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



: Kaukinen U, Lyytikainen S, Mikkola S, Lonnberg H

Publisher: OXFORD UNIV PRESS

: 2002

: Nucleic Acids Research

: NUCLEIC ACIDS RESEARCH

: NUCLEIC ACIDS RES

: 30

: 2

: 468

: 474

: 7

: 0305-1048

DOI: https://doi.org/10.1093/nar/30.2.468


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 35degreesC. 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.



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