Analysis of melting transitions of the DNA hairpins formed from the oligomer sequences d[GGATAC(X)₄GTATCC] (X = A, T, G, C)

Abstract

Optical melting transitions of the short DNA hairpins formed from the self-complementary DNA oligomers d[GGATACX4GTATCC] where X = A, T, G, or C measured in 100 mM NaCl are presented. A significant dependence of the melting transitions on loop sequence is observed and transition temperatures, tm, of the hairpins vary from 58.3 degrees C for the T4 loop hairpin to 55.3 degrees C for the A4 loop. A nearest-neighbor sequence-dependent theoretical algorithm for calculating melting curves of DNA hairpins is presented and employed to analyze the experimental melting transitions. Experimental melting curves were fit by adjustment of a single theoretical parameter, Fend(n), the weighting function for a hairpin loop comprised of n single-strand bases. Empirically determined values of Fend(n) provide an evaluation of the free-energy of hairpin loop formation and stability. Effects of heterogeneous nearest-neighbor sequence interactions in the duplex stem on hairpin loop formation were investigated by evaluating Fend(n) in individual fitting procedures using two of the published sets of nearest-neighbor stacking interactions in DNA evaluated in 100 mM NaCl and given by Wartell and Benight, 1985. In all cases, evaluated values of Fend(n) were obtained that provided exact theoretical predictions of the experimental transitions. Results of the evaluations indicate: (1) Evaluated free-energies of hairpin loop formation are only slightly dependent on loop sequences examined. At the transition temperature, Tm, the free-energy of forming a loop of four bases is approximately equal for T4, G4, or C4 loops and varies from 3.9 to 4.8 kcal/mole depending on the set of nearest-neighbor interactions employed in the evaluations. This result suggests, in light of the observed differences in stability between the T4, G4, and C4 loop hairpins, that sequence-dependent interactions between base residues of the loop are most likely not the source of the enhanced stability of a T4 loop.(ABSTRACT TRUNCATED AT 400 WORDS)

A single base permutation in any loop of a folded intramolecular quadruplex influences its structure and stability

“…Hence, changing a single base in a loop changes its conformation due to differences in stacking. Sequence context plays a role in the structure and stability of DNA duplexes due to differences in base stacking for DNAs of identical GC content [24][25][26][27][28] and also plays a role in stacking of bases in single strand loops in duplex DNA [29,30]. The folding motifs of quadruplexes are dependent upon loop formation for the non G-rich segments and theses short loops are conformational restricted.…”

Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins

“…The equilibrium model is based on the one-dimensional Ising model that allows for only two states for each base pair, broken or intact (25). Nearest-neighbor sequence dependence in the stacking interactions is included for each base pair, with parameters taken from the work of Benight and coworkers (4,26). In our calculation, the statistical weight of the loop for each microstate in the ensemble depends on the size of the loop and is expressed in terms of a persistence length characterizing the flexibility of the single-stranded chain.…”

“…Knowing the time scales and mechanism of formation of these loops is an essential first step toward understanding the folding problem. Although the stability of hairpin loops and the kinetics of hairpin formation have been a subject of intense investigation for over 30 years (1)(2)(3)(4)(5), our understanding of the kinetics is limited. In particular, there is no simple physical model that describes in a consistent way both the thermodynamics and kinetics of hairpin formation.…”

Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes

“…The free energy landscape ΔG(i, j) is obtained by calculating the free energy for each (i, j)-state with respect to the native state at (0, 0), using the thermodynamic parameters employed by Kuznetsov et al [21] Following the assumption made by Poland and Scheraga, [22] each base pair is allowed to be either broken or intact, with the energetics determined by base pairing, nearest-neighbor stacking, and loop formation. [23,24] The relative free energy of any state (i, j) is calculated by (2) The terms in eqn (2) are defined as follows. ΔH p,s (i, j) and ΔS p,s (i, j) are the differences in pairing-stacking enthalpies and entropies, respectively, between the state (i, j) and the native state (0, 0); each term represents the sum over all base pairs of state (i, j).…”