Thermodynamic and structural features of ultrastable DNA and RNA hairpins Bele ´n Herna ´ndez a,b , Vladimir Baumruk c , Nicolas Leulliot a,b , Catherine Gouyette d , Tam Huynh-Dinh d , Mahmoud Ghomi a,b, * a Laboratoire de Physicochimie Biomole ´culaire et Cellulaire (LPBC), UMR CNRS 7033, Universite ´ P. & M. Curie, Case 138, 4 Place de Jussieu, 75252 Paris Cedex 05, France b Laboratoire de Physicochimie Biomole ´culaire et Cellulaire (LPBC), UMR CNRS 7033, UFR SMBH, Universite ´ Paris 13, 74 rue Marcel Cachin, 93017 Bobigny Cedex, France c Institute of Physics, Charles University, Ke Karlovu 5, 12116 Prague 2, Czech Republic d Unite ´ de Chimie Organique, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France Received 3 September 2002; accepted 16 September 2002 Abstract Short RNA and DNA hairpins have been analysed in aqueous phase by means of UV absorption and vibrational spectroscopy in the following oligodeoxynucleotide and oligoribonucleotide sequences: 5 0 -d(GC-GAA-GC)-3 0 ,5 0 -r(CGC-GNRA-GCG)-3 0 (where N ¼ U, A, C, G and R ¼ A, G) and 5 0 -r(GCG-UGAA-CGC)-3 0 . These hairpins contain GAA triloop, GNRA and UGAA tetraloops stabilised by two or three GC base pairs in their stems. The analysis of UV absorption melting profiles allowed us to confirm the high (to very high) thermodynamic stability of these hairpins through the estimation of their melting temperature ðT m Þ: FT-IR spectra revealed the presence of N-type and/or S-type sugar puckers in the hairpins. Raman spectra at the temperatures below T m provided information on the conformations of certain nucleosides involved in the hairpins, as well as on the global conformation (A or B forms) of their stems. Raman spectra recorded as a function of temperature, are consistent with the hairpin-to-random coil conformational transitions through the breakdown of interbase H-bonds, and the loss of stacking between the bases. A discussion has been carried out on the agreement between vibrational data and those available from NMR on a few number of these hairpins. q 2003 Elsevier Science B.V. All rights reserved. Keywords: Hairpin; Oligodeoxynucleotide; Oligoribonucleotide 1. Introduction Hairpins are elementary structural units respon- sible for nucleic acid (NA) folding. A hairpin consists of an intramolecular antiparallel double helix (stem) capped by a certain number of unpaired nucleotides (loop). In RiboNucleic Acid (RNA), hairpins allow 0022-2860/03/$ - see front matter q 2003 Elsevier Science B.V. All rights reserved. PII: S0022-2860(02)00627-0 Journal of Molecular Structure 651–653 (2003) 67–74 www.elsevier.com/locate/molstruc * Corresponding author. Address: Laboratoire de Physicochimie Biomole ´culaire et Cellulaire (LPBC), UMR CNRS 7033, Universite ´ P. & M. Curie, Case 138, 4 Place de Jussieu, 75252 Paris Cedex 05, France. Tel.: þ33-1-442-77555; fax: þ 33-1-442-77560. E-mail addresses: ghomi@lpbc.jussieu.fr (M. Ghomi), hernandez@lpbc.jussieu.fr (B. Herna ´ndez).