title: Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases.
abstract: Urea titration of RNA by urea is an effective approach to investigate the forces stabilizing this biologically important molecule. We used all atom molecular dynamics simulations using two urea force fields and two RNA constructs to elucidate in atomic detail the destabilization mechanism of folded RNA in aqueous urea solutions. Urea denatures RNA by forming multiple hydrogen bonds with the RNA bases and has little influence on the phosphodiester backbone. Most significantly we discovered that urea engages in stacking interactions with the bases. We also estimate, for the first time, the m-value for RNA, which is a measure of the strength of urea-RNA interactions. Our work provides a conceptual understanding of the mechanism by which urea enhances RNA folding rates.
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA.
authors.forename: U Deva
authors.initials: UD
authors.lastname: Priyakumar
authors.forename: Changbong
authors.initials: C
authors.lastname: Hyeon
authors.forename: D
authors.initials: D
authors.lastname: Thirumalai
authors.forename: Alexander D
authors.initials: AD
authors.lastname: Mackerell
mesh_terms: D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D014508:Urea / Q000737:chemistry*
chemical_list: D012313:RNA; D014508:Urea