title: Importance of phosphate contacts for sequence recognition by EcoRI restriction enzyme.
abstract: We have studied the importance of charge and hydrogen-bonding potential of the phosphodiester backbone for binding and cleavage by EcoRI restriction endonuclease. We used 12-mer oligodeoxynucleotide substrates with single substitutions of phosphates by chiral methylphosphonates at each position of the recognition sequence -pGpApApTpTpCp-. Binding was moderately reduced between 4- and 400-fold more or less equally for the R(P) and S(P)-analogues mainly caused by missing charge interaction. The range of cleavage effects was much wider. Four substrates were not cleaved at all. At both flanking positions and in the purine half of the sequence up to the central position, cleavage was more impaired than binding and differences between R(P) and S(P) diastereomeres were more pronounced. These effects are easily interpreted by direct phosphate contacts seen in the crystal structure. For the effects of substitutions in the pyrimidine half of the recognition sequence, more indirect effects have to be discussed.
authors.affiliation: Zentrum Biochemie, Medizinische Hochschule Hannover, Hannover 30623, Germany.
authors.forename: Olaf
authors.initials: O
authors.lastname: Rosati
authors.forename: Tushar K
authors.initials: TK
authors.lastname: Srivastava
authors.forename: Seturam B
authors.initials: SB
authors.lastname: Katti
authors.forename: Jürgen
authors.initials: J
authors.lastname: Alves
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D015246:Deoxyribonuclease EcoRI / Q000737:chemistry / Q000378:metabolism*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009838:Oligodeoxyribonucleotides / Q000737:chemistry* / Q000378:metabolism*; D009943:Organophosphorus Compounds / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D013379:Substrate Specificity
chemical_list: D009838:Oligodeoxyribonucleotides; D009943:Organophosphorus Compounds; C032627:methylphosphonic acid; D015246:Deoxyribonuclease EcoRI