title: Molecular dynamics study of intrinsic stability in six RNA terminal loop motifs.
abstract: Single stranded RNA molecules can assume a wide range of tertiary structures beyond the canonical A-form double helix. Certain sequences, termed motifs, are more common than a random distribution would suggest. The existence of such motifs can be rationalized in structural terms. In this study, we have investigated the intrinsic structural stability of RNA terminal loop motifs using multiple MD simulations in explicit water. Representative loops were chosen from the major tetraloop motifs, including also the U-turn motif. Not all loops retain their folded starting structure, but lowering the temperature to 277 K, or adding adjacent base pairs from the stem to which the motif is attached, helps stabilizing the folded loop structure.
authors.affiliation: Karolinska Institutet, Department of Biosciences and Nutrition, SE-141 57 Huddinge, Sweden.
authors.forename: Boel
authors.initials: B
authors.lastname: Nyström
authors.forename: Lennart
authors.initials: L
authors.lastname: Nilsson
mesh_terms: D001483:Base Sequence; D002151:Calorimetry; D003198:Computer Simulation; D004355:Drug Stability; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009843:Oligoribonucleotides / Q000737:chemistry; D012313:RNA / Q000737:chemistry*
chemical_list: D009843:Oligoribonucleotides; D012313:RNA