Synthesis and biochemical evaluation of RNA containing an intrahelical disulfide crosslink

AbstractBackground: Several factors impede the elucidation of RNA structure and function by X-ray and NMR methods, including the complexity of folded RNA motifs, the tendency of RNA to aggregate, and its ability to fold into multiple isomeric structures. The ability to constrain the process of RNA folding to give a single, homogeneous product would assist these investigations. We therefore set out to develop a synthetic procedure for the site-specific insertion of a disulfide crosslink into oligoribonucleotides. We also examined the ability of a crosslinked species to serve as a substrate for ricin, an RNA glycosylase.Results: A convertible nucleoside derivative (C) suitable for the site-specific introduction of N4-alkyl-cytidine residues into RNA has been developed. The corresponding C phosphoramidite was employed in the synthesis of an 8-mer oligonucleotide, 5′-CGGAGACG-3′, which was then efficiently converted to an 8-mer containing two S-protected N4-(2-thioethyl)C residues. Upon deprotection and air oxidation, the 8-mer efficiently formed an intramolecular disulfide bond, yielding a GAGA tetraloop presented on a two base-pair CPG disulfide crosslinked ministem. We show that this ministem-loop is an excellent substrate for ricin. Control 8-mers lacking the disulfide crosslink were substantially poorer substrates for ricin.Conclusions: The nucleoside chemistry described here should be generally useful for the site-specific introduction of a range of non-native functional groups into RNA. We have used this chemistry to constrain an RNA ministem through introduction of an intrahelical disulfide crosslink. That this tetraloop substrate linked to a two base-pair ministem is efficiently processed by ricin is clear evidence that ricin makes all of its energetically favorable contacts to the extreme end of the stem-loop structure, and that the two base pairs of the stem abutting the loop remain intact during recognition and processing by ricin