Hydrophobic properties of tRNA with varied conformations evaluated by an aqueous two-phase system

Keishi Suga, Hibiki Tomita, Seishiro Tanaka, Hiroshi Umakoshi

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)

Abstract

The surface properties of transfer RNA (tRNA) were analyzed using a polyethylene gly-col)/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 (θ265) 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.

Original languageEnglish
Pages (from-to)1188-1196
Number of pages9
JournalInternational Journal of Biological Sciences
Volume8
Issue number8
DOIs
Publication statusPublished - 2012 Oct 15
Externally publishedYes

Keywords

  • Hydrophobicity
  • Transfer RNA

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Applied Microbiology and Biotechnology
  • Molecular Biology
  • Developmental Biology
  • Cell Biology

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