title: Thermodynamics of DNA target site recognition by homing endonucleases.
abstract: The thermodynamic profiles of target site recognition have been surveyed for homing endonucleases from various structural families. Similar to DNA-binding proteins that recognize shorter target sites, homing endonucleases display a narrow range of binding free energies and affinities, mediated by structural interactions that balance the magnitude of enthalpic and entropic forces. While the balance of DeltaH and TDeltaS are not strongly correlated with the overall extent of DNA bending, unfavorable DeltaH(binding) is associated with unstacking of individual base steps in the target site. The effects of deleterious basepair substitutions in the optimal target sites of two LAGLIDADG homing endonucleases, and the subsequent effect of redesigning one of those endonucleases to accommodate that DNA sequence change, were also measured. The substitution of base-specific hydrogen bonds in a wild-type endonuclease/DNA complex with hydrophobic van der Waals contacts in a redesigned complex reduced the ability to discriminate between sites, due to nonspecific DeltaS(binding).
authors.affiliation: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025 Seattle, WA 98109, USA.
authors.forename: Jennifer H
authors.initials: JH
authors.lastname: Eastberg
authors.forename: Audrey
authors.initials: A
authors.lastname: McConnell Smith
authors.forename: Lei
authors.initials: L
authors.lastname: Zhao
authors.forename: Justin
authors.initials: J
authors.lastname: Ashworth
authors.forename: Betty W
authors.initials: BW
authors.lastname: Shen
authors.forename: Barry L
authors.initials: BL
authors.lastname: Stoddard
mesh_terms: D020137:Base Pair Mismatch; D002151:Calorimetry; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004251:DNA Transposable Elements; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D019281:Dimerization; D004706:Endodeoxyribonucleases / Q000737:chemistry* / Q000145:classification / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D015202:Protein Engineering; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
chemical_list: D004251:DNA Transposable Elements; D004268:DNA-Binding Proteins; D004247:DNA; D004706:Endodeoxyribonucleases