Intra- and intermolecular interactions influence the reactivity of RNA oligonucleotides




Linjalahti H, Mikkola S

PublisherWILEY-V C H VERLAG GMBH

2007

Chemistry and Biodiversity

CHEMISTRY & BIODIVERSITY

CHEM BIODIVERS

4

12

2938

2947

10

1612-1872

DOIhttps://doi.org/10.1002/cbdv.200790243



The transesterification of RNA oligonucleotides was studied over a wide pH range. The rate constants obtained indicate that, under neutral conditions, oligonucleotides with an adenosine moiety as the 5'-linked nucleoside can be up to 1000-fold more reactive than the reference oligonucleotide, a 13-mer oligo-U (1). Experiments with the modified oligonucleotide with N-6,N-6-dimethyladenosine (9) as the 5'-Iinked nucleoside moiety suggest that the exocyclic amino group is involved in the reaction, influencing the reactivity of the neighboring phosphodiester bond. In addition to such intramolecular interactions, weak intermolecular interactions most probably contribute to the reactivity.



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