In this report, the characterization of labeled oligonucleotides was discussed from the view points of base sequence analysis and structural analysis of nucleic acids in solution. Oligonucleotides site specifically spin labeled with TEMPO and fluorescent labeled with fluorescein were prepared and used for those analyses. The changes of ESR lines and rotational correlation time (tau) of the spin labeled oligonucleotide (S-probe) were dependent on the base sequence of S-probe, diastereoisomers, and the manner of hybridization. These results suggest that the conformation of the hybrid largely affected the local mobility of TEMPO and that tau value of S-probe reflected the local structure of the hybrid. When S-probe which was complementary to a single strand region of 5S RNA, was mixed with 5S RNA, tau value largely changed, indicating that the S-probe could form hybrid with 5S RNA in solution. Similar results were also obtained in the fluorescence depolarization analysis using fluorescent labeled oligonucleotide (F-probe). These results suggest that S-probe and F-probe are capable for the recognition of the secondary structure of 5S RNA in solution and useful for the analysis of the secondary structure of other nucleic acids in solution.