title: Hydrophobic properties of tRNA with varied conformations evaluated by an aqueous two-phase system.
abstract: The surface properties of transfer RNA (tRNA) were analyzed using a poly(ethylene glycol)/dextran aqueous two-phase system (ATPS), where the surface net hydrophobicity (HFS) and the local hydrophobicity (LH) were evaluated based on the partition coefficient of tRNA in the ATPS. According to the evaluated HFS values, the surface of the tRNA molecule was hydrophilic at 20° -40 °C, and it became hydrophobic at 50° -80 °C because of the exposure of the intrinsic nucleobases of tRNA. In contrast, the LH values were found to be maximal at 20° -40 °C. The conformation of tRNA was investigated by Raman and circular dichroism (CD) spectroscopies, corroborating the results with the calculated prediction of its secondary structure (Mfold). It was shown that 66% of A-form structure existed at room temperature; the base stacking (θ(265)) was gradually decreased, and the A-form structure (θ(208)) was denatured along with a sigmoid curve against the temperature increase; the denatured secondary structures were observed above 50° C by Mfold prediction. The HFS value of the DNA duplex was found to be hydrophilic, compared to that of the single-stranded DNA, indicating that the exposure of nucleobases is a key factor of the hydrophobic properties of nucleotides. We conclude that the hydrophobic property of the tRNA surface was directly affected by its conformational transition.
authors.affiliation: Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Osaka, Japan.
authors.forename: Keishi
authors.initials: K
authors.lastname: Suga
authors.forename: Hibiki
authors.initials: H
authors.lastname: Tomita
authors.forename: Seishiro
authors.initials: S
authors.lastname: Tanaka
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Umakoshi
mesh_terms: D002942:Circular Dichroism; D003911:Dextrans; D057927:Hydrophobic and Hydrophilic Interactions; D009690:Nucleic Acid Conformation; D011092:Polyethylene Glycols; D012343:RNA, Transfer / Q000737:chemistry*; D013059:Spectrum Analysis, Raman; D013499:Surface Properties; D013696:Temperature
chemical_list: D003911:Dextrans; D011092:Polyethylene Glycols; D012343:RNA, Transfer
keywords: hydrophobicity; transfer RNA