DNA-stacking interactions Determine the Sequence Specificity of the Deoxyribonuclease Activity of 1,10-Phenanthroline-copper Ion

Chemical Probing Shows That the Intron-encoded Endonuclease I-SceI Distorts DNA through Binding in Monomeric Form to Its Homing Site

“…4, B and C). A sharp change in the direction of the helix axis at the step T Ϫ1 A 1 is also fully consistent with the decrease in the OP 2 Cu ϩ reactivity of positions ϩ1, ϩ2 on the top strand and positions Ϫ1, Ϫ2 on the bottom strand in complexed compared to free DNA because the model of OP 2 Cu ϩ binding involves the long axis of one phenanthroline ring parallel with the minor groove axis (9). The absence of the band corresponding to the dimer T 9 T 10 in the cleavage pattern of the bottom strand agrees also with the protein binding-kinking proposed to interpret copper complexes footprinting results (see above).…”

“…Note first the significant variation of OP 2 Cu ϩ cleavage frequency at individual phosphodiester bonds along the DNA sequence in the absence of I-SceI, reflecting the high binding specificity of the tetrahedral coordination complex ( Fig. 4; A, lanes 2 and 7; and B) (9). Binding of I-SceI to DNA results, on the one hand, in the full protection of the DNA segment delimited by the positions 7 and 13 on the top strand 5 and 11 on the bottom strand and in contrast in the increase in the OP 2 Cu ϩ cleavage frequency at positions ϩ2 to ϩ4 on the top strand ϩ1 to ϩ3 on the bottom strand and, though to a lesser extent, at positions Ϫ6 to Ϫ3 and Ϫ8 and Ϫ10 on the top strand only.…”

“…We then used chemical probing agents to characterize the conformation of DNA in the complex. I-SceI protein-DNA complex was thus submitted to the nucleolytic attack of the cuprous complexes of 1,10-phenanthroline (OP 2 Cu ϩ and Phe-OP 2 Cu ϩ ), which results from the abstraction of C-1Ј hydrogen atom by a tetrahedral copper-oxo species bound within the minor groove (13,14,15,9) and to UVA/4Ј,5Ј-dihydro-7-methylpyrido [3,4-c]psoralen (DHMePyPs) photosensitization, which requires prior intercalation of the pyridopsoralen at selective 5Ј-TTA-3Ј sites (10). We also employed chemical modification agents of base and sugar residues (for a review, see Ref.…”

“…In an attempt to reveal intrinsic helical properties of the I-SceI nucleic acid target, we used this sequence as substrate in earlier studies analyzing the mechanisms of DNA chemical reactions and photosensitization processes (9,10,11,12). We found evidence that the conformation of the helix deviates from the ideal B-form duplex along two segments of three and five base pairs located at a distance of approximately one helical turn, respectively, upstream and downtream from the site of junction of the two exons (9). In the present study, we first performed DNase I footprinting and gel retardation assays to identify the complex formed between I-SceI and its target in the absence of a divalent metal ion.…”

Copper(II) complexes of 1,10-phenanthroline-derived ligands: Studies on DNA binding properties and nuclease activity

“…It has been suggested that the cuprous complex [Cu(phen) 2 ] + cleaves B-form DNA much faster than it does A-form DNA because the complex has stronger affinity for the minor groove of B-form DNA than for that of A-form [42][43][44][45][46]. The present results suggest that the difference in the coordination structures of [Cu(phen) 2 ] 2+ bound to A-and Bforms of DNA may be another factor responsible for the difference in the rate of the reaction [47]. It should be also noted that the change in the rhombic EPR line shape with U quite resembles that observed for 5; the g i signals observed at U = 0° (Fig.…”