors either leads to no change (left) or a 2<i>π</i> difference (right) in twist. Taking <i>α</i> into account resolves the 2<i>π</i> difference. (E) Cases where the twist definition of Britton et al. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003756#pcbi.1003756-Britton1" target="_blank">[56]</a> would fail to give reasonable answers.</p

Torsional persistence length from the simulations.

<p>(A, C) DNA_default. (B, D) RNA_default. (A, B) Effective torsional persistence lengths at different stretching forces, fitted to Moroz-Nelson model. Only the last six points are used in the fit since Moroz-Nelson model is a high-force expansion. (C, D) Torque vs. the target link constraint plots in link-constrained simulations, at 7 pN stretching forces. Data are fitted to straight lines.</p

Link-extension coupling constants from the simulations.

<p>(A, C) DNA_default. (B, D) RNA_default. (A, B) Link per kbp vs. force plot (black dots) with a linear fit (blue solid lines). The link values are offset such that the first point (at 0.04 pN stretching force) has a link of zero. The corresponding twist (green triangles) and writhe (red squares) component for each link data point, as well as linear fits (dotted and dashed lines) are also shown in the figures. In panel A, the writhe is close to zero, and the link and twist are almost undistinguishable. (C, D) Extension vs. target link constraint in link-constrained simulations with linear fits, at 7 pN stretching forces. The first and last data points are not used for fitting as the linear relationship breaks down at high numbers of turns.</p

Force vs. extension plots from the simulations.

<p>Data are fitted to extensible WLC model by Bouchiat et al. (A) DNA_default. (B) RNA_default.</p

Measurements of ¹³C Multiple-Quantum Coherences in Amyloid Fibrils under Magic-Angle Spinning

The excitation and detection of high-order multiple quantum coherences among ¹³C nuclear spins are demonstrated in the samples of [1-¹³C]-l-alanine and ¹³C labeled amyloid fibrils at a spinning frequency of 20 kHz. The technique is based on the double-quantum average Hamiltonian prepared by the DRAMA-XY4 pulse sequence. Empirically, we find that multiple supercycles are required to suppress the higher-order effects for real applications. Measurements for the fibril samples formed by the polypeptides of PrP(113–127) provide the first solid-state NMR evidence for the stacking of multiple β-sheet layers at the structural core of amyloid fibril

Files required for app implementation and their role.

<p>Files required for app implementation and their role.</p