We describe a conceptual framework for understanding the way large RNA molecules fold based on the notion that their free-energy landscape is rugged. A key prediction of our theory is that RNA folding can be described by the kinetic partitioning mechanism (KPM). According to KPM a small fraction of molecules folds rapidly to the native state whereas the remaining fraction is kinetically trapped...

Commonly used RNA folding programs compute the minimum free energy structure of a sequence under the pseudoknot exclusion constraint. They are based on Zuker's algorithm which runs in time O(n(3)). Recently, it has been claimed that RNA folding can be achieved in average time O(n(2)) using a sparsification technique. A proof of quadratic time complexity was based on the assumption that computat...

The paper presents some aspects correlating thermal stability of RNA folding and the occurrence of structural motifs in natural ribonucleic acids. Particularly, the thermodynamic stability of 2'-5' and 3'-5' linked RNA and the contribution of unpaired terminal nucleotides (dangling ends) in secondary (2D) and tertiary (3D) structures of RNA are discussed. Both examples suggest that during evolu...

RNA molecules with novel functions have revived interest in the accurate prediction of RNA three-dimensional (3D) structure and folding dynamics. However, existing methods are inefficient in automated 3D structure prediction. Here, we report a robust computational approach for rapid folding of RNA molecules. We develop a simplified RNA model for discrete molecular dynamics (DMD) simulations, in...

Metrics for indirectly predicting the folding rates of RNA sequences are of interest. In this letter, we introduce a simple metric of RNA structural complexity, which accounts for differences in the energetic contributions of RNA base contacts toward RNA structure formation. We apply the metric to RNA sequences whose folding rates were previously determined experimentally. We find that the metr...

Abstract Regardless of the scale it is built at, geometric principles origami make an architecture both constrained by act folding and imbued with dynamics folding. From space stations to molecules, solutions are inspiring a new type design that considers its deployment as integral part structure. In this essay, I will explain some surprising similarities between ancient art paper RNA at nanosc...

Native polyacrylamide gel electrophoresis is a powerful approach for visualizing RNA folding states and folding intermediates. Tris-borate has a high-buffering capacity and is therefore widely used in electrophoresis-based investigations of RNA structure and folding. However, the effectiveness of Tris-borate as a counterion for RNA has not been systematically investigated. In a recirculated Hep...

Tetraloops with the generic sequence GNRA are commonly found in RNA secondary structure, and interactions of such tetraloops with "receptors" elsewhere in RNA play important roles in RNA structure and folding. However, the contributions of tetraloop-receptor interactions specifically to the kinetics of RNA tertiary folding, rather than the thermodynamics of maintaining tertiary structure once f...

UNLABELLED Three-dimensional RNA structure prediction and folding is of significant interest in the biological research community. Here, we present iFoldRNA, a novel web-based methodology for RNA structure prediction with near atomic resolution accuracy and analysis of RNA folding thermodynamics. iFoldRNA rapidly explores RNA conformations using discrete molecular dynamics simulations of input ...

Barrier trees consisting of local minima and their connecting saddle points imply a natural coarse-graining for the description of the energy landscape of RNA secondary structures. Here we show that, based on this approach, it is possible to predict the folding behavior of RNA molecules by numerical integration. Comparison with stochastic folding simulations shows reasonable agreement of the re...