RNAstructural

RNAstructural is an interdisciplinary field focused on the structure, dynamics, and function of ribonucleic acids (RNA). It combines experimental approaches and computational modeling to understand how RNA sequences fold into three-dimensional structures that govern biological activity in cells, viruses, and synthetic systems.

Key concepts include RNA secondary structure—helices, loops, bulges, and pseudoknots—along with higher-order tertiary interactions. Structure determines catalytic activity in ribozymes, regulation in riboswitches, and the binding properties of RNA-protein complexes. RNA structure can be dynamic, with conformational changes in response to ligands, temperature, or ion concentrations.

Experimental methods range from X-ray crystallography, nuclear magnetic resonance spectroscopy, and cryo-electron microscopy to chemical and enzymatic probing (such as SHAPE and DMS), cross-linking, and footprinting techniques. High-throughput methods enable parallel assessment of structure in many RNAs. Computational methods include sequence- and structure-based folding algorithms (MFold, RNAfold, RNAstructure), energy models, covariation analysis, and three-dimensional modeling (Rosetta FARFAR, MC-SYM) and molecular dynamics simulations.

Data resources include three-dimensional RNA structures in the Protein Data Bank, RNA structures in the PDB and NDB, RNAcentral aggregating RNA sequences and structures, Rfam families, and specialized RNA structural analysis tools. Community-wide benchmarks exist to assess prediction accuracy and guide method development.

Applications of RNAstructural research span fundamental biology and biotechnology, including riboswitch mechanism elucidation, ribozyme design, RNA-based therapeutics, and RNA engineering in synthetic biology.