DINAMelt web server for nucleic acid melting prediction

Abstract

The DINAMelt web server simulates the melting of one or two single-stranded nucleic acids in solution. The goal is to predict not just a melting temperature for a hybridized pair of nucleic acids, but entire equilibrium melting profiles as a function of temperature. The two molecules are not required to be complementary, nor must the two strand concentrations be equal. Competition among different molecular species is automatically taken into account. Calculations consider not only the heterodimer, but also the two possible homodimers, as well as the folding of each single-stranded molecule. For each of these five molecular species, free energies are computed by summing Boltzmann factors over every possible hybridized or folded state. For temperatures within a user-specified range, calculations predict species mole fractions together with the free energy, enthalpy, entropy and heat capacity of the ensemble. Ultraviolet (UV) absorbance at 260 nm is simulated using published extinction coefficients and computed base pair probabilities. All results are available as text files and plots are provided for species concentrations, heat capacity and UV absorbance versus temperature. This server is connected to an active research program and should evolve as new theory and software are developed. The server URL is http://www.bioinfo.rpi.edu/applications/hybrid/.

Figure 1

A typical concentration plot, resulting from the simulation of 10 μM of each of A = 5′-GTGTTTATATACTGCGGCAGTATGTAGACAC-3′ and B = 5′-GTGTTTATATACTGCTGCAGTATAAACAC-3′ with [Na⁺] = 1 M and [Mg²⁺] = 0 M. The mole fraction of each species is plotted as a function of temperature. The red and green lines indicate the concentrations of the unfolded single strands, and the blue and magenta lines show the folded single strands. The yellow and cyan curves correspond to the two homodimers and the black curve to the heterodimer.

Figure 2

Heat capacity and absorbance curves for the example from Figure 1. The heat capacity (left axis label) is plotted with a solid line, while the absorbance (right axis label) is plotted with a dotted line.