Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides

Abstract

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 ∼20°C) than that of the hairpin (by ∼10°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.

Master sensors of pathogenic RNA – RIG-I like receptors

“…In our experience, one-time size fractionation of hairpin RNA is not sufficient to exclude contamination of transcripts with small size differences completely. On the other hand, it has to be considered that hairpins are in equilibrium with their self-complementary duplex (Nakano et al 2007), which is supposed to be a more active ligand than the monomeric hairpin (Binder et al 2011). Thus, small contaminations can cause substantial effects.…”

Synthesis and Hybridization Properties of Modified Oligodeoxynucleotides Carrying Non‐Natural Bases

“…Low salt and low oligomer concentration favors the formation of the hairpin [15][16][17][18]. In our case, it is expected that the introduction of a central mismatch will decrease the stability of the bimolecular duplex without affecting the stability of the hairpin, thus favoring the formation of hairpin relative to the bimolecular duplex.…”

“…Dickerson-Drew dodecamer, as all self-complementary oligonucleotides, can form both a unimolecular hairpin and a bimolecular duplex [15][16][17][18]. Low salt and low oligomer concentration favors the formation of the hairpin [15][16][17][18].…”

1.25 Å resolution structure of an RNA 20-mer that binds to the TREX2 complex

“…The formation of duplexes from hairpins is favoured at the high ionic strength and RNA concentrations employed for crystallization (Nakano et al, 2007).…”