Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here we report that many pseudoknots can be predicted through long-time-scale RNA-folding simulations, which follow the stochastic closing and opening of individual RNA helices. The numerical efficacy of these stochastic simulations relies on an ᏻ(n 2 ) clustering algorithm that computes time averages over a continuously updated set of n reference structures. Applying this exact stochastic clustering approach, we typically obtain a 5-to 100-fold simulation speed-up for RNA sequences up to 400 bases, while the effective acceleration can be as high as 10 5 -fold for short, multistable molecules (<150 bases). We performed extensive folding statistics on random and natural RNA sequences and found that pseudoknots are distributed unevenly among RNA structures and account for up to 30% of base pairs in G؉C-rich RNA sequences (online RNA-folding kinetics server including pseudoknots: http:͞͞ kinefold.u-strasbg.fr).T he folding of RNA transcripts is driven by intramolecular GC͞AU͞GU base-pair stacking interactions. This primarily leads to the formation of short, double-stranded RNA helices connected by unpaired regions. Ab initio RNA-folding prediction restricted to tree-like secondary structures is now well established (refs. 1-7, ref. 8 and references therein, www.bioinfo.rpi.edu͞applications͞mfold, and www.tbi. univie.ac.at) and has become an important tool to study and design RNA structures, which remain by and large refractory to many crystallization techniques. Yet, the accuracy of these predictions is difficult to assess, despite the precision of stacking interaction tables (7), due to their a priori dismissal of pseudoknot helices (Fig. 1A).Pseudoknots are regular double-stranded helices that provide specific structural rigidity to the RNA molecule by connecting different ''branches'' of its otherwise more flexible, tree-like secondary structure ( Fig. 1 A and B). Many ribozymes, which require a well defined 3D enzymatic shape, have pseudoknots (9-17). Pseudoknots are also involved in mRNA-ribosome interactions during translation initiation and frameshift regulation (18). Still, the overall prevalence of pseudoknots has proved difficult to ascertain from the limited number of RNA structures known to date. This recently has motivated several attempts to include pseudoknots in RNA secondary structure predictions (19-21).There are two main obstacles to include pseudoknots in RNA structures: a structural modeling problem and a computational efficiency issue. In the absence of databases for pseudoknot energy parameters, their structural features have been modeled at various descriptive levels by using polymer theory (19,21,22). From a computational perspective, pseudoknots have proved not easily amenable to classical polynomial minimization algorithms (20) because of their intrinsic nonnested nature. Instead, simulating RNA-folding dynamics has provided an alternati...

In this study we pursue a closer analysis of the photodamage promoted on giant unilamellar vesicles membranes made of dioleoyl-sn-glycero-3-phosphocholine (DOPC) or 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), by irradiating methylene blue present in the giant unilamellar vesicles solution. By means of optical microscopy and electro-deformation experiments, the physical damage on the vesicle membrane was followed and the phospholipids oxidation was evaluated in terms of changes in the membrane surface area and permeability. As expected, oxidation modifies structural characteristics of the phospholipids that lead to remarkable membrane alterations. By comparing DOPC- with POPC-made membranes, we observed that the rate of pore formation and vesicle degradation as a function of methylene blue concentration follows a diffusion law in the case of DOPC and a linear variation in the case of POPC. We attributed this scenario to the nucleation process of oxidized species following a diffusion-limited growth regime for DOPC and in the case of POPC a homogeneous nucleation process. On the basis of these premises, we constructed models based on reaction-diffusion equations that fit well with the experimental data. This information shows that the outcome of the photosensitization reactions is critically dependent on the type of lipid present in the membrane.

An original coarse-grained model for peroxidised phospholipids is presented, based on the MARTINI lipid force field. This model results from a combination of thermodynamic modelling and structural information on the area per lipid, which have been made available recently. The resulting coarse-grained lipid molecules form stable bilayers, and a set of elastic coefficients (compressibility and bending moduli) is obtained. We compare the compressibility coefficient to the experimental values [Weber et al., Soft Matter, 2014, 10, 4241]. Predictions for the mechanical properties, membrane thickness and lateral distribution of hydroperoxide groups in the phospholipid bilayer are presented.