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Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
The intricate network of interactions observed in RNA three-dimensional structures is often described in terms of a multitude of geometrical properties, including helical parameters, base pairing/stacking, hydrogen bonding and backbone…
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and…
Post-transcriptional modifications are crucial for RNA function, with roles ranging from the stabilization of functional RNA structures to modulation of RNA--protein interactions. Additionally, artificially modified RNAs have been suggested…
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
Ribonucleic acids (RNA) are unique in that they can store genetic information, replicate and perform catalysis. Importantly, RNA molecules are highly dynamic, and thus determining the ensemble of conformations that they populate is crucial…
The tertiary structures of functional RNA molecules remain difficult to decipher. A new generation of automated RNA structure prediction methods may help address these challenges but have not yet been experimentally validated. Here we apply…
A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural…
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal…
All-atom simulations have become increasingly popular to study conformational and dynamical properties of nucleic acids as they are accurate and provide high spatial and time resolutions. This high resolution however comes at a heavy…
Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence databases, we analyze nucleotide coevolution across homologous sequences via…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
Mechanical properties of the cell are important biomarkers for probing its architectural changes caused by cellular processes and/or pathologies. The development of microfluidic technologies have enabled measuring cell mechanics at…
Structured RNA plays many functionally relevant roles in molecular life. Structural information, while required to understand the functional cycles in detail, is challenging to gather. Computational methods promise to complement…
Non-coding RNA molecules fold into precise base pairing patterns to carry out critical roles in genetic regulation and protein synthesis. We show here that coupling systematic mutagenesis with high-throughput SHAPE chemical mapping enables…
The relationship between RNA structure and function has recently attracted interest within the deep learning community, a trend expected to intensify as nucleic acid structure models advance. Despite this momentum, the lack of standardized,…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…