DINAMelt

DINAMelt predicts hybridization and secondary structure formation of finite-length DNA and RNA molecules using equilibrium thermodynamic and statistical mechanical ensemble methods to compute species mole fractions and thermodynamic properties across temperatures.

Key Features:

• Comprehensive modeling: Models self-folding and hybridization of finite-length DNA and RNA, including matched pairs, mismatches, symmetric and asymmetric interior loops, bulges, and single-base stacking at duplex ends or helix termini.
• Stacking-derived enthalpy: Accounts for stacking interactions between neighboring nucleotide residues in unfolded strands as a source of enthalpy change during helix formation.
• Equilibrium melting profiles: Simulates full equilibrium melting profiles as a function of temperature and permits noncomplementary and unequal strand concentrations to predict competition among species.
• Free energy and ensemble properties: Computes free energies for heterodimers, homodimers, and single-strand folding by summing Boltzmann factors and predicts species mole fractions and ensemble properties such as free energy, enthalpy, entropy, and heat capacity.
• UV absorbance simulation: Simulates ultraviolet absorbance at 260 nm using published extinction coefficients combined with computed base pair probabilities.

Scientific Applications:

• RNA secondary-structure analysis: Improves prediction accuracy of RNA secondary structures by including stacking contributions and detailed loop and mismatch modeling.
• Helix–helix interface thermodynamics: Provides thermodynamic parameters for helix–helix interfaces to assess sequence-dependent binding affinities for short duplexes and interfaces.
• Temperature-dependent thermodynamics: Enables analysis of enthalpic and entropic contributions to hybridization and folding by modeling species distributions and heat capacity across temperatures.

Methodology:

Uses a statistical mechanical ensemble approach to model single- and double-stranded species, computes free energies by summing Boltzmann factors, models base pairing, mismatches, interior loops, bulges and end stacking, calculates species mole fractions and ensemble thermodynamic properties as a function of temperature, and simulates UV 260 nm absorbance using published extinction coefficients and computed base pair probabilities.