Nucleic Acids Research Advance Access originally published online on December 14, 2006
Nucleic Acids Research 2007 35(2):486-494; doi:10.1093/nar/gkl1073
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Nucleic Acids Research, 2007, Vol. 35, No. 2 486-494
© 2006 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides
1 Frontier Institute for Biomolecular Engineering Research (FIBER) 8–9–1 Okamoto, Higashinada–ku, Kobe 658–8501, Japan 2 Department of Chemistry, Faculty of Science and Engineering, Konan University 8–9–1 Okamoto, Higashinada–ku, Kobe 658–8501, Japan 3 Faculty of Engineering, Gunma University 1-5-1 Tenjin-chou, Kiryu, Gunma 376-8515, Japan 4 PRESTO, Japan Science and Technology Agency (JST) Saitama 332-0012, Japan
*To whom correspondence should be addressed. Tel: +81 78 435 2497; Fax: +81 78 435 2539; Email: sugimoto{at}konan-u.ac.jp
Received July 27, 2006. Revised November 9, 2006. Accepted November 10, 2006.
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.
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