title: Computational Approach to Explore the B/A Junction Free Energy in DNA.
abstract: Protein-DNA interactions induce conformational changes in DNA such as B- to A-form transitions at a local level. Such transitions are associated with a junction free energy cost at the boundary of two different conformations in a DNA molecule. In this study, we performed umbrella sampling simulations to find the free energy values of the B-A transition at the dinucleotide and trinucleotide level of DNA. Using a combination of dinucleotide and trinucleotide free energy costs obtained from simulations, we calculated the B/A junction free energy. Our study shows that the B/A junction free energy is 0.52 kcal mol(-1) for the A-philic GG step and 1.59 kcal mol(-1) for the B-philic AA step. This observation is in agreement with experimentally derived values. After excluding junction effects, we obtained an absolute free energy cost for the B- to A-form conversion for all the dinucleotide steps. These absolute free energies may be used for predicting the propensity of structural transitions in DNA.
authors.affiliation: Department of Chemistry, Indian Institute of Science Education and Research, Pune-, 411008, India.
authors.forename: Mandar
authors.initials: M
authors.lastname: Kulkarni
authors.affiliation: Department of Chemistry, Indian Institute of Science Education and Research, Pune-, 411008, India. arnab.mukherjee@iiserpune.ac.in.
authors.forename: Arnab
authors.identifier: http://orcid.org/0000-0001-5691-6120
authors.initials: A
authors.lastname: Mukherjee
mesh_terms: D001483:Base Sequence; D044704:DNA, A-Form / Q000737:chemistry*; D059371:DNA, B-Form / Q000737:chemistry*; D004735:Energy Transfer; D008956:Models, Chemical; D014867:Water / Q000737:chemistry
chemical_list: D044704:DNA, A-Form; D059371:DNA, B-Form; D014867:Water
keywords: DNA; computational chemistry; dinucleotide step; free energy; umbrella sampling simulations