The B goes to Z transition of poly(dG-dC) . poly(dG-dC) modified by some platinum derivatives

Metal ion-promoted conformational changes of oligonucleotides

The review will discuss the influence of metal ions on conformational changes of oligonucleotides. First, a short definition of the torsion angles is given, followed by a concise yet critical overview of the commonly applied experimental techniques. Finally, the possible role of metals upon the following conformational changes of oligonucleotides is discussed: (i) the denaturation of double-strands, (ii) the transition from B- to A-DNA, (iii) the transition from right- to left-handed DNA and RNA, (iv) the condensation, (v) and other conformational changes. We conclude with a summary and outlook.

Circular dichroism study of the irreversibility of conformational changes induced by polyamine-linked dinuclear platinum compounds

In this work, the reversibility of both the B-->Z and B-->A conformational change in polymer DNA induced by polynuclear platinum compounds was studied. The compounds examined were: [[trans-PtCl(NH(3))(2)](2)[NH(2) (CH(2))(6)NH(2)]](2+) (BBR3005); [[trans-PtCl(NH(3))(2)](2)[mu-spermine-N1,N12]](4+) (BBR3535); [[trans-PtCl(NH(3))(2)](2)[mu-spermidine-N1,N8]](3+) (BBR3571); [[trans-PtCl(NH(3))(2)](2)[mu-BOC-spermidine]](2+) (BBR3537); and [[trans-PtCl(NH(3))(2)](2)[mu-trans-Pt(NH(3))(2)(H(2)N(CH(2))(6)NH(2))(2)]](4+) (BBR3464). The conformational changes were assessed by circular dichroism and the reversibility of the transitions was tested by subsequent titration with the DNA intercalator ethidium bromide (EtBr). Fluorescent quenching was also used to assess the ability of ethidium bromide to intercalate into A and/or Z-DNA induced by the compounds. The results were compared with those produced by the simple hexamminecobalt cation [Co(NH(3))(6)](3+). The data suggest that while conformational changes induced by electrostatic interactions are confirmed to be reversible, covalent binding induces irreversible changes in both the A and Z conformation. The relevance of these changes to the novel biological action of polynuclear platinum compounds is discussed.

A comparative study of calf thymus DNA binding to Cr(III) and Cr(VI) ions. Evidence for the guanine N-7-chromium-phosphate chelate formation

Chromium(VI) salts are well known to be mutagens and carcinogens and to easily cross the cell membranes. Because they are powerful oxidizing agents, Cr(VI) reacts with intracellular materials to reduce to trivalent form, which binds DNA. This study was designed to investigate the interaction of calf thymus DNA with Cr(VI) and Cr(III) in aqueous solution at pH 6.5-7.5, using Cr(VI)/DNA(P) molar ratios (r) of 1:20 to 2:1 and Cr(III)/DNA(P) molar ratios (r) of 1:80 to 1:2. UV-visible and Fourier transform infrared (FTIR) difference spectroscopic methods were used to determine the metal ion-binding sites, binding constants, and the effect of cation complexation on DNA secondary structure. Spectroscopic results showed no interaction of Cr(VI) with DNA at low anion concentrations (r = 1:20 to 1:1), whereas some perturbations of DNA bases and backbone phosphate were observed at very high Cr(VI) contents (r > 1) with overall binding constant of K = 508 M(-1). Cr(III) chelates DNA via guanine N-7 and the nearest PO(2) group with overall binding constant of K = 3.15 x 10(3) M(-1). Evidence for cation chelate formation comes from major shiftings and intensity variations of the guanine band at 1717 and the phosphate asymmetric stretching vibration at 1222 cm(-1). At low Cr(III) concentration (r = 1:40), the number of Cr(III) ions bound to DNA were 6-7 cations/500 base pairs, and this increased to 30-35 cations/500 base pairs at high metal ion content (r = 1:4). DNA condensation occurred at high cation concentration (r = 1:10). No major alteration of DNA conformation was observed, and the biopolymer remained in the B family structure upon chromium complexation.

Comparison of the mode of action of a dinuclear platinum complex containing a pyridine derivative with its monomeric analog

The DNA binding and interstrand cross-linking properties of the dinuclear platinum complex [¿cis-Pt(NH3)2Cl¿2bpsu](NO3)2 (bpsu is 4,4'-dipyridyl sulfide) (II) and the mononuclear complex [cis-Pt(NH3)2Cl(4-methylpyridine)]NO3 (I) were compared with those of [¿cis-Pt(NH3)2Cl¿2H2N(CH2)4NH2](NO3)2 (III) in order to understand the mode of action of complexes I and II. Both compound I and compound II caused significantly different changes of conformation in poly(dG-dC) x poly(dG-dC) than compound III did. Studies of DNA binding, interstrand cross-linking and fluorescence assay suggest that compound I monofunctionally binds to DNA and compound II bifunctionally binds to DNA, that the dinuclear platinum complex II more efficiently interacts with DNA compared to its monomeric analog, and that platinum I and II complexes both interact with DNA in a non-intercalative mode. All the results indicate that the mode of action of the dinuclear complex II is different from that of the mononuclear complex I.

A circular dichroism study of ethidium bromide binding to Z-DNA induced by dinuclear platinum complexes

Dinuclear bis(platinum) complexes have been shown previously to induce the B-->Z transition in synthetic DNAs (Nucleic Acids Res. 7, 1697-1703, J. Inorganic Biochem. 54, 207-220). In this paper, the reversibility of the Z conformation back to the B form was assessed by treatment of the induced Z form in poly(dG-dC).poly(dG-dC) with ethidium bromide (Etd). Z-DNA induced by the tetra-amine cations [{Pt(NH3)3}2(H2N(CH2)nNH2)]4+, which are capable of only electrostatic interactions with the polynucleotide, was readily reversible. The spectroscopic data mirrored that of ethidium bromide/poly(dG-dC).poly(dG-dC) in the presence of 4.4 M NaCl. In contrast, Z-DNA induced by the bifunctional complexes [{trans-PtCl(NH3)2}2(H2N(CH2)nNH2)]2+ did not produce spectra typical of Etd intercalation and reversal to B-form DNA. The original Z-form CD spectra of DNA treated with the bifunctional complexes could be reobtained following removal of Etd by extensive dialysis. The bifunctional complexes are very effective interstrand cross-linking agents. The data suggest that interstrand cross-linking by dinuclear complexes can stabilize or "lock" the Z-conformation prohibiting its reversal to the B-form. The implications for the biological activity of the dinuclear complexes are briefly discussed.

A novel DNA structure induced by the anticancer bisplatinum compound crosslinked to a GpC site in DNA

The bifunctional platinum compound, [(trans-PtCI(NH)3)2)2(H2N(CH2)4NH2)]2+, forms a stable adduct with the self-complementary DNA oligomer CATGCATG, with the two platinum atoms coordinated at the N7 positions of the two symmetrical G4 nucleotides. The NMR-derived structure shows that the DNA octamer forms a novel hairpin structure with the platinated G4 residue adopting a syn conformation and the guanine base in the minor groove. Two such hairpins stack end-over-end and are linked together by the butanediamine tether to form a dumbbell structure. Such unusual structural distortion is different from that of the anticancer drug cisplatin-DNA adduct and may provide clues to explain the distinct biological activities of the two compounds.

Restriction-enzyme cleavage of DNA modified by platinum(II) complexes

The effect of binding of cis-diamminedichloroplatinum(II), its trans isomer and diethylenetriaminechloroplatinum(II) chloride to DNA on the splicing effectiveness of BamHI, EcoRI and SalI restriction endonucleases has been determined by means of gel electrophoresis. All three platinum complexes inhibit the cleavage of linearized plasmid DNA. In addition, the three platinum complexes bound to DNA constitute a barrier across which the linear diffusion of EcoRI on DNA is difficult. We interpret these findings to mean that the splicing effectiveness of restriction enzymes is influenced by bifunctional and monofunctional DNA adducts of platinum via both steric interference and DNA conformational distortions. Whereas the platinum adducts in the restriction sites or in their very close proximity inhibit the cleavage, the lesions occurring a greater distance from the restriction site can slow down the process of the localization of recognition sequences.

Nonclassical platinum antitumor agents: perspectives for design and development of new drugs complementary to cisplatin

Studies over the last few years have shown that the range of platinum complexes with useful cytotoxicity and antitumor activity is not strictly limited to structural analogs of cisplatin. In general, we can expect that cells will process structurally different species in different manners. The metabolic chemistry and DNA binding will be altered in in comparison to the cis-[PtX2 (amine)2] class. This point is of particular importance because any altered pattern of antitumor activity of structural analogs of cisplatin is likely to be due to unpredictable pharmacokinetic, rather than truly mechanistic, factors. The fact that discrete cisplatin-DNA adducts vary in their biological activity further supports the hypothesis that complexes structurally dissimilar to cisplatin may produce biological activity complementary to the parent drugs. The mechanism of action of nonclassical complexes is different from that of cisplatin and its analogs. Their pattern of antitumor activity is also altered with respect to cisplatin--thus, not all platinum-containing drugs need necessarily be similar in their clinical profile to cisplatin. Note that both the dinuclear bis(platinum) complexes and the trans complexes give their own distinct patterns of tumor specificity--different from cisplatin and each other (see Tables 1 and 3). New cytotoxic mechanisms for platinum complexes may also be placed in context with cisplatin resistance. Modes of overcoming cisplatin resistance may reside at the various levels of uptake, interaction with "detoxifying" intracellular thiols, and DNA repair. Likewise complexes with novel mechanisms of action may circumvent resistance by more than one unique route. Indeed, the three major routes to resistance are all affected to varying degrees by the complexes outlined above. From the discovery of cisplatin, the development of analogs has essentially been an empirical exercise. Because of their similar mechanism of action, much comparison has been made between platinum complexes and the classic alkylating agents. Yet the alkylating agents represent a good example where a number of structurally distinct drugs with different anticancer activities are clinically available. This desirable feature may be achieved for platinum complexes by emphasis on complexes structurally dissimilar to the presently used agents. The dinuclear bis(platinum) complexes and mononuclear complexes in the trans geometry are of special interest. Comparison of common features and differences between different classes may point to guidelines for the rational design of complexes with a different spectrum of clinical antitumor activity to cisplatin and activity against cisplatin-resistant tumors.

B----Z DNA conformational changes induced by a family of dinuclear bis(platinum) complexes

The reactions of bis(platinum) complexes of general formula [(PtClm(NH3)3-m)2(NH2(CH2)nNH2)]2(2-m)+ were studied with poly(dG-dC).poly(dG-dC), poly(dG-m5dC).poly(dG-m5dC) and poly(dG).poly(dC). When m = 0 (Complexes II, n = 2,4) the complexes are saturated 4+ cations capable only of electrostatic interactions with the polynucleotide. Where m = 1 the complexes contain two monodentate platinum coordination spheres with the chloride trans to the diamine bridge (Complexes I, n = 2,4, 1,1/t,t). Complexes I give CD spectra characteristic of a 'Z-like' conformation upon reaction with poly(dG-dC).poly(dG-dC) and poly(dG-m5dC).poly(dG-m5dC) but not poly(dG).poly(dC). The B----Z transition appears independent of interplatinum diamine chain length. As little as 1 bis(platinum) complex per 25-30 base pairs is sufficient to observe the Z-like spectrum. Covalent binding is however not a prerequisite for Z-DNA formation because the polyvalent cations II are also very effective in inducing the B----Z transition in either poly(dG-dC).poly(dG-dC) or poly (dG-m5dC).poly(dG-m5dC). In these cases, the concentrations of II required are significantly lower than analogous monomeric agents such as [Co(NH3)6]3+. The possible biological consequences of the Z-DNA induction by bis(platinum) complexes are discussed.

Biophysical studies of the modification of DNA by antitumour platinum coordination complexes

Cisplatin (cis-diamminedichloroplatinum(II] is widely used in the treatment of various human tumours. A large body of experimental evidence indicates that the reaction of cisplatin with DNA is responsible for the cytostatic action of this drug. Several platinum-DNA adducts have been identified and their effect on the conformation of DNA has been investigated. Structural studies of platinum-DNA adducts now permit a reasonably good explanation of the biophysical properties of platinated DNA. Antitumouractive platinum compounds induce in DNA, at low levels of binding, local conformational alterations which have the character of non-denaturing distortions. It is likely that these changes occur in DNA due to the formation of intrastrand cross-links between two adjacent purine residues. On the other hand, the modification of DNA by antitumour-inactive complexes results in the formation of more severe local denaturation changes. Conformational alterations induced in DNA by antitumour-active platinum compounds may be reparable with greater difficulty than those induced by the inactive complexes. Alternatively, non-denaturation change induced in DNA by antitumour platinum drugs could represent more significant steric hindrance against DNA replication as compared with inactive complexes.

Furazolidone-induced interstrand cross-links in Vibrio cholerae DNA. Study of conformational change by circular dichroism

Vibrio cholerae DNA bearing furazolidone-induced interstand cross-links show a change in the characteristic circular dichroism spectra of the DNA itself in dilute buffer. The change in c.d. spectra was characterized by a shift of the positive band around 272 nm to lower wavelength and a loss of ellipticity of the negative band around 242 nm, and is similar to that exhibited by mitomycin linked Vibrio cholerae DNA under identical conditions and is suggestive of a conformational change of DNA bearing such cross-links. Both furazolidone-induced and mitomycin-induced cross-linking of Vibrio cholerae DNA inhibited the salt-induced conformation change, i.e. increase in winding angle of DNA, the percentage inhibition being greater for mitomycin-linked DNA.

Slow exchanging protons in the Z-form of G-C and A-C alternating polymers by using a rapid dialysis method

Using a dialysis method we have measured the hydrogen exchange (HX) kinetics in poly(dG-dC).poly(dG-dC), poly(dG-m5dC).poly(dG-m5dC), poly(dG-br5dC).poly(dG-br5dC) and platinated poly(dA-br5dC).poly(dG-dT) under experimental conditions in which these polymers adopt the Z-conformation. The latter polymer has one slow exchanging proton with a half-time of about 2 h, whereas the other G-C alternating polymers display a slow class of two protons with exchange half-time of about 6 h. These exchange half-times are independent of ionic strength and of the nature of the salt for all these polymers in the Z-form. The slow proton exchange appears to be strongly correlated to the Z-conformation but rather independent of the Z-DNA sequence. The comparison of the proton exchange rates with the corresponding B in equilibrium Z transition rates is not in favour of the same rate limiting step for both processes.

Characterization of the ternary complexes formed in the reaction of cis-diamminedichloroplatinum (II), ethidium bromide and nucleic acids

The purpose of this study was to characterize the ternary complexes formed in the reaction of cis-diamminedichloroplatinum (II) (cis-DDP) and nucleic acids, in the presence of the intercalating compound ethidium bromide (EtBr). In these ternary complexes, some EtBr is tightly bound to the nucleic acids. Tight binding is defined by resistance to extraction with butanol, assayed by filtration at acid pH or thin layer chromatography at basic pH. These ternary complexes are formed with double stranded but not with single stranded nucleic acids. They are not formed if cis-DDP is replaced by transdiamminedichloroplatinum(II). The amount of tightly bound EtBr depends upon the sequence of the nucleic acid, being larger with poly (dG-dC).poly(dG-dC) than with poly(dG).poly(dC). Spectroscopic results support the hypothesis that the tight binding of the dye is due to the formation of a bidentate adduct (guanine-EtBr)cis-platin. The visible spectrum of the ternary complexes is blue-shifted as compared to that of EtBr intercalated between the base pairs of unplatinated DNA and it depends upon the conformation of the ternary complex. The fluorescence quantum yield of the ternary complexes is lower than that of free EtBr in water. Tightly bound EtBr stabilizes strongly the B form versus the Z form of the ternary complex poly(dG-dC)-Pt-EtBr and slows down the transition from the B form towards the Z form. The sequence specificity of cis-DDP binding to a DNA restriction fragment in the absence or presence of EtBr is mapped by means of the 3'----5' exonuclease activity of T4 DNA polymerase. In the absence of the dye, all the d(GpG) sites and all the d(ApG) sites but one in the sequence d(TpGpApGpC) are platinated. The d(GpA) sites are not platinated. In the presence of EtBr, some new sites are detected. These results might help to explain the synergism for drugs used in combination with cis-DDP and in the design of new chemotherapeutic agents.

Reaction of nucleic acids and cis-diamminedichloroplatinum(II) in the presence of intercalating agents

The reaction of cis-diamminedichloroplatinum(II) and several synthetic or natural double-stranded polydeoxyribonucleotides has been carried out in the presence of such intercalating agents as ethidium bromide, proflavine, and acridine. After incubation of the reaction mixtures at 37 degrees C for 24 hr, some ethidium or proflavine, but no acridine, molecules are tightly bound to nucleic acids. Tight binding is defined by resistance to extraction with butanol, assayed by filtration at acid pH or by thin-layer chromatography at basic pH. In the ternary complexes, there is about one tightly bound ethidium (or proflavine) per platinum residue. At 37 degrees C, but not at 4 degrees C, tightly bound ethidium exchanges with free ethidium, whereas platinum residues do not exchange. The binding and the release of tightly bound ethidium are very slow (several hours). It is suggested that in the ternary complexes, nucleic acid-cis-Pt(NH3)2-intercalating agent, a bidentate adduct (guanine-ethidium or -proflavine)-cis-Pt(NH3)2, is formed. No tightly bound ethidium or proflavine is found when cis-diamminedichloroplatinum(II) is replaced by trans-diamminedichloroplatinum(II). Competition experiments between cis-diamminedichloroplatinum(II), poly(dG-dC), and poly(dG)-poly(dC) or poly(dA-dT) show that the presence of ethidium bromide, proflavine, or acridine interferes with the distribution of platinum between the polynucleotides. These results might help to explain the synergism for drugs used in combination with cis-diamminedichloroplatinum(II) and in the design of new chemotherapeutic agents.

DNA modified by platinum derivatives cannot adopt the A-form

DNA fragments from chicken erythrocytes were modified by cis-diamminedichloroplatinum(II), its trans-isomer and chlorodiethylenetriaminoplatinum(II) chloride. The conformation of the modified DNA fragments in ethanolic solutions was studied by circular dichroism spectroscopy. Non-modified DNA adopted the A-form in 81% ethanol. The modification of DNA by the three platinum compounds inhibited the B to A transition of DNA induced by high concentrations of ethanol roughly to the same extent. The results support the view that the binding of the platinum complexes to B-DNA lowers the conformational freedom of DNA so that it cannot acquire the A-conformation.

The low ionic strength form of the sodium salt of poly(dm5C-dG) is a B DNA

The low-salt Z form of poly(dm5C-dG) reported in the literature was shown to be due to minute amounts of bivalent cations. If the polymer was purified by dialysis against 1 mM EDTA, poly(dm5C-dG) showed the normal B form. No change in this B form was observed up to 0.8 M NaCl. Very small amounts of Mg2+ or Ca2+ (10(-6) to 10(-5) M) induced the characteristic Z form CD spectrum, which could easily and rapidly be reverted to B-DNA by addition of EDTA.

Comparison between poly(dG-dC).poly(dG-dC) and DNA modified by cis-diamminedichloroplatinum (II): immunological and spectroscopic studies

The importance of the base composition and of the conformation of nucleic acids in the reaction with the drug cis-diamminedichloroplatinum(II) has been studied by competition experiments between the drug and several double-stranded polydeoxyribonucleotides. Binding to poly(dG).poly(dC) is larger than to poly (dG-dC).poly(dG-dC). There is no preferential binding in the competition between poly(dG-dC).poly(dG-dC), poly(dA-dC).poly(dG-dT) and poly(dA-dG).poly(dC-dT). In the competition between poly(dG-dC).poly (dG-dC) (B conformation) and poly(dG-br5dC).poly(dG-br5dC) (Z conformation), the drug binds equally well to both polynucleotides. In natural DNA, modification of guanine residues in (GC)n.(GC)n sequences by the drug has been revealed by the inhibition of cleavage of these sequences by the restriction enzyme BssHII. By means of antibodies to platinated poly(dG-dC), it is shown that some of the adducts formed in platinated poly(dG-dC) are also formed in platinated pBR322 DNA. The type of adducts recognized the antibodies is not known. Thin layer chromatography of the products after chemical and enzymatic hydrolysis of platinated poly(dG-dC) suggests that interstrand cross-links are formed. Finally, the conformations of poly(dG-dC) modified either by cis-diamminedichloroplatinum(II) or by trans-diamminedichloroplatinum (II) have been compared by circular dichroism. Both the cis-isomer and the trans-isomer stabilize the Z conformation when they bind to poly(dG-m5dC) in the Z conformation. When they bind to poly(dG-m5dC) in the B conformation, the conformations of poly(dG-m5dC) modified by the cis or the trans-isomer are different. Moreover, the cis-isomer facilitates the B form-Z form transition of the unplatinated regions while the trans-isomer makes it more difficult.

Application of polyelectrolyte theory to the study of the B-Z transition in DNA (1)

We have used the polyelectrolyte theory to study the ionic strength dependence of the B-Z equilibrium in DNA. A DNA molecule is molded as an infinitely long continuously charged cylinder of radius a with reduced linear charge density q. The parameters a and q for the B and Z forms were taken from X-ray data: aB = 1nm, qB = 4.2, aZ = 0.9 nm and qZ = 3.9. A simple theory shows that at low ionic strengths (when Debye screening length rD much greater than a) the electrostatic free energy difference FelBZ = FelZ - FelB increases with increasing ionic strength since qB greater than qZ. At high ionic strengths (when rD much less than a) the FelBZ would go on growing with increasing ionic strength if the inequality qB/aB greater than qZ/aZ were valid. In the converse case when qZ/qB greater than aZ/aB the FelBZ value decreases with increasing salt concentration at high ionic strength. Since X-ray data correspond to the latter case, theory predicts that the FelBZ value reaches a maximum at an intermediate ionic strength of about 0.1 M (where rD approximately a). We also performed rigorous calculations based on the Poisson-Boltzmann equation. These calculations have confirmed the above criterion of nonmonotonous behaviour of the FelBZ value as a function of ionic strength. Different theoretical predictions for the B-Z transition in linear and superhelical molecules are discussed. Theory predicts specifically that at a very low ionic strength the Z form may prove to be more stable than the B form.(ABSTRACT TRUNCATED AT 250 WORDS)

Z-DNA is formed by poly (dC-dG) and poly (dm5C-dG) at micro or nanomolar concentrations of some zinc(II) and copper(II) complexes

We report studies on the interaction of some zinc(II) and copper(II) complexes of amines and amino acids with poly(dC-dG) and poly(dm5C-dG). Of the zinc complexes the species zinc-tris(2-aminoethyl) amine is found to be the most efficient for inducing Z-DNA giving a mid point at low ionic strength of 1.4 microM (poly(dC-dG] and 44nM (poly(dm5C-dG). While an antagonistic effect on raising the ionic strength is observed, the transition occurs at only 2 microM for poly(dm5C-dG) at 150mM NaCl. The most efficient copper(II) complex is that of diethylene triamine, though copper(II) complexes are generally less efficient than zinc(II) complexes. We also report kinetic and thermodynamic studies upon the B-Z transition induced by these complexes. A model is proposed for the interaction of one of the zinc complexes which involves not only direct zinc-DNA binding but also the formation of hydrogen bonds between the metal bond amine groups and the residues adjacent to the coordination site.

Unwinding of supercoiled DNA by cis- and trans-diamminedichloroplatinum(II): influence of the torsional strain on DNA unwinding

The effective unwinding angle, phi, for cis-diamminedichloroplatinum(II) (cis-DDP) and trans-DDP was determined by utilizing high resolution gel electrophoresis and supercoiled phi X174 RF DNA as a substrate. The effective unwinding angle was calculated by equating the reduction in mobility of the DDP-modified DNA to the removal of a number of superhelical turns. The value of the effective unwinding angle for both DDP isomers was greatest at the low levels of DDP bound and decreased with increasing amounts of unwinding agent. The cis-isomer is a better unwinding agent than is the trans-isomer, being nearly twice as effective in unwinding the supercoiled DNA at the DDP levels investigated. A comparison of the magnitude of phi below rb values of 0.005 and those at high levels of binding reveals that the extent of torsional strain in the supercoiled DNA influences the magnitude of the unwinding of the DNA by these complexes. When this method is used in the analysis of the unwinding angle for a covalently bound species on supercoiled DNA, it may provide a more reliable estimate of the magnitude of phi at high degrees of supercoiling and at low levels of modification.

Electron microscopic measurement of chain flexibility of poly(dG-dC).poly(dG-dC) modified by cis-diamminedichloroplatinum(II)

The antitumor drug cis-diamminedichloroplatinum (II) (cis-Pt) forms bidentate adducts with guanine residues of poly(dG-dC).poly(dG-dC). The secondary structure of the polymer is altered. In this work, high resolution pictures of naked molecules, obtained by dark field electron microscopy reveal DNA chain distortions with radii as small as 30 A. The extent of distortion increases with the drug/nucleotide ratio (rb). These alterations of the secondary structure are responsible for the apparent shortening of the molecules. Measurements of the persistence lengths of the polymer as well as the end-to-end distances of elementary segments of various lengths, are obtained from digitized electron micrographs. The measurements are used to monitor and quantify the observed modifications of polymer structure upon cis-Pt binding at various rb or incubation times. Poly(dG-m5dC).poly(dG-m5dC) in the B and Z forms have different persistence lengths. In the B form, this polymer is more altered by cis-Pt than in the Z one.

Effect of chromium(III) on poly(dG-dC) conformation

The interaction of chromium(III) with poly(dG-dC) inhibits the B to Z transition and results in the condensation of the polymer at high Cr/nucleotide ratios. At low Cr/nucleotide ratios chromium(III) enhanced the ability of ethanol to induce the B to Z transition of poly(dG-dC). The effects of chromium(III) on the conformation of DNA may be related to the carcinogenicity of chromium compounds.

Presence of Z-DNA specific antibodies in Crohn's disease, polyradiculoneuritis and amyotrophic lateral sclerosis

Two modified polynucleotides having the Z-DNA conformation (poly [dG-dC] dien Pt and poly [dG-br5dC] . poly [dG-br5dC]) have been used for determination of antibodies to Z-DNA. Such antibodies were found in sera of patients with systemic lupus erythematosus and with Crohn's disease. They were scarcely observed in polyradiculoneuritis and in amyotrophic lateral sclerosis. In Crohn's disease sera, no antibodies to B-DNA were ever found but presence of two different families of antibodies to Z-DNA was demonstrated.

Platinum determination in cis-dichlorodiammineplatinum(II)-DNA complexes by differential pulse polarography

A simple polarographic assay for platinum determination in cis-dichlorodiammineplatinum(II)-DNA complexes is described. The method makes it possible to determine the free (unbound) drug in the presence of DNA or platinum-DNA complex, i.e., without a separation of free drug and macromolecular components of the solution to be analyzed. This method is based on the polarographic activity of intact cis-dichlorodiammineplatinum(II) at -1.5 V, which can be measured by differential pulse polarography even in the presence of DNA or platinum-DNA complex. The lower level of analytical utility of this method is ca. 1 X 10(-6) M (195 ng of platinum/ml).

Inner and outer complexes of Pt-coordination compounds with DNA probed by SERS spectroscopy

Surface enhanced Raman scattering (SERS) spectroscopy has been used to study the interfacial behaviour of DNA modified by cis-Pt(NH3)2Cl2, (cis-DDP) and [Pt-(dien)Cl]Cl bidentate and monodentate platinum coordination compounds, respectively. Two stereochemical configurations of Pt-DNA complexes can be deduced from the adsorption behaviour of the Pt adducts. The antitumoral inactive [Pt-(dien)Cl] Cl forms an outer complex whereas the antitumoral active cis-DDP favours an inner complex.

Z-DNA immunoreactivity in fixed metaphase chromosomes of primates

Antibodies against Z-DNA bind to fixed metaphase chromosomes of man and Cebus albifrons (Platyrrhini, Primate). By indirect immunofluorescence and indirect immunoperoxidase techniques, a heavy staining is detected in some segments of chromosomes of C. albifrons. These segments correspond to R-band-positive heterochromatin, which has a high G + C-base content. Euchromatin of human and Cebus chromosomes show a weak and heterogeneous staining that consistently reproduces an R- and T-banding pattern in both species. Because chromosome homologies previously were demonstrated between these distantly related species by chromosome banding, our results suggest that Z-DNA has been conserved during the course of primate evolution.

Similar binding of the carcinostatic drugs cis-[Pt(NH3)2Cl2] and [Ru(NH3)5Cl] Cl2 to tRNAphe and a comparison with the binding of the inactive trans-[Pt(NH3)2Cl2] complex - reluctance in binding to Watson-Crick base pairs within double helix

A comparative study of the binding of square planar cis- and trans-[Pt(NH3)2Cl2] complexes and the octahedral [Ru(NH3)5(H2O)]3+ complex to tRNAphe from yeast was carried out by X-ray crystallography. Both of the carcinostatic compounds, cis-[Pt(NH3)2Cl2] and [Ru(NH3)5(H2O)]3+ show similarities in their mode of binding to tRNA. These complexes bind specifically to the N(7) positions of guanines G15 and G18 in the dihydrouridine loop. [Ru(NH3)5(H2O)]3+ has an additional binding site at N(7) of residue G1 after extensive soaking times (58 days). A noncovalent binding site for ruthenium is also observed in the deep groove of the acceptor stem helix with shorter (25 days) soaking time. The major binding site for the inactive trans-[Pt(NH3)Cl2] complex is at the N(1) position of residue A73, with minor trans-Pt binding sites at the N(7) positions of residues Gm34, G18 and G43. The similarities in the binding modes of cis-[Pt(NH3)2Cl2] and [Ru(NH3)5(H2O)]3+ are expected to be related to their carcinostatic properties.

Intercalative and nonintercalative binding of large cationic porphyrin ligands to polynucleotides

The interactions of two positional isomers and one analogue of meso-tetra (4-N-methylpyridyl) porphine, with the synthetic polynucleotides poly[d(A-T)] . poly[d(A-T)] and poly[d(G-C)] . poly[d(G-C)] have been investigated by circular dichroism. All four porphyrins were found to bind to the polynucleotides as shown by the induction of circular dichroism in their Soret bands. Furthermore, the sign of the induced ellipticity reflects selective occupation of binding sites by the porphyrin ligands. The conformational lability of poly[d(A-T)] X poly[d(A-T)] was found to be appreciable as micromolar amounts of meso-substituted 4-N-methylpyridyl, 3-N-methylpyridyl, and p-N-trimethylanilinium porphines induced a CD spectrum similar but not identical to that of DNA in the Z-form, i.e. a negative band at 280 nm and a positive band at 259 nm. The effect of porphyrin binding to poly[d(G-C)] X poly[d(G-C)] was less pronounced and dissimilar to that seen in the AT polymer.

cis-Platinum induced distortions in DNA. Conformational analysis of d(GpCpG) and cis-pt(NH3)2[d(GpCpG)], studied by 500-MHz NMR

Proton NMR studies at 500 MHz in aqueous solution were carried out on the G-G chelated deoxytrinucleosidediphosphate platinum complex cis-Pt(NH3)2[d(GpCpG], on the uncoordinated trinucleotide d(GpCpG) and on the constituent monomers cis-Pt(NH3)2[d(Gp)]2, cis-Pt(NH3)2[d(pG)]2, d(Gp), d(pCp) and d(pG). Complete NMR spectral assignments are given and chemical shifts and coupling constants are analysed to obtain an impression of the detailed structure of d(GpCpG) and the distortion of the structure due to chelation with [cis-Pt(NH3)2]2+. Platination of the guanosine monophosphates affects the sugar conformational equilibrium to favour the N conformation of the deoxyribose ring. This feature is also apparent in ribose mononucleotides and is possibly caused by an increased anomeric effect. In cis-Pt(NH3)2[d(pG)]2 the phase angle of pseudorotation of the S-type sugar ring is 20 degrees higher than in 'free' d(pG) which might be an indication for an ionic interaction between the positive platinum and the negatively charged phosphate. It appears that d(GpCpG) reverts from a predominantly random coil to a normal right-handed B-DNA-like single-helical structure at lower temperatures, whereas the conformational features of cis-Pt(NH3)2[d(GpCpG)] are largely temperature-independent. In the latter compound much conformational freedom along the backbone angles is seen. The cytosine protons and deoxyribose protons exhibit almost no shielding effect as should normally be exerted by the guanine bases in stacking positions. This is interpreted in terms of a 'turning away' of the cytosine residue from both chelating guanines. Conformational features of cis-Pt(NH3)2[d(GpCpG)[ are compared with the 'bulge-out' of the ribose-trinucleotide m6(2)ApUpm6(2)A.