DINAMelt web server for nucleic acid melting prediction

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ID: 300492
2005
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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/.
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openalex_W2088998577 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Nicholas R. Markham, Michael Zuker
Journal Nucleic Acids Research
Year 2005
DOI
10.1093/nar/gki591
URL
https://doi.org/10.1093/nar/gki591
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