Mechanical Identities of RNA and DNA Double Helices Unveiled at the Single-Molecule Level

• Published in: Journal of the American Chemical Society Vol. 135; no. 1; pp. 122 - 131
• Main Authors: Herrero-Galán, Elías, Fuentes-Perez, Maria Eugenia, Carrasco, Carolina, Valpuesta, José M, Carrascosa, José L, Moreno-Herrero, Fernando, Arias-Gonzalez, J. Ricardo
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 09.01.2013
• Subjects: DNA - chemistry; Microscopy, Atomic Force; RNA - chemistry
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja3054755

Double-stranded (ds) RNA is the genetic material of a variety of viruses and has been recently recognized as a relevant molecule in cells for its regulatory role. Despite that the elastic response of dsDNA has been thoroughly characterized in recent years in single-molecule stretching experiments, an equivalent study with dsRNA is still lacking. Here, we have engineered long dsRNA molecules for their individual characterization contrasting information with dsDNA molecules of the same sequence. It is known that dsRNA is an A-form molecule unlike dsDNA, which exhibits B-form in physiological conditions. These structural types are distinguished at the single-molecule level with atomic force microscopy (AFM) and are the basis to understand their different elastic response. Force–extension curves of dsRNA with optical and magnetic tweezers manifest two main regimes of elasticity, an entropic regime whose end is marked by the A-form contour-length and an intrinsic regime that ends in a low-cooperative overstretching transition in which the molecule extends to 1.7 times its A-form contour-length. DsRNA does not switch between the A and B conformations in the presence of force. Finally, dsRNA presents both a lower stretch modulus and overstretching transition force than dsDNA, whereas the electrostatic and intrinsic contributions to the persistence length are larger.