Stretching instability of intrinsically curved semiflexible biopolymers:A lattice model approach

We apply a Monte Carlo simulation method to lattice systems to study the effect of an intrinsic curvature on the mechanical property of a semiflexible biopolymer.We find that when the intrinsic curvature is sufficiently large,the extension of a semiflexible biopolymer can undergo a first-order transition at finite temperature.The critical force increases with increasing intrinsic curvature.However,the relationship between the critical force and the bending rigidity is structuredependent.In a triangle lattice system,when the intrinsic curvature is smaller than a critical value,the critical force increases with the increasing bending rigidity first,and then decreases with the increasing bending rigidity.In a square lattice system,however,the critical force always decreases with the increasing bending rigidity.In contrast,when the intrinsic curvature is greater than the critical value,the larger bending rigidity always results in a larger critical force in both lattice systems.

Thermal properties of a two-dimensional intrinsically curved semiflexible biopolymer

We study the behaviors of mean end-to-end distance and specific heat of a two-dimensional intrinsically curved semiflexible biopolymer with a hard-core excluded volume interaction. We find the mean square end-to-end distance R2 N∝ Nβ at large N, with N being the number of monomers. Bothβ and proportional constant are dependent on the reduced bending rigidity κ and intrinsic curvature c. The larger the c, the smaller the proportional constant, and 1.5 ≥β ≥ 1. Up to a moderate κ = κc, or down to a moderate temperature T = Tc, β = 1.5, the same as that of a self-avoiding random walk, and the larger the intrinsic curvature, the smaller the κc. However, at a large κ or a low temperature,β is close to 1, and the conformation of the biopolymer can be more compact than that of a random walk. There is an intermediate regime with 1.5 〉β 〉 1 and the transition fromβ = 1.5 toβ= 1 is smooth. The specific heat of the system increases smoothly with increasing κ or there is no peak in the specific heat. Therefore, a nonvanishing intrinsic curvature seriously affects the thermal properties of a semiflexible biopolymer, but there is no phase transition in the system.

Conserved Curvature of RNA Polymerase Ⅰ Core Promoter Beyond rRNA Genes: The Case of the Tritryps

In trypanosomatids, the RNA polymerase I （RNAPI）-dependent promoters controlling the ribosomal RNA （rRNA） genes have been well identified. Although the RNAPI transcription machinery recognizes the DNA conformation instead of the DNA sequence of promoters, no con- formational study has been reported for these promoters. Here we present the in silico analysis of the intrinsic DNA curvature of the rRNA gene core promoters in Trypanosoma brucei, Trypanosoma cruzi, and Leiskmania major. We found that, in spite of the absence of sequence conservation, these promoters hold conformational properties similar to other eukaryotic rRNA promoters. Our results also indicated that the intrinsic DNA curvature pattern is conserved within the Leishmania genus and also among strains of T. cruzi and T. brucei. Furthermore, we analyzed the impact of point mutations on the intrinsic curvature and their impact on the promoter activity. Furthermore, we found that the core promoters of protein-coding genes transcribed by RNAPI in T. brucei show the same conserved conformational characteristics. Overall, our results indicate that DNA intrinsic curvature of the rRNA gene core promoters is conserved in these ancient eukaryotes and such con- served curvature might be a requirement of RNAPI machinery for transcription of not only rRNA genes but also protein-coding genes.