Thermodynamics of RNA-RNA duplexes with 2- or 4-thiouridines: Implications for antisense design and targeting a group I intron

Stephen M. Testa, Matthew D. Disney, Douglas H. Turner, Ryszard Kierzek

Research output: Contribution to journalArticlepeer-review

104 Scopus citations

Abstract

Antisense compounds are designed to optimize selective hybridization of an exogenous oligonucleotide to a cellular target. Typically, Watson-Crick base pairing between the antisense compound and target provides the key recognition element. Uridine (U), however, not only stably base pairs with adenosine (A) but also with guanosine (G), thus reducing specificity. Studies of duplex formation by oligonucleotides with either an internal or a terminal 2- or 4-thiouridine (s2U or s4U) show that s2U can increase the stability of base pairing with A more than with G, while s4U can increase the stability of base pairing with G more than with A. The latter may be useful when binding can be enhanced by tertiary interactions with a s4U-G pair. To test the effects of s2U and s4U substitutions on tertiary interactions, binding to a group I intron ribozyme from mouse-derived Pneumocystis carinii was measured for the hexamers, r(AUGACU), r(AUGACs2U), and r(AUGACs4U), which mimic the 3' end of the 5' exon. The results suggest that at least one of the carbonyl groups of the 3' terminal U of r(AUGACU) is involved in tertiary interactions with the catalytic core of the ribozyme and/or thio groups change the orientation of a terminal U-G base pair. Thus thio substitutions may affect tertiary interactions. Studies of transsplicing of 5' exon mimics to a truncated rRNA precursor, however, indicate that thio substitutions have negligible effects on overall reactivity. Therefore, modified bases can enhance the specificity of base pairing while retaining other activities and, thus, increase the specificity of antisense compounds targeting cellular RNA.

Original languageEnglish
Pages (from-to)16655-16662
Number of pages8
JournalBiochemistry
Volume38
Issue number50
DOIs
StatePublished - Dec 14 1999

ASJC Scopus subject areas

  • Biochemistry

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