In order to understand the interaction mechanism between the assemblies and the nucleic acids, analyses of the surface properties of nucleic acids are necessary. The interaction of supermolecular assemblies (i.e., the liposome) with various types of nucleic acids has been reported 3 - 5. The physiochemical properties of the surface of the biomacromolecule are likely to have an important role in the molecular recognition, however, the relationship between the surface properties and the conformation in the nucleic acids has not yet been fully determined. These attracting forces may depend on the surface properties of the biomacromolecule, which are likely related to its conformation. Such molecular recognition requires several possible driving forces: (i) electrostatic and (ii) hydrophobic interaction, or (iii) hydrogen bond. Transfer RNA (tRNA) is one of the well-studied ribonucleotides (ribozymes) that transfers amino acids to the ribosome. RNA is a polynucleotide which carries genetic information such as DNA, and it also possesses a catalyst function, which is known as the "ribozyme." The conformation of RNA is a key to the regulation of its functions: the recognition of amino acids or aminoacyl tRNA synthetase, the reading of genetic information on mRNA, the peptidyl transfer of ribosomal RNA, etc. The various types of functional nucleic acids play important roles in biological events. We conclude that the hydrophobic property of the tRNA surface was directly affected by its conformational transition. 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. 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 conformation of tRNA was investigated by Raman and circular dichroism (CD) spectroscopies, corroborating the results with the calculated prediction of its secondary structure (Mfold). In contrast, the LH values were found to be maximal at 20° -40 ☌. According to the evaluated HFS values, the surface of the tRNA molecule was hydrophilic at 20° -40 ☌, and it became hydrophobic at 50° -80 ☌ because of the exposure of the intrinsic nucleobases of tRNA. 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.
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