Secondary structure change of oligonucleotide induced by salts

Formation of a unimolecular structure is essential for many biological processes such as transcription and translation, and the (deoxy)ribozyme activities. Since such nucleic acids consist of self-complementary sequence, they also have a potential to form a bimolecular structure as well. In this study, we designed 13 RNA and DNA sequences which can potentially form a hairpin loop structure by one strand and a duplex by two strands. On the basis of the UV melting and CD spectra measurements, we found that an RNA oligomer of rGCAAGCAAGCUUGC adopted different secondary structures depending on NaCl concentration, for example, a duplex at 1 M NaCl and a hairpin loop structure at 10 mM NaCl. On the other hand, the structure of DNA oligomer with the same sequence was unchanged. This observation indicates that the structural transition by the change of the NaCl concentration is not due to the nature of the sequence.