title: DNA-DNA sequence homology recognition: physical mechanisms and open questions.
abstract: First, we summarize recent experimental facts on homologous DNA pairing in vitro and discuss possible mechanisms of DNA-DNA sequence recognition. Then, we overview the mechanism of DNA-DNA recognition based on complementarity of DNA charge patterns. The theory predicts the recognition energy up to 10 k(B) T for close parallel homologous DNA fragments of gene-relevant lengths. We argue why this estimate cannot be directly applied to pairing of homologous DNA loci in experiments on yeast chromosomes. Namely, DNA-DNA distances assessed from experiments are much larger than those typically used in theory. Finally, we suggest some experiments that could help to judge whether short-range electrostatic forces indeed govern DNA pairing. This viewpoint paper introduces recently developed theoretical concepts to molecular biologists, with a hope to generate a junction between theory and future experiments on DNA recognition.
authors.affiliation: IFF-2/IAS, Research Centre Jülich, 52425 Jülich, Germany. a.cherstvy@gmail.com
authors.forename: A G
authors.initials: AG
authors.lastname: Cherstvy
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D012689:Sequence Homology, Nucleic Acid; D013816:Thermodynamics
chemical_list: D004247:DNA