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Nucleic Acids Research, 2002, Vol. 30, No. 2 468-474
© 2002 Oxford University Press

The reactivity of phosphodiester bonds within linear single-stranded oligoribonucleotides is strongly dependent on the base sequence

Ulla Kaukinen, Sari Lyytikäinen, Satu Mikkola* and Harri Lönnberg

Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland

The cleavage of short chimeric oligonucleotides containing only one reactive ribonucleoside unit, all other nucleosides being 2'-O-methylated, has been studied at pH 8.5 and 35°C. Among the 20 different sequences that did not exhibit any tendency to form a defined secondary structure, the scissile 5'-UpA-3' and 5'-CpA-3' phosphodiester bonds experienced >100- and up to 35-fold reactivity differences, respectively. Compared with dinucleoside monophosphates, both rate accelerations and retardations of more than one order of magnitude were observed. Even a change of a single base several nucleosides away from the scissile bond markedly affected the reaction rate. Duplex formation at the 3'- and/or 5'-side of the scissile bond was also studied and observed to be strongly rate retarding. The origin of the high sensitivity of phosphodiester bonds to the molecular environment is discussed.

* To whom correspondence should be addressed. Tel: +358 2 333 6785; Fax: +358 2 333 6700; Email: satu.mikkola@utu.fi


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