A Periodic Table of Tandem Mismatches in RNA

Abstract

The stabilities and structures of a series of RNA octamers containing symmetric tandem mismatches were studied by UV melting and imino proton NMR. The free energy increments for tandem mismatch formation are found to depend upon both mismatch sequence and adjacent base pairs. The observed sequence dependence of tandem mismatch stability is UGGU > GUUG > GAAG > or = AGGA > UUUU > CAAC > or = CUUC approximately UCCU approximately CCCC approximately ACCA approximately AAAA, and the closing base pair dependence is 5'G3'C > 5'C3'G > 5'U3'A approximately 5'A3'U. These results differ from expectations based on models used in RNA folding algorithms and from the sequence dependence observed for folding of RNA hairpins. Imino proton NMR results indicate the sequence dependence is partially due to hydrogen bonding within mismatches.

Effects of magnesium ions on the stabilization of RNA oligomers of defined structures

“…mation in 1 M NaCl melt buffer are within experimental error of those measured previously+ The ⌬G8 37 value for the AG tandem pair is Ϫ0+2 kcal/mol+ The effect of Mg 2ϩ ion on the thermal stability of the oligomers with tandem GA pairs is shown in Figure 3A,B+ The melting temperature for the GA oligomer increases by 11+8 8C in 50 mM Mg 2ϩ ion and that of the AG oligomer by 9+4 8C (Table 2)+ These increases are nearly the same as those observed for the regular Watson-Crick octamer duplex+ The data for the tandem GA oligomers were then fitted to the two models for Mg 2ϩ binding and the results are displayed in Figure 4C,D+ Fitting the data to model 1 results in a slope that corresponds to ⌬n values of 0+52 (GA) and 0+40 (AG; Fig+ 4C Figure 5A displays the geometry of the tandem GA pair and Figure 5B shows the helix structure with the narrow deep groove produced by the trans Hoogsteen/sugar edge GA pairs+ The BD simulation shows an accumulation of metal-binding sites within the deep groove+ The narrow deep groove of the tandem GA helix features high occupancy sites for both 1+2-and 2+2-Å spheres near the center of the helix (Fig+ 5B)+ Again, space-filling representations of the low occupancy sites (Fig+ 5C) indicate that the deep groove is lined with potential binding sites+ Figure 6A displays the geometry of the tandem AG pair and Figure 6B shows the helix structure with the widened deep groove produced by the cis WatsonCrick/Watson-Crick AG pairs+ The BD simulation shows an accumulation of metal binding sites within the deep groove (Fig+ 6B)+ The wider deep groove of the tandem AG helix features high occupancy sites not only at the center of the helix (near the AG pairs) but also near the helix ends for the 1+2-Å spheres+ The high occupancy 2+2-Å spheres sites are located M.J. Serra et al at the center of the helix+ The low occupancy sites modeled in Figure 6C as spheres line the deep groove+ Phylogenetic analysis of rRNAs has shown that the symmetrical sequence 59-UG/GU is the most prevalent non-Watson-Crick tandem (Gutell et al+, 1992;Gutell, 1994)+ This motif has been shown to be more stable than other tandem non-Watson-Crick pairs (He et al+, 1991)+ The tandem GU in the opposite orientation 59GU/UG is less prevalent (Gautheret et al+, 1995) and its stability depends upon the identity of the flanking base pairs (Wu et al+, 1995)+ The nonsymmetrical 59GG/UU tandem motif is intermediate both in abundance and stability relative to the two symmetrical GU motifs (Gautheret et al+, 1995;Xia et al+, 1997)+ The structure and properties of GU pairs and tandem have recently been reviewed (Masquida & Westhof, 2000)+ The structures of three different tandem GU pairs have been determined by X-ray diffraction …”

Hairpins in a DNA site for topoisomerase II studied by1H-and31P-NMR

“…Actually, GT is among the most stable mismatch base pairs (39,45). It could further, through the slight distortions that it imposes to the DNA backbone of the loop, facilitate both the creation of an additional base pairing between the two A residues of the central loop and favourable base stackings, these incrementing the stability of the homoduplex.…”

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

“…Internal loop free energy parameters are revised on the basis of recent measurements (58)(59)(60)(61) and the previously assembled database (8,45,46,(62)(63)(64)(65)(66)(67)(68)(69). In the program described here, measured values are used when available for 1 ϫ 1, 1 ϫ 2, and 2 ϫ 2 internal loops, but approximations are used for most internal loops.…”

“…The ⌬G°3 7 GG(2 ϫ 2) term (Ϫ1.3 Ϯ 0.2 kcal͞mol) is applied to loops with a GG pair adjacent to an AA or any noncanonical pair with a pyrimidine. Values for ⌬ p and ⌬G°37 GG were obtained by linear regression on the 2 ϫ 2 loop database (8,58,62,64,65,68). Other internal loops are approximated by ⌬G°3 7 loop(n) ϭ ⌬G°37 loop initiation(n) ϩ ⌬G°37 AU͞GUϩ ͉n1 Ϫ n2͉ ⌬G°3 7 asym ϩ ⌬G°37 first noncanonical pairs(except for 1 ϫ (n Ϫ 1) for n Ͼ 3).…”

“…For example, an isoenergetic bulged C in 5ЈUGU͞3ЈACCA can occur in two positions. ⌬G°3 7 (special C bulge), Ϫ0.9 Ϯ 0.3 kcal (1 cal ϭ 4.18 J)͞mol, is an empirical bonus applied to bulged C residues adjacent to at least one C. The ⌬G°3 7 bulge initiation for single nucleotide bulges is 3.81 Ϯ 0.08 kcal͞mol.Internal loop free energy parameters are revised on the basis of recent measurements (58-61) and the previously assembled database (8,45,46,(62)(63)(64)(65)(66)(67)(68)(69)). In the program described here, measured values are used when available for 1 ϫ 1, 1 ϫ 2, and Abbreviation: RT, reverse transcription.…”