title: Binding energies of nucleobase complexes: Relevance to homology recognition of DNA.
abstract: The binding energies of complexes of DNA nucleobase pairs are evaluated using quantum mechanical calculations at the level of dispersion corrected density functional theory. We begin with Watson-Crick base pairs of singlets, duplets, and triplets and calculate their binding energies. At a second step, mismatches are incorporated into the Watson-Crick complexes in order to evaluate the variation in the binding energy with respect to the canonical Watson-Crick pairs. A linear variation of this binding energy with the degree of mismatching is observed. The binding energies for the duplets and triplets containing mismatches are further compared to the energies of the respective singlets in order to assess the degree of collectivity in these complexes. This study also suggests that mismatches do not considerably affect the energetics of canonical base pairs. Our work is highly relevant to the recognition process in DNA promoted through the RecA protein and suggests a clear distinction between recognition in singlets, and recognition in duplets or triplets. Our work assesses the importance of collectivity in the homology recognition of DNA.
authors.affiliation: Institute for Computational Physics, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.|Departamento de Ciencias Naturales, Escuela Colombiana de Ingeniería Julio Garavito, AK 45 205-59, Bogotá, Colombia.
authors.forename: Sergio Cruz
authors.initials: SC
authors.lastname: León
authors.affiliation: Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA.
authors.forename: Mara
authors.initials: M
authors.lastname: Prentiss
authors.affiliation: Institute for Computational Physics, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
authors.forename: Maria
authors.initials: M
authors.lastname: Fyta
mesh_terms: D020029:Base Pairing; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D004734:Energy Metabolism; D012689:Sequence Homology, Nucleic Acid
chemical_list: D004247:DNA