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Nucleic Acids Research 2005 33(16):5082-5093; doi:10.1093/nar/gki789
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Published online 9 September 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes

Elzbieta Kierzek1,2, Anna Ciesielska2, Karol Pasternak2, David H. Mathews3,4, Douglas H. Turner1,3,* and Ryszard Kierzek2

1Department of Chemistry and Department of Pediatrics, University of Rochester RC Box 270216, Rochester, NY 14627-0216, USA 2Institute of Bioorganic Chemistry, Polish Academy of Sciences 60-714 Poznan, Noskowskiego 12/14, Poland 3Center for Molecular Pediatric Research, University of Rochester School of Medicine and Dentistry Rochester, New York, 14642, USA 4Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry Rochester, New York, 14642, USA

*To whom correspondence should be addressed. Tel: +1 585 275 3207; Fax: +1 585 276 0205; Email: turner{at}chem.rochester.edu

Received June 6, 2005. Revised August 8, 2005. Accepted August 8, 2005.

The influence of locked nucleic acid (LNA) residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes is reported. Optical melting studies indicate that LNA incorporated into an otherwise 2'-O-methyl RNA oligonucleotide usually, but not always, enhances the stabilities of complementary duplexes formed with RNA. Several trends are apparent, including: (i) a 3' terminal U LNA and 5' terminal LNAs are less stabilizing than interior and other 3' terminal LNAs; (ii) most of the stability enhancement is achieved when LNA nucleotides are separated by at least one 2'-O-methyl nucleotide; and (iii) the effects of LNA substitutions are approximately additive when the LNA nucleotides are separated by at least one 2'-O-methyl nucleotide. An equation is proposed to approximate the stabilities of complementary duplexes formed with RNA when at least one 2'-O-methyl nucleotide separates LNA nucleotides. The sequence dependence of 2'-O-methyl RNA/RNA duplexes appears to be similar to that of RNA/RNA duplexes, and preliminary nearest-neighbor free energy increments at 37°C are presented for 2'-O-methyl RNA/RNA duplexes. Internal mismatches with LNA nucleotides significantly destabilize duplexes with RNA.


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