Open AccessInfluence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides
Author(s) -
Shuichi Nakano,
Toshimasa Kirihata,
Satoshi Fujii,
Hiroshi Sakai,
Masayasu Kuwahara,
Hiroaki Sawai,
Naoki Sugimoto
Publication year - 2006
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/gkl1073
Subject(s) - oligonucleotide , duplex (building) , dna , circular dichroism , rna , nucleotide , cationic polymerization , biology , biophysics , molecule , nucleic acid denaturation , triple helix , palindromic sequence , crystallography , biochemistry , chemistry , stereochemistry , palindrome , base sequence , organic chemistry , crispr , gene
A self-complementary nucleotide sequence can form both a unimolecular hairpin and a bimolecular duplex. In this study, the secondary structures of the self-complementary DNA and RNA oligonucleotides with different sequences and lengths were investigated under various solution conditions by gel electrophoresis, circular dichroism (CD) and electron paramagnetic resonance (EPR) spectroscopy and a ultraviolet (UV) melting analysis. The DNA sequences tended to adopt a hairpin conformation at low cation concentrations, but a bimolecular duplex was preferentially formed at an elevated cationic strength. On the other hand, fully matched RNA sequences adopted a bimolecular duplex regardless of the cation concentration. The thermal melting experiments indicated a greater change in the melting temperature of the bimolecular duplexes (by approximately 20 degrees C) than that of the hairpin (by approximately 10 degrees C) by increasing the NaCl concentration from 10 mM to 1 M. Hairpin formations were also observed for the palindrome DNA sequences derived from Escherichia coli, but association of the complementary palindrome sequences was observed when spermine, one of the major cationic molecules in a cell, existed at the physiological concentration. The results indicate the role of cations for shifting the structural equilibrium toward a nucleotide assembly and implicate nucleotide structures in cells.