DNA Distortion in bis-Intercalated Complexes

Abstract

The bis-intercalators Flexi-Di and ditercalinium are synthetic dimers that bis-intercalate into DNA and cause cell death in prokaryotes from futile and abortive repair of DNA. Each is composed of two 7H-pyridocarbazole units and a linker. Flexi-Di has a flexible spermine-like linker while ditercalinium has a rigid bis(ethylpiperidinium) linker. This report, describing the 2.5-A X-ray structure of Flexi-Di complexed with [d(BrCGCG)]2, appears to be the first report of a three-dimensional structure of a DNA complex with a bis-intercalator with a flexible linker. DNA complex formation with a ditercalinium analog having a flexible linker was not anticipated to yield unstacked and bent DNA as was observed in the previously reported ditercalinium.[d(CGCG)]2 complex. Surprisingly, the DNA in the Flexi-Di complex is bent to a degree exceeding that of the ditercalinium complex. A comparison of the DNA complexes of Flexi-Di and ditercalinium has allowed us to propose a mechanism by which these bis-intercalators distort DNA. We propose that this class of bis-intercalators pulls the internal base pairs into the major groove and pushes the external base pairs into the minor groove. The result is a bend toward the minor groove. It appears that hydrogen bonds between the linker and the internal guanines effectively pull the central base pairs of the complex out into the major groove. At the external regions of the complex, stacking interactions between the chromophores and terminal base pairs effectively push the terminal base pairs into the minor groove. The result of this push/pull combination is to bend the DNA.

Crosslinking of DNA duplexes: a novel binding mode by bisacridine derivatives

“…Therefore, bisacridines linked through linkers with appropriate length are expected to have the highestaffinity binding by a dual intercalating mode. A number of crystallographic data have demonstrated the classic bisintercalation in which both chromophores of the bisintercalators bind to the same DNA duplex [1,2]. However, a novel crosslinking binding mode by two bisacridine derivatives has been observed in our laboratory recently, in which the bisacridines with a positively charged linker are found to be capable of crosslinking different DNA duplexes.…”

Molecular Dynamics Simulations of the Bis-Intercalated Complexes of Ditercalinium and Flexi-Di with the Hexanucleotide d(GCGCGC)2: Theoretical Analysis of the Interaction and Rationale for the Sequence Binding Specificity

“…34,35 In the case of the ditercalinium complex, initial difficulties for solving the structure by molecular replacement were precisely due to a wrong positioning of the linker, and the crystal was later found to diffract to only 2.5 Å resolution in the cell direction approximately perpendicular to the DNA helical axis. 21 The Flexi-Di linker is reported to have been constructed from coordinates of a spermine molecule and added to the model; 23 this fact, together with the intermediate resolution of this crystal structure, precludes the accurate location of the linker atoms, which nevertheless are highly disordered. We thus felt it was justified to reoptimize the geometry of both linkers.…”

“…The X-ray crystal structures of the complexes between d(CGCG)2 and ditercalinium (1.7 Å resolution, R-factor ) 22.5%), 21 and between d( Br CGCG)2 and Flexi-Di (2.5 Å resolution, R-factor ) 23.9%) 23 were retrieved from the Brookhaven Data Bank. 27 Hydrogen atoms were added to the molecules using standard geometries.…”

“…22 It came then as a surprise that the crystal structure of the same DNA sequence complexed with Flexi-Di revealed many similar features and an even higher degree of bending. 23 Since the orientation of the N,N′-diethyl-1,6-hexanediammonium linker of Flexi-Di increases the hydrogen bonding potential of this linker over that of the more rigid bis(ethylpiperidinium) spacer of ditercalinium, it was proposed that DNA bending originates in these complexes by a concerted push/pull effect mechanism involving specific hydrogen bonding and base pairchromophore stacking interactions. 23 We thought it would be of considerable interest to analyze these stacking interactions in detail because we have previously shown their relative importance in determining binding specificity 24 and dictating DNA conformational preferences 25,26 in other bis-intercalator-DNA complexes.…”

“…23 Since the orientation of the N,N′-diethyl-1,6-hexanediammonium linker of Flexi-Di increases the hydrogen bonding potential of this linker over that of the more rigid bis(ethylpiperidinium) spacer of ditercalinium, it was proposed that DNA bending originates in these complexes by a concerted push/pull effect mechanism involving specific hydrogen bonding and base pairchromophore stacking interactions. 23 We thought it would be of considerable interest to analyze these stacking interactions in detail because we have previously shown their relative importance in determining binding specificity 24 and dictating DNA conformational preferences 25,26 in other bis-intercalator-DNA complexes. We were also interested in probing, by simulation methods, to what extent the amount and the direction of bending could be influenced by lattice forces and by the presence of surrounding complexes in the crystal, which must surely give rise to a very different electrostatic environment from that of the complex in aqueous solution.…”