Remarkable Stability of Hairpins Containing 2‘,5‘-Linked RNA Loops
- 13 November 2001
- journal article
- Published by American Chemical Society (ACS) in Journal of the American Chemical Society
- Vol. 123 (49), 12368-12374
- https://doi.org/10.1021/ja011336r
Abstract
We report here the results of a comparative study of hairpin loops that differ in the connectivity of phosphodiester linkages (3‘,5‘- versus 2‘,5‘-linkages). In addition, we have studied the effect of changing the stem composition on the thermodynamic stability of hairpin loops. Specifically, we constructed hairpins containing one of six stem duplex combinations, i.e., DNA:DNA (“DD”), RNA:RNA (“RR”), DNA:RNA (“DR”), 2‘,5‘-RNA:RNA (“RR”), 2‘,5‘-RNA:DNA (“RD”), and 2‘,5‘-RNA:2‘,5‘-RNA (“RR”), and one of three tetraloop compositions, i.e., 2‘,5‘-RNA (“R”), RNA (“R”), and DNA (“D”). All hairpins contained the conserved and well-studied loop sequence 5‘-...C(UUCG)G...-3‘ [Cheong et al. Nature 1990, 346, 680−682]. We show that the 2‘,5‘-linked loop C(UUCG)G, i.e., ...C3‘p5‘U2‘p5‘U2‘p5‘C2‘p5‘G2‘p5‘G3‘p5‘..., like its “normal” RNA counterpart, forms an unusually stable tetraloop structure. We also show that the stability imparted by 2‘,5‘-RNA loops is dependent on base sequence, a property that is shared with the regioisomeric 3‘,5‘-RNA loops. Remarkably, we find that the stability of the UUCG tetraloop is virtually independent of the hairpin stem composition (DD, RR, RR, etc.), whereas the native RNA tetraloop exerts extra stability only when the stem is duplex RNA (R:R). As a result, the relative stabilities of hairpins with a 2‘,5‘-linked tetraloop, e.g. ggac(UUCG)gtcc (Tm = 61.4 °C), are often superior to those with RNA tetraloops, e.g. ggac(UUCG)gtcc (Tm = 54.6 °C). In fact, it has been possible to observe the formation of a 2‘,5‘-RNA:DNA hybrid duplex by linking the hybrid's strands to a (UUCG) loop. These duplexes (RD), which are not stable enough to form in an intermolecular complex [Wasner et al. Biochemistry1998, 37, 7478−7486], were stable at room temperature (Tm ∼ 50 °C). Thus, 2‘,5‘-loops have potentially important implications in the study of nucleic acid complexes where structural data are not yet available. Furthermore, they may be particularly useful as structural motifs for synthetic ribozymes and nucleic acid “aptamers”.Keywords
This publication has 20 references indexed in Scilit:
- Physicochemical and Biochemical Properties of 2‘,5‘-Linked RNA and 2‘,5‘-RNA:3‘,5‘-RNA “Hybrid” Duplexes,Biochemistry, 1998
- Über die Aktivität 2′,5′‐verknüpfter RNA in der templatgesteuerten Oligomerisierung von MononucleotidenAngewandte Chemie, 1997
- Regiospecific Solid-Phase Synthesis of Branched Oligonucleotides. Effect of Vicinal 2‘,5‘- (or 2‘,3‘-) and 3‘,5‘-Phosphodiester Linkages on the Formation of Hairpin DNABioconjugate Chemistry, 1997
- Selective Binding of RNA, but Not DNA, by Complementary 2‘,5‘-Linked DNAJournal of the American Chemical Society, 1996
- Structure of the P1 Helix from Group I Self-splicing IntronsJournal of Molecular Biology, 1995
- Exceptionally Stable Nucleic Acid HairpinsAnnual Review of Biophysics and Biophysical Chemistry, 1995
- An Efficient Method for the Isolation and Purification of OligoribonucleotidesNucleosides and Nucleotides, 1995
- Sequence Specific Thermodynamic and Structural Properties for DNA.cntdot.RNA DuplexesBiochemistry, 1994
- Structure of an unusually stable RNA hairpinBiochemistry, 1991
- Solution structure of an unusually stable RNA hairpin, 5GGAC(UUCG)GUCCNature, 1990