Folding Cooperativity in RNA and DNA Is Dependent on Position in the Helix

Abstract

Secondary structural motifs play essential roles in the folding and function of RNA and DNA molecules. Previous work from our lab compared the folding of small DNA and RNA hairpin loops containing a sheared GA pair [Moody, E. M., Feerar, J. C., and Bevilacqua, P. C. (2004) Biochemistry 43, 7992-7998]. We found that the small DNA hairpins fold in a highly cooperative manner with indirect coupling, while their RNA counterparts fold in a much less cooperative fashion and display direct coupling. Herein, we extend this study to the double-stranded helix. We carried out double mutant cycles on base pairs having identical nearest-neighbor contexts but located in either external or internal helical registers. In the external register, both RNA and DNA exhibit extensive folding cooperativity between the penultimate and terminal base pair, which is independent of mismatch identity. In contrast, DNA exhibits virtually no folding cooperativity in the center of the helix, while RNA maintains substantial coupling, which is dependent on mismatch identity. Two models account for these non-nearest-neighbor effects: one involves the unfavorable entropy of helix initiation common to DNA and RNA, and the other involves steric and electrostatic strain peculiar to RNA. These data show that RNA can display cooperativity less than, greater than, or equal to that of DNA depending on context and position.

Driving Forces for Nucleic Acid pKa Shifting in an A+·C Wobble: Effects of Helix Position, Temperature, and Ionic Strength

“…Sharpening of this resonance in WT at low pH supports nearby A þ 3 C wobble formation (13), while absence of this resonance at high pH in -1 suggests that base pair 3 breaks with the AC wobble. Additionally, the resonance for base pair 3 is effectively absent from the spectra of the -2 and -3 constructs at both low and high pH (Supporting Information), which supports the earlier finding that -2 does not exhibit an observable pK a (Figure 2), as well as our earlier studies in which a terminal base pair did not form in the absence of a penultimate base pair (36).…”

“…We opt to label this sequence as "WT" herein because variants were designed on the basis of this core sequence. We used a similar WT nomenclature in another report (36).…”

Thermodynamic characterization of naturally occurring RNA tetraloops

“…Non-nearest-neighbor effects have been observed previously for a wide variety of RNA secondary structure motifs (Longfellow et al 1990;Kierzek et al 1999;Badhwar et al 2007;Davis and Znosko 2007;Siegfried et al 2007;Wright et al 2007); however, current algorithms that predict the stability of RNA from sequence (Zuker 1989;Mathews et al 1999Mathews et al , 2004Hofacker 2003;Zuker 2003;Lu et al 2006) ignore non-nearest-neighbor effects. Hairpins are a convenient motif to investigate non-nearest-neighbor effects on motif stability because they are situated at the end of a helix and have nonnearest neighbors in only one direction.…”

Thermodynamic examination of the pyrophosphate sensor helix in the thiamine pyrophosphate riboswitch

“…2; Table 2); the CdA/CdA construct is z0.6 kcal/mol more stable than the AdC/AdC construct in both conditions. These differences may be indicative of differing interactions with the two helical stems and are likely indicative of nonnearest neighbor interactions (Kierzek et al 1999;Siegfried et al 2007;Chen et al 2009). The helical context of the internal loop has been seen to have an effect on RNA stability in previous studies, indicating that other nonnearest neighbor interactions contribute to internal loop stability (Schroeder and Turner 2000).…”