NMR Structures of (rGCUGAGGCU)₂ and (rGCGGAUGCU)₂:  Probing the Structural Features That Shape the Thermodynamic Stability of GA Pairs^,

Abstract

The NMR structures of and are reported. The internal loop, , is about 2 kcal/mol more stable than at 37 °C. The duplexes assemble into similar global folds characterized by the formation of tandem sheared GA pairs. The different stabilities of the loops are accompained by differences in the local structure of the closing GU pairs. In the internal loop, the GU pairs form canonical wobble configurations with two hydrogen bonds, whereas in the GU pairs form a single hydrogen bond involving the amino group, GH22, to the carbonyl group, UO4. This pairing is similar to the GU closing pair of the 690 hairpin loop found in E. coli 16S rRNA. The and structures reveal how the subtle interplay between stacking and hydrogen bonding determines sequence dependent conformation and thermodynamic stability. Thus, this work provides

Stacking Effects on Local Structure in RNA: Changes in the Structure of Tandem GA Pairs when Flanking GC Pairs Are Replaced by isoG−isoC Pairs

“…11,60 This is also consistent with the mixed sugar pucker observed here for the (iCGAiG) 2 loop and with observations on tandem GA pairs closed by GU pairs. 15 The current results, however, suggest this is not a strict correlation because the (iGGAiC) 2 internal loop has a favorable free energy increment, but the G has a mixture of C3′ and C2′-endo sugars. Nonetheless, loop stability and sugar pucker are correlated for the GC to iGiC replacements.…”

“…In the minor conformation: (1) the iG6H1′ proton is shifted 1.27 ppm upfield relative to the major conformation ( Figure S1 and Table S4), consistent with the shift induced by the adenine ring of a sheared GA pair, as observed for iC6H1′ in (GCiGGAiCGCA) 2 and other structures; 8,14,64 (2) the G4 imino proton is shifted upfield to 9.8 ppm (Figure 2, 3, and Table S4), consistent with an imino proton not involved in a hydrogen bond; and (3) the G4 ribose ring is observed to exist partially in the C2′-endo conformation ( Figure S4), consistent with the observation that in several structures involving thermodynamically less stable sheared GA pairs, the G ribose is found to be in the C2′-endo conformation. 11,14,15,60,64 It cannot be determined, however, whether the C2′-endo pucker occurs when the GA pair is in the major or minor conformation or both.…”

“…The stability [1][2][3][4][5][6][7] and three-dimensional structure [7][8][9][10][11][12][13][14][15] of RNA tandem GA pairs are dependent on sequence context. Tandem sheared GA (trans Hoogsteen/ Sugar edge A-G) pairs ( Figure 1) form with cross-strand base stacking in the symmetric contexts (CGAG) 2 with loop free energy of −0.7 kcal/mol 1,3,8 and (UGAA) 2 with loop free energy of 0.7 kcal/mol.…”

“…7,9,16 Different shapes of GA pairs in turn provide different molecular features, e.g., van der Waals and electrostatic surface, and hydrogen bonding donors and acceptors, for higher order RNA folding and molecular recognition. [13][14][15][17][18][19] The Watson-Crick like iGiC pair, with the amino and carbonyl groups transposed relative to the Watson-Crick GC pair, provides an expanded alphabet [20][21][22][23][24][25][26] for further understanding interactions that shape nucleic acid structure (Figure 1). 7,[25][26][27][28][29][30][31][32] Here, thermodynamic studies of tandem GA pairs flanked by iGiC pairs are reported along with NMR structures of the RNA duplexes (GCiGGAiCGCA) 2 and (GGiCGAiGCCA) 2 .…”

29 Accelerating nucleic acid design using pre-selected sequences

“…Previous solution structures showed that these tandem GA base pairs adopt either imino (cis-Watson-Crick/cisWatson-Crick interaction) or sheared (trans-Hoogsteen/ trans-Hoogsteen interaction) pairing depending upon the sequence and orientation of the adjacent base pairs. In our simulations, we modeled (GCGGACGC) 2 (Wu and Turner 1996) and (GCGGAUGC) 2 (Tolbert et al, 2007), experimentally preferred as imino and sheared, respectively. Besides the experimentally preferred conformation, we constructed models of the nonnative conformations by changing cytosine to uracil or uracil to cytosine.…”