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Published online 9 January 2004

Nucleic Acids Research, 2004, Vol. 32, No. 1 248-254
© 2004 Oxford University Press

Hydration of short DNA, RNA and 2'-OMe oligonucleotides determined by osmotic stressing

Eriks Rozners* and Janelle Moulder

Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA

*To whom correspondence should be addressed. Tel: +1 617 373 5826; Fax: +1 617 373 8795; Email: e.rozners{at}neu.edu

Studies on hydration are important for better understanding of structure and function of nucleic acids. We compared the hydration of self-complementary DNA, RNA and 2'-O-methyl (2'-OMe) oligonucleotides GCGAAUUCGC, (UA)6 and (CG)3 using the osmotic stressing method. The number of water molecules released upon melting of oligonucleotide duplexes, {Delta}nW, was calculated from the dependence of melting temperature on water activity and the enthalpy, both measured with UV thermal melting experiments. The water activity was changed by addition of ethylene glycol, glycerol and acetamide as small organic co-solutes. The {Delta}nW was 3–4 for RNA duplexes and 2–3 for DNA and 2'-OMe duplexes. Thus, the RNA duplexes were hydrated more than the DNA and the 2'-OMe oligonucleotide duplexes by approximately one to two water molecules depending on the sequence. Consistent with previous studies, GC base pairs were hydrated more than AU pairs in RNA, whereas in DNA and 2'-OMe oligonucleotides the difference in hydration between these two base pairs was relatively small. Our data suggest that the better hydration of RNA contributes to the increased enthalpic stability of RNA duplexes compared with DNA duplexes.


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