Binding of quinoline analogues of echinomycin to deoxyribonucleic acid. Role of the chromophores

Abstract

Two novel antibiotics were isolated, designated compounds 1QN and 2QN respectively, having quinoline rings in place of one or both of the quinoxaline chromophores of echinomycin. Each removes and reverses the supercoiling of closed circular duplex DNA from bacteriophage PM2 in the fashion characteristic of intercalating drugs. For compound 1QN, the unwinding angle at I0.01 is almost twice that of ethidium, whereas for compound 2QN the value is indistinguishable from that of ethidium. Binding of both analogues produced changes in the viscosity of sonicated rod-like DNA fragments corresponding to double the helix extension found with ethidium, a feature characteristic of bifunctional intercalation by quinoxaline antibiotics. These results suggest that both compounds 1QN and 2QN behave as bifunctional intercalators but that compound 2QN produces only half the helix unwinding seen with compound 1QN and the natural quinoxalines. Binding curves for the interaction of both analogues with a variety of synthetic and naturally occurring nucleic acids were determined by solvent-partition analysis. Values for compound 2QN were also obtained by a fluorimetric method and found to agree well with the solvent-partition measurements. Compound 1QN bound most tightly to Micrococcus lysodeikticus DNA and, like echinomycin, exhibited a broad preference for (G + C)-rich DNA species. For compound 2QN no marked (G + C) preference was indicated, and the tightest binding among the natural DNA species studied was found with DNA from Escherichia coli. The two analogues also displayed different patterns of specificity in their interaction with synthetic nucleic acids. Compound 2QN bound to poly(dA-dT) slightly more tightly than to poly-(dG-dC), whereas compound 1QN displayed a large (approx. 11-fold) preference in the opposite sense. There was evidence of co-operativity in the binding to poly(dA-dT). It may be concluded that the chromophore moieties play an active role in determining the capacity of quinomycin antibiotics to recognize and bind selectively to specific sequences in DNA.

Effect of phosphate and amino acids on echinomycin biosynthesis by Streptomyces echinatus

“…In the presence of quinaldic acid, echinomycin was not detected; however, a chromatographically faster-moving component was seen. The Rf of that compound was consistent with the migration of the bis-quinoline derivative of echinomycin (6). DISCUSSION Previous investigators (1,13) speculated that variability in yields of echinomycin might be due to its inherent sensitivity to progressive increases in pH during incubation.…”

Changes in contour length of polydeoxynucleotide fragments

“…Nucleic acid concentrations are expressed with respect to nucleotides and are based on the following values of e(P)26o: poly(dA-dT), 6700 [10]; poly(dG-dC), 7100 [11]. Molar extinction coefficients of the quinoxallne antibiotics were taken from [7,12]. Concentrations of other drugs, were based on the following extinction coefficients: actinomycin D, 24 450 (440 nm) [13]; ethidium bromide, 5900 (480 nm) [14 I.…”

“…Complexes of ethidium and actinomycin D with the polynucleotides were prepared by direct addition of small amounts of a concentrated drug solution to the DNA in the viscometer as in [18]. Estimates of the binding.ratio, r, were based on published values of association constants and site-sizes in buffer of 10 mM ionic strength [7,12,19]. Figure 2 shows helix extension plots for echinomycin binding to poly(dA-dT) and poly(dG-dC).…”

“…Echinomycin was the first bifunctional intercalator to be identified [3] and consequently its DNA-binding properties have been extensively characterised: it does indeed display considerable sequence-selectivity, which is evident in its interaction with natural DNAs as well as with synthetic polynucleotides [4]. The same is true of other quinoxaline antibiotics but their patterns of sequenceselectivity differ radically from that seen with echinomycin, especially as regards their binding to poly(dA-dT) and poly(dG-dC) [5][6][7]. To date, however, there has been no direct evidence that the nature of the complex formed with a synthetic polynucleotide resembles that formed with natural DNA, though it has generally been assumed that all such complexes involve bifunctional intercalation.…”

Two-Dimensional1H and31P NMR Spectra of a Decamer Oligodeoxyribonucleotide Duplex and a Quinoxaline ([MeCys3, MeCys7]TANDEM) Drug Duplex Complex

“…Studies have centered primarily around acridine dimers, ethidium dimers, ditercalinium, and more recently echinomycin, triostin A, and their derivatives (17)(18)(19)(20)(21)(22)(23)(24). The latter two are members of the quinoxaline class of naturally occurring antibiotic, antimicrobial, and antitumor drugs (25)(26)(27).…”