Intercalation proflavine

C2 Z = 4 Dx = 1.41 R = 0.102 for 4,115 intensities. The structure is a 3 2 complex of proflavine and CpG. The asymmetrical unit contains one CpG molecule, 1.5 proflavine molecules, 0.5 sulfate ion, and 11 5 water molecules. Two CpG molecules form an antiparallel, Watson-Crick, miniature duplex, with a proflavine intercalated between the base pairs through the wide groove. The double helix has exact (crystallographic), two-fold symmetry, and the crystallographic, two-fold axis passes through the C-9-N-10 vector of the intercalated proflavine. A second and a third molecule of proflavine are stacked on top of the C - G pairs ... 

In addition to the intercalated proflavine, there is a proflavine molecule that is sandwiched by adjacent, CpA dimer duplexes. The intercalated proflavine stacks more extensively with the C-C pair than with the A-A pair. The sandwiched proflavine stacks extensively with both the A - A and C-C pairs. Both proflavine molecules exhibit disorder. In each... 

Several complexes that involve intercalation of an acridine in a portion of a nucleic acid have been studied by X-ray crystallographic techniques. These include complexes of dinucleoside phosphates with ethidium bromide, 9-aminoacridine, acridine orange, proflavine and ellipticine (65-69). A representation of the geometry of an intercalated proflavine molecule is illustrated in Figure 6 (b) this is a view of the crystal structure of proflavine intercalated in a dinucleoside phosphate, cytidylyl- -S ) guano-sine (CpG) (70, TV). For comparison an example of the situation before such intercalation is also illustrated in Figure 6 (a) by three adjacent base pairs found in the crystal structure of a polynucleotide (72, 73). In this latter structure the vertical distance (parallel to the helix axis) between the bases is approximately... 

Fig. 10.7 Sketches representing the secondary structure of normal DNA (left) and DNA containing intercalated proflavine molecules (right). The helix is drawn as iewed from a remote point, so that the base-pairs and the intercalated proflavine appear only in edgewise projection, and the phosphate deoxyribose backbone appears as a smooth coil. (Redrawn from Lerman, 1964b.)...

Effect of DNA and DNA-Histone Complexes on the Inhibition of Poly(ADP-Ribose) Glycohydrolase by Intercalators. The inhibition of glycohydrolase activity by intercalators (proflavine, ellipticine, tilorone R10,556 DA) is relieved by the addition of 100 Mg mr calf thymus DNA (data not shown). This is probably due to the well-known binding of the intercalators to the added DNA. However, addition of DNA-histone complexes (100 jug nil" of each) slightly increases the inhibition of the glycohydrolase activity by those intercalators which are inhibitory (Table 1). These include ethacridine, tilorone R10,556 DA, eUipticine, daunomycin and proflavine. 

Fig. 2. Position of intercalated acridine molecules. 1 A, structure of normal DNA B, structure of DNA containing intercalated proflavine molecules. (After Ler-man, L. S., 1964.) 2 A, the relative position of an acridine nucleus and a base pair in the intercalation model according to Lerman (1964) b, the relative position of the acridine nucleus and the purine of a base pair in the intercalation model of...

The effect of intercalating drugs on DNA polymerization probably results from an increase in the energy required to separate the two strands. Acting on RNA polymerization, the intercalated proflavine has been shown to decrease the number of binding sites for the enzyme on the DNA template. Thus acridines, in contrast... 

As described in section 4.1, the DNA double helix must unwind to allow access ofthe polymerase enzymes to produce two new strands ofDNA. This is facilitated by DNA gyrase, the target of the quinolones. Some agents interfere with the unwinding of the chromosome by physical obstruction. These include the acridine dyes, of which the topical antiseptic proflavine is the most familiar, and the antimalarial acridine, mepacrine. They prevent strand separation by insertion (intercalation) between base pairs from each strand, but exhibit very poor selective toxicity. 

Thus complete intercalation of the aromatic PAH between the bases of DNA, in the manner described above for flat molecule such as proflavine, did not seem to be a likely mechanism for the carcinogenic action of these compounds. Since alkylation and intercalation are not simultaneously possible for steric reasons, and since one molecule is wedge-shaped and the other is flatter, it was considered more likely that the action of these compounds arose from their alkylating ability they could alkylate a base of DNA and then, since the bulky aromatic hydrophobic group would possibly not remain protruding into the hydrophilic environment, it is possible that the aromatic PAH group could then lie in one of the grooves of DNA. 

Figure 30. Schematic diagrams of overlap of ring systems in (a) the alkylated nucleoside described here, (b) daunomycin intercalated in a hexanucleotide (143), (c) proflavine intercalated in a dinucleoside phosphate (70), Td) a model of a diol epoxide of DMBA semi-intercalated in a manner analogous to that in (a) so that N2 of guanine may be alkylated, (e) a model of a diol epoxide of DMBA semi-intercalated in a manner analogous to that in (c) so that 06 of guanine may be alkylated.

The steady-state FPA of large ( 500bp) calf thymus DNA/ethidium complexes is unaffected by addition of proflavine up to one per two base pairs. From this, it is concluded that the torsion constant is unaltered(168) by intercalation of proflavine. However, in our time-resolved FPA studies of linear pBR322 DNA/ethidium complexes, the torsion constant is reduced by the factor 0.60 as proflavine is added from zero to one per two base pairs.(173) Whether this discrepancy is due to a real difference between these DNAs or... 

When the stretched DNA-lipid film was soaked in an aqueous solution of ethidium bromide (itmax = 480 nm) for a day at room temperature, the transparent film turned red (itmax = 520 nm) and the aqueous solution became clear (Fig. 9a). Thus, the ethidium intercalated completely between base pairs of the DNA film. When the film was moved into the new aqueous buffer solution, the intercalated dye molecules were hardly removed from the film at least for a day. Similar intercalation behavior into the film was observed for other dyes such as proflavine, acridine orange, and safranine T [14-17]. 

Cationic amphiphiles 2Ci8-glu-N spread on pure water, in the solution of 10 xM DNA containing 10 xM intercalating dyes (proflavine). The dye-intercalated DNA anions were expected to adsorb to the cationic lipid mono-layer due to electrostatic interactions and was transferred to a hydrophobized glass plate at a surface pressure of 35 mN m at 20 °C. From a moving area of a barrier, two layers of the monolayer were confirmed to be transferred in each one cycle (Y-type deposition). When the QCM plate was employed as a transfer plate, the transferred mass could be calculated from frequency decreases (mass increase on the QCM) [29-31]. It was confirmed that 203 10 ng of two lipid monolayers and 74 5 ng of DNA strands were transferred on to the substrate per dipping cycle, which means ca. 95% of the monolayer area was covered by DNA molecules. 

We first describe the NMR parameters for the duplex to strand transition of the synthetic DNA poly(dA-dT) (18) with occasional reference to poly(dA-dU) (24) and poly(dA- brdU) and the corresponding synthetic RNA poly(A-U) (24). This is followed by a comparison of the NMR parameters of the synthetic DNA in the presence of 1 M Na ion and 1 M tetramethylammonium ion in an attempt to investigate the effect of counterion on the conformation and stability of DNA. We next outline structural and dynamical aspects of the complexes of poly(dA-dT) with the mutagen proflavine (25) and the anti-tumor agent daunomycin (26) which intercalate between base pairs and the peptide antibiotic netropsin (27) which binds in the groove of DNA. 

Planar dyes such as proflavine can bind to DNA by intercalation between base pairs or by stacking along the groove of the helix. The former process is favored when the nucleic acid is in excess (Nuc/D 4) and in high salt solution. We are interested in the intercalation process and hence our NMR studies have focussed on an investigation of the proflavine poly(dA-dT) complex as a function of the Nuc/D ratio in 1 M NaCl in an attempt to probe the structure and dynamics of mutagen-nucleic acid interactions in solution (25). 

Overlap Geometry A schematic representation of the proposed overlap geometry for proflavine intercalated into a deoxy pyrimidine(3 -5 )purine site is presented below with the (o) symbols representing the location of the phenanthridine ring protons. The mutual overlap of the two base pairs at the intercalation site involves features observed in the crystal structures of a platinum metallointercalator miniature dC-dG duplex complex (55) and the more recent proflavine miniature dC-dG duplex complex (48), as well as features derived in a linked-atom conformational calculation of the intercalation site in the proflavine DNA complex (51). [4]... 

The relative magnitude of the large proflavine upfield complexation shifts requires that the dye intercalate into the duplex with its long axis colinear to the direction of the Watson-Crick hydrogen bonds of adjacent base pairs. This results in significant overlap of the proflavine ring system and base pairs at the intercalation site. 

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