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

Schaeffer, Francis; Rimsky, Sylvie; Spassky, Annick

doi:10.1006/jmbi.1996.0419

Cited by 27 publications

(22 citation statements)

References 53 publications

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“…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).…”

Section: -Pheop 2 Cusupporting

confidence: 72%

“…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.…”

Section: Resultsmentioning

confidence: 96%

“…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.…”

mentioning

confidence: 99%

“…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.…”

mentioning

confidence: 99%

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

Beylot¹,

Spassky

2001

Journal of Biological Chemistry

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Despite its small size (27.6 kDa), the group I intronencoded I-SceI endonuclease initiates intron homing by recognizing and specifically cleaving a large intronless DNA sequence. Here, we used gel shift assays and footprinting experiments to analyze the interaction between I-SceI and its target. I-SceI was found to bind to its substrate in monomeric form. Footprinting using DNase I, hydroxyl radical, phenanthroline copper complexes, UV/DH-MePyPs photosensitizer, and base-modifying reagents revealed the asymmetric nature of the interaction and provided a first glimpse into the architecture of the complex. The protein interacts in the minor and major grooves and distorts DNA at three distinct sites: one at the intron insertion site and the other two, respectively, downstream (؊8, ؊9) and upstream (؉9, ؉10) from this site. The protein appears to stabilize the DNA curved around it by bridging the minor groove on one face of the helix. The scissile phosphates would lie on the outside of the bend, facing in the same direction relative to the DNA helical axis, as expected for an endonuclease that generates 3 overhangs. An internally consistent model is proposed in which the protein would take advantage of the concerted flexibility of the DNA sequence to induce a synergistic binding/kinking process, resulting in the correct positioning of the enzyme active site.I-SceI is a homing endonuclease encoded by the mobile group I intron of the large rRNA gene of Saccharomyces cerevisiae (1, 2). This family of enzymes mediates the propagation of the intron by cutting intronless genes at the site of intron insertion (reviewed in Ref.3). Like restriction enzymes, homing endonucleases cleave double-stranded DNA with high specificity in the presence of divalent metal ions. However, they differ from restriction endonucleases in their recognition properties and structures, as well as in their genomic location (4). In particular, whereas restriction enzymes have short recognition sequences (3-8 bp), 1 homing endonucleases, despite their small size, recognize long DNA sequences (12-40 bp). They have been classified into four families on the basis of both their sequence motifs and DNA cleavage mechanism (3). to cleave DNA within its recognition sequence and leaves a 4-bp overhang presenting a 3Ј-hydroxyl terminus (5, 6). The enzyme displays a low turnover, probably because of its strong affinity for one of the products of the cleavage reaction (7).The interaction of homing endonucleases with their substrates raises an interesting question common to all the gene-regulatory proteins, namely: how can a small protein specifically recognize and modify a long DNA sequence? Understanding the molecular basis of such a mechanism is essential for elucidating many aspects of cellular control and is a prerequisite in any rational drug design program. It is clearly established that local and global DNA structural features that are highly sequence-dependent, play a primary role in the dynamics of protein-DNA recognition (8). Sequence recognition would...

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Section: -Pheop 2 Cusupporting

confidence: 72%

Section: Resultsmentioning

confidence: 96%

mentioning

confidence: 99%

mentioning

confidence: 99%

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

Beylot¹,

Spassky

2001

Journal of Biological Chemistry

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“…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.…”

Section: Dna Fiber Epr Spectral Studymentioning

confidence: 77%

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

Hirohama¹,

Kuranuki²,

Ebina³

et al. 2005

Journal of Inorganic Biochemistry

195

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Geometries of stacking interactions between phenanthroline ligands in crystal structures of square-planar metal complexes

et al. 2010

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Stacking interactions of phenanthroline square-planar complexes in crystal structures were studied by analyzing data from the Cambridge Structural Database. In most of the crystal structures, two phenanthroline complexes were oriented "head to tail." Phenanthroline complexes show a wide range of overlap geometries in stacking interactions, while short metal-metal distances were not observed. Stacking chains with alternating overlaps were the predominant type of packing in the crystal structures.

show abstract

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

Cited by 27 publications

References 53 publications

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

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

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

Geometries of stacking interactions between phenanthroline ligands in crystal structures of square-planar metal complexes

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