The geometrical origin of the strain-twist coupling in double helices

The geometrical coupling between strain and twist in double helices is investigated. Overwinding, where strain leads to further winding, is shown to be a universal property for helices, which are stretched along their longitudinal axis when the initial pitch angle is below the zero-twist angle (39.4 deg). Unwinding occurs at larger pitch angles. The zero-twist angle is the unique pitch angle at the point between overwinding and unwinding, and it is independent of the mechanical properties of the double helix. This suggests the existence of zero-twist structures, i.e. structures that display neither overwinding, nor unwinding under strain. Estimates of the overwinding of DNA, chromatin, and RNA are given.Comment: 8 pages, 4 figures; typos fixed; added ref. and acknowledgemen

The ancient art of laying rope

We describe a geometrical property of helical structures and show how it accounts for the early art of ropemaking. Helices have a maximum number of rotations that can be added to them -- and it is shown that this is a geometrical feature, not a material property. This geometrical insight explains why nearly identically appearing ropes can be made from very different materials and it is also the reason behind the unyielding nature of ropes. The maximally rotated strands behave as zero-twist structures. Under strain they neither rotate one or the other way. The necessity for the rope to be stretched while being laid, known from Egyptian tomb scenes, follows straightforwardly, as does the function of the top, an old tool for laying ropes.Comment: 6 pages, 3 figures; v2: discussion of flexibility included; added refs. and acknowledgement, v3: minor modification

Transcription and the Pitch Angle of DNA

The question of the value of the pitch angle of DNA is visited from the perspective of a geometrical analysis of transcription. It is suggested that for transcription to be possible, the pitch angle of B-DNA must be smaller than the angle of zero-twist. At the zero-twist angle the double helix is maximally rotated and its strain-twist coupling vanishes. A numerical estimate of the pitch angle for B-DNA based on differential geometry is compared with numbers obtained from existing empirical data. The crystallographic studies shows that the pitch angle is approximately 38 deg., less than the corresponding zero-twist angle of 41.8 deg., which is consistent with the suggested principle for transcription.Comment: 7 pages, 3 figures; v2: minor modifications; v3: major modifications compared to v2. Added discussion about transcription, and reference

Cartan Ribbonization of Surfaces and a Topological Inspection

We develop the concept of Cartan ribbons and a method by which they can be used to ribbonize any given surface in space by intrinsically flat ribbons. The geodesic curvature along the center curve on the surface agrees with the geodesic curvature of the corresponding Cartan development curve, and this makes a rolling strategy successful. Essentially, it follows from the orientational alignment of the two co-moving Darboux frames during the rolling. Using closed center curves we obtain closed approximating Cartan ribbons that contribute zero to the total curvature integral of the ribbonization. This paves the way for a particular simple topological inspection -- it is reduced to the question of how the ribbons organize their edges relative to each other. The Gauss-Bonnet theorem leads to this topological inspection of the vertices. Finally, we display two examples of ribbonizations of surfaces, namely of a torus using two ribbons, and of an ellipsoid using its closed curvature lines as center curves for the ribbons. The topological inspection of the torus ribbonization is particularly simple as it has no vertex points, giving directly the Euler characteristic $0$. The ellipsoid has $4$ vertices -- corresponding to the $4$ umbilical points -- each of degree one and each therefore contributing one-half to the Euler characteristic

The size of the nucleosome

The structural origin of the size of the 11 nm nucleosomal disc is addressed. On the nanometer length-scale the organization of DNA as chromatin in the chromosomes involves a coiling of DNA around the histone core of the nucleosome. We suggest that the size of the nucleosome core particle is dictated by the fulfillment of two criteria: One is optimizing the volume fraction of the DNA double helix; this requirement for close-packing has its root in optimizing atomic and molecular interactions. The other criterion being that of having a zero strain-twist coupling; being a zero-twist structure is a necessity when allowing for transient tensile stresses during the reorganization of DNA, e.g., during the reposition, or sliding, of a nucleosome along the DNA double helix. The mathematical model we apply is based on a tubular description of double helices assuming hard walls. When the base-pairs of the linker-DNA is included the estimate of the size of an ideal nucleosome is in close agreement with the experimental numbers. Interestingly, the size of the nucleosome is shown to be a consequence of intrinsic properties of the DNA double helix.Comment: 11 pages, 5 figures; v2: minor modification