Thermodynamic Characterization of the Complete Set of Sequence Symmetric Tandem Mismatches in RNA and an Improved Model for Predicting the Free Energy Contribution of Sequence Asymmetric Tandem Mismatches

Abstract

Because of the availability of an abundance of RNA sequence information, the ability to rapidly and accurately predict the secondary structure of RNA from sequence is becoming increasingly important. A common method for predicting RNA secondary structure from sequence is free energy minimization. Therefore, accurate free energy contributions for every RNA secondary structure motif are necessary for accurate secondary structure predictions. Tandem mismatches are prevalent in naturally occurring sequences and are biologically important. A common method for predicting the stability of a sequence asymmetric tandem mismatch relies on the stabilities of the two corresponding sequence symmetric tandem mismatches [Mathews, D. H., Sabina, J., Zuker, M., and Turner, D. H. (1999) J. Mol. Biol. 288, 911-940]. To improve the prediction of sequence asymmetric tandem mismatches, the experimental thermodynamic parameters for the 22 previously unmeasured sequence symmetric tandem mismatches are reported. These new data, however, do not improve prediction of the free energy contributions of sequence asymmetric tandem mismatches. Therefore, a new model, independent of sequence symmetric tandem mismatch free energies, is proposed. This model consists of two penalties to account for destabilizing tandem mismatches, two bonuses to account for stabilizing tandem mismatches, and two penalties to account for A-U and G-U adjacent base pairs. This model improves the prediction of asymmetric tandem mismatch free energy contributions and is likely to improve the prediction of RNA secondary structure from sequence.

Thermodynamic characterization of naturally occurring RNA tetraloops

“…The synthesis and purification of the oligonucleotides followed standard procedures that were described previously (Davis and Znosko 2007;Wright et al 2007;Christiansen and Znosko 2008).…”

“…Melting curves (absorbance versus temperature) were obtained, and duplex thermodynamics (for terminal mismatches) were determined as described previously (Davis and Znosko 2007;Wright et al 2007;Christiansen and Znosko 2008). All stem-loops were melted about nine times with approximately a 50-fold concentration range.…”

“…Updated values for parameters in previous predictive models and values for new predictive models were derived by linear regression as described previously (Badhwar et al 2007;Davis and Znosko 2007;Wright et al 2007;Christiansen and Znosko 2008;Davis and Znosko 2008). The calculated experimental contribution of the tetraloop to stem-loop stability was used as a constant when doing linear regression.…”

Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops

“…Studies started with self-complementary sequences 72 designed to form symmetric duplexes with a central 2×2 nt internal loop. As discussed below, however, there were conditions in which NMR showed that the sequences can also form a hairpin, thus revealing an unexpected conformational pliability for GU pairs.…”

“…The other numbers are nearest neighbor parameters taken from Xia et al and J. Chen et al 63, 70 The calculated value of 3.58 kcal/mol for loop formation is more stable than the 6.00 kcal/mol previously reported. 72 The difference is that the previous calculation subtracted the measured ΔG° 37 of −11.2 kcal/mol for (5′CG GGUC CG) 2 73 and added the best value of 1.29 kcal/mol for the (5′GU/3′UG) middle nearest neighbor available at that time. 36 Use of the measured value for (5′CG GGUC CG) 2 , however, neglects the fact that the 5′GGUC/3′CUGG quartet is unusually stable 63, 73 but absent in (5′CGG GCAU CCG) 2 .…”