Hairpin thermodynamic stability

Blanco et al. 209 have studied the thermodynamic stability of another P-hairpin model sequence by use of NMR spectroscopy. This work was extended by Munoz et al. 201 by analysis of the T-jump-induced unfolding kinetics (with fluorescence monitoring) which revealed significantly longer time scales (ps) for bringing the two arms of the hairpin together than had previously been found for zipping the a-helix (180 ns). 

A hairpin consists of a helix bridged by a loop of unpaired nucleotides (Fig. 1.1). The hairpin loop is a frequent target for protein interactions and also functions as nucleation site for RNA folding. In particular the tetraloop hairpins, a group of loop sequences, UNCG, GNRA and CUUG, exhibit unusual thermodynamic stability. 

Without providing a detailed sensitivity analysis for this specific yeast screen, we want to add that sensitivity highly depends on the ncRNA class. MicroRNAs, for example are easy to detect because of the high thermodynamic stability of the hairpin precursor. On the other hand, C/D type snoRNAs for example are generally difficult to detect because they lack a pronounced secondary structure. We completely miss ncRNAs, which do not depend on a secondary structure for their function, as for example the yeast SER3 regulating RNA (2), which, as expected, does not show up in this screen. 

Singh and Kollman reported on the first FEP calculations conducted to investigate the thermodynamic stability of mutant RNA hairpins. They were able to attribute the increased observed stability of an UUCG over an UUUG loop to a phosphate-base interaction which favors cytosine over uracil by 6 kcal mor. MD simulations on RNA/DNA hybrids have been conducted by Cheatham et al, ... 

Termination positions are defined by the thermodynamic stability of the polymerase complex, whereas the efficiencies of termination are determined by a kinetic competition between RNA elongation and release at each position (94). The termination efficiency is affected mostly by the strength of the stem—loop, the presence of the U-tract, and also by the concentration of NTP substrates. The efficiency of transcription termination also depends on other factors such as the size and shape of the hairpin, not just its stability, most likely involving interactions with the polymerase. Different RNA hairpins exert varying effects on transcription termination, while a cruciform structure may have no or some attenuating effect on transcription. Furthermore, certain changes in the stem sequence designed to maintain or raise the stability of the stem (AG = —18 kcal/mol) lead to a decrease... 

The preference has both thermodynamic and structural reasons. Initially the sequence dependence of the hairpin-loop thermodynamic stability was attributed... 

Model peptides that can adopt the (3-sheet conformation have until recently been confined to ones that form intermolecular (3-sheets, t96,104,105 Peptides that can form intramolecular (3-sheets have been avidly sought because the coil-(3 transition1 06 in such peptides would provide thermodynamic data on the effects of sequence and individual residues on (3-sheet stability like those obtainable from model a-helical peptides. Two types of models have been developed 107 (3-hairpins, i.e. two-stranded (3-sheets, and three-stranded (3-sheets. 

Proctor DJ, Ma H, Kierzek E, Kierzek R, Gruebele M, Bevilac-qua PC. Folding thermodynamics and kinetics of YNMG RNA hairpins specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate. Biochemistry 2004 43 14004-14014. 

Thermodynamic Parameters. The thermodynamic parameters are taken from previous studies of RNA folding (2,5) with the exception of recently studied motifs. Changes have been made in the stabilities of internal loops of 1 by 2 nucleotides (one unpaired nucleotide opposite two unpaired nucleotides) and 2 by 2 nucleotides (two unpaired nucleotides opposite two unpaired nucleotides), hairpin loops, and multibranch loops. The complete tables of parameters are available on the Turner Lab Homepage at http //ma.chem.rochester.edu. 

What are the structural features of a hairpin A priori, a hairpin requires a self-complementary oligonucleotide to form the double-helical stem and a variable number of nucleotides to form the loop. The stability and dynamics of a hairpin thus depend on contributions from the stem as well as the loop. Thermodynamic studies have shown that four or five bases are optimal to form a loop in DNA as well as in RNA (102). Among all possible hairpin structures, a tetranucleotide loop or tetraloop is the predominant species in 16S and 23S rRNAs (103), transcription terminators (104), and the phage T4 genome (105). About 70% of these tetraloops have the consensus loop sequences UNCG or GNRA (where N is A, C, G, or U), while the closing base pairs tend to be C G or less preferably G C. 

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