Ionic strength-dependent persistence lengths of single-stranded RNA and DNA

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 109; no. 3; pp. 799 - 804
• Main Authors: Chen, Huimin, Meisburger, Steve P, Pabit, Suzette A, Sutton, Julie L, Webb, Watt W, Pollack, Lois
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 17-01-2012; National Acad Sciences
• Subjects: Biological Sciences; Chemical bases; Deoxyribonucleic acid; DNA; DNA, Single-Stranded - chemistry; Electrostatics; Fluorescence; Fluorescence Resonance Energy Transfer; Ions; Magnesium Chloride - pharmacology; Models, Molecular; Molecules; Nucleic acids; Osmolar Concentration; Pliability - drug effects; Polymers; Ribonucleic acid; RNA; RNA - chemistry; Salts; Scattering, Small Angle; single-stranded DNA; Sodium Chloride - pharmacology; translation (genetics); X-Ray Diffraction
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1119057109

Dynamic RNA molecules carry out essential processes in the cell including translation and splicing. Base-pair interactions stabilize RNA into relatively rigid structures, while flexible non-base-paired regions allow RNA to undergo conformational changes required for function. To advance our understanding of RNA folding and dynamics it is critical to know the flexibility of these un-base-paired regions and how it depends on counterions. Yet, information about nucleic acid polymer properties is mainly derived from studies of ssDNA. Here we measure the persistence lengths (lp) of ssRNA. We observe valence and ionic strength-dependent differences in lp in a direct comparison between 40-mers of deoxythymidylate (dT40) and uridylate (rU40) measured using the powerful combination of SAXS and smFRET. We also show that nucleic acid flexibility is influenced by local environment (an adjoining double helix). Our results illustrate the complex interplay between conformation and ion environment that modulates nucleic acid function in vivo.