Viscosity, nicking, thermal and alkaline denaturation studies on three classes of DNA-platinum complex

Melting of cross-linked DNA IV. Methods for computer modeling of total influence on DNA melting of monofunctional adducts, intrastrand and interstrand cross-links formed by molecules of an antitumor drug

A theoretical method is developed for calculation of melting curves of covalent complexes of DNA with antitumor drugs. The method takes into account all the types of chemical modifications of the double helix caused by platinum compounds and DNA alkylating agents: 1) monofunctional adducts bound to one nucleotide; 2) intrastrand cross-links which appear due to bidentate binding of a drug molecule to two nucleotides that are included into the same DNA strand; 3) interstrand cross-links caused by bidentate binding of a molecule to two nucleotides of different strands. The developed calculation method takes into account the following double helix alterations at sites of chemical modifications: 1) a change in stability of chemically modified base pairs and neighboring ones, that is caused by all the types of chemical modifications; 2) a change in the energy of boundaries between helical and melted regions at sites of chemical modification (local alteration of the factor of cooperativity of DNA melting), that is caused by all the types of chemical modifications, too; 3) a change in the loop entropy factor of melted regions that include interstrand cross-links; 4) the prohibition of divergence of DNA strands in completely melted DNA molecules, which is caused by interstrand cross-links only. General equations are derived, and three calculation methods are proposed to calculate DNA melting curves and the parameters that characterize the helix-coil transition.

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.

Melting of cross-linked DNA: II. Influence of interstrand linking on DNA stability

In the previous paper (D.Y. Lando, J. Biomol. Struct. Dynam, 15, 129-140 (1997)) the melting of cross-linked DNA with N base pairs and omega interstrand cross-links has been considered theoretically. In the present study on the basis of these results, two simple schemes are developed for the computation of melting curves of cross-linked DNA. The investigation of influence of interstrand linking on DNA stability has been carried out by computer simulation. It is shown that the relative concentration of cross-links, CCT = omega/N, their distribution along a DNA molecule, and particular values of the entropy factors of small loops formed by cross-links in melted regions strongly affect the DNA melting temperature, Tm. On the contrary, for DNA without cross-links, a ten-fold increase or decrease in the entropy factors of small loops does not cause the Tm variation. The comparison of the results of calculation with experimental data suggests that the majority of types of cross-link neither maintain ordered parallel orientation of bases in melted regions nor increase considerably the thermostability of cross-linked base pairs. Four different ways of influence of interstrand cross-linking on the DNA double helix stability are considered. It is shown that cross-linking significantly enhances the influence of single strand stiffness in melted regions on DNA melting behavior.

Melting of cross-linked DNA: I. Model and theoretical methods

Covalent and strong coordination binding to DNA of a large number of antitumour drugs and other compounds leads to interstrand cross-link formation. To investigate cross-link influence on double helix stability, two methods are developed for the calculation of melting curves. The first method is based on Poland's approach. It requires computer time proportional to u.N, where u is the average distance (in base pairs) between neighboring cross-links and N is the number of base pairs in the DNA chain. The method is more suitable when u is not large, and small loops formed by interstrand cross-links in melted regions strongly affect DNA melting. The computer time for the second method, based on the Fixman-Freire approach, does not depend on the number of cross-links and is proportional to I.N (I is the number of exponential functions used for a decomposition of the loop entropy factor). It is more appropriate when N and u are large, and therefore particular values of the entropy factors of small loops do not influence DNA melting behavior.

Palladium(II) compounds with potential antitumour properties and their platinum analogues: a comparative study of the reaction of some orotic acid derivatives with DNA in vitro

Ethidium bromide was used to study perturbations induced in salmon sperm DNA complexed with a series of platinum and palladium compounds obtained from chloro and orotic acid derivatives as leaving ligands. The antitumoral activity of these compounds against Sarcoma 180 cells grafted intraperitoneally into mice is correlated with their capacity to interact with DNA in vitro and to perturb its secondary structure. Nevertheless, among these compounds, [Pt(Dach)(3-methyl-orot)] and [Pt(Dach)(5-fluoro-orot)] do not interact with DNA in vitro and are inactive against Sarcoma 180 cells. This lack of activity originates from the fact that strong chelating properties of the ligand prevent hydrolysis of the compounds which are unable to give rise to aquo species which are the reactive ones. On the other hand, the interaction with DNA is not the only prerequisite in order that a compound be active towards tumour cells. In fact, cis-[Pd(NH3)2Cl2] and cis[Pd(Dach)Cl2] are not antitumoral. It is well known that the former undergoes an inactive trans-conformation and that the two compounds hydrolyse very fast assuming that they interact in vivo with a lot of molecules particularly proteins preventing them to reach the DNA, their pharmacological target. By contrast, [Pd(Dach)(3-methyl-orot)] (T/C = 267%) and [Pd(Dach)(5-fluoro-orot)] (T/C = 270%) display significant antitumour activity.

Effect of the amine non-leaving group on the structure and stability of DNA complexes with cis-[Pt(R-NH2)2(NO3)2]

The antitumor compound cis-[Pt(NH3)2Cl2] (cisplatin), conserves two ammine ligands during the reaction with its cellular target DNA. Modifications of these non-leaving groups change the antineoplastic properties of this compound and its genotoxic effects. It is therefore of interest to determine the influence of non-leaving groups on the structure and stability of DNA in vitro. We have investigated platinum-DNA adducts formed by cis-[Pt(R-NH2)2(NO3)2] (where R-NH2 = NH3, methylamine, cyclobutylamine, cyclopentylamine and cyclohexylamine) as a function of DNA binding. All compounds quantitatively reacted with DNA in less than 1 h at 37 degrees C. They formed bifunctional adducts with adjacent nucleotides judging from the displacement of the intercalating molecule ethidium bromide, ultraviolet absorption spectroscopy and circular dichroism. Substitution of a H on the NH3 ligand by alkyl groups dramatically destabilized the platinum-DNA complex. Thermal stability decreased progressively with an increasing number of carbon atoms, delta tm = -4.4 degrees C for 3 cyclohexylamine-platinum-DNA adducts/1000 nucleotides, conditions where cisplatin had no effect. DNA adducts with cyclobutylamine and cyclohexylamine ligands inhibited the hydrolysis of platinum-DNA complexes by S1 nuclease. Km for the digestion of DNA containing these lesions was 2.3 times greater than for cisplatin, indicating steric inhibition of enzyme-substrate complex formation. These results show that the non-leaving groups of substituted cis-Pt(II) compounds may destabilize DNA and interfere with protein-DNA interactions. These perturbations may have consequences for the genotoxic and antitumor activities of platinum compounds.

Evidence for lack of mitochondrial DNA repair following cis-dichlorodiammineplatinum treatment

The purpose of this study was to determine whether cis-dichlorodiammineplatinum (cisplatin) causes mitochondrial DNA (mtDNA) damage. A specific and sensitive method for quantitation of damage to mtDNA was used, by which the physical forms of mtDNA (supercoiled, open circular and linear forms) were separated by gel electrophoresis. The DNA specificity was then obtained by hybridizing with a mtDNA probe. In vitro incubation of mtDNA with cisplatin showed that the drug did not induce any changes in the proportion of physical forms; similar results were obtained in vivo. Since cisplatin did not cause any strand scission in mtDNA but induces strand breaks in nuclear DNA, which is an indirect effect, a lack of repair for cisplatin-induced adducts in mtDNA is suggested.

The effect of combined treatment with platinum complexes and ionizing radiation on DNA in vitro

The conformation of isolated calf-thymus DNA treated with cis-diamminedichloroplatinum(II) (cis-DDP) or its trans-isomer (trans-DDP) and gamma radiation in combination was investigated by means of differential pulse polarography and circular dichroism spectroscopy. The results revealed that combined treatment with antitumour active cis-DDP enhanced the extent of double-stranded distorted regions in DNA molecules. If irradiation preceded the platination, the combined effect was purely additive, while the reverse order of application of the two agents resulted in an increased effect over and above what may be expected from using the two modalities separately. These results were explained on the basis of the hypothesis that favours as a major mechanism of this combined effect the fixation by the binding of cis-DDP of DNA lesions introduced during radiation. Combined treatment with antitumour inactive trans-DDP resulted in the enhancement of single-stranded, denatured DNA yield. However, more extensive alterations in DNA conformation were observed if DNA was platinated after irradiation. The different effects of the combined treatments with cis- and trans-DDP were thought to be connected with the different destabilizing effects resulting from distinct conformational distortions induced by the two isomers.

DNA degradation after interaction of cis- and trans-diamminedichloroplatinum (II) with calf thymus nuclei

DNA samples isolated from control nuclei and nuclei treated by cis- and trans-diamminedichloroplatinum (DDP) were analyzed by gel electrophoresis. There were no changes in Mr when DNA isolated from nuclei treated with trans-DDP was analyzed. Scans of DNA isolated from nuclei treated with cis-DDP revealed significant changes in Mr. This DNA bears, however, no signs of regular fragmentation. The possible involvement of endonuclease activity in the degradation process is discussed.

A simple model for DNA elution from filters

DNA chain scission, induced both in vitro and in vivo by various agents, is an event of great biological relevance. The damage is currently evaluated by empirical membrane separation techniques; the results are quite reproducible and the sensitivity higher than 1 single strand break per 10(9) Daltons. We outline a simple theory of the filtration of coiled macrosolutes, having a random size distribution, through porous membranes, considered as being in quasi-steady flow. The basic transport equation Jj = cj (1 - sigma)Jv is solved by considering that the value of sigma j, the reflection coefficient of component j, (1 less than or equal to j less than or equal to N), is given by (1 - KjRj), where Kj is the partition constant between pore and solution, a function of the conformational entropy loss of the coil, and Rj accounts for the frictional force experienced by a particle moving along the pore. The problem of evaluating the volume Vs filled up with solute has been approached according to a simplified theory of the excluded volume for flexible polymers; the result is Vs = sigma nj4/3 pi(rGj)3 where rGj is the jth radius of gyration. The solution of the resulting set of N differential equations gives nj, the number of molecules of component j remaining on the filter, as a function of the elution volume V. The theory demonstrates that the process is governed by the average dimensions of the coil, so affording a universal calibration of filter elution methods, in excellent agreement with the experiments.

Kinetics of the reaction of cis-platinum compounds with DNA in vitro

The kinetics of the reaction of a series of cis-platinum(II) compounds with DNA in vitro has been studied using their ability to disturb the secondary structure of the macromolecule. The complexation modifies the stacking of the base pairs and causes an inhibition of the intercalation of ethidium bromide which is correlated with the number of platinum atoms bound per nucleotide. The compounds fall into three groups which react in a few minutes, in a few hours or in several days. The inhibition of the complexation by chloride and carboxylato ions indicates that the interaction occurs through hydrolysed species and that hydrolysis is the rate limiting step. In addition the results indicate that the carboxylato entities are able to react with DNA in vitro without enzymatic activation and that there is no correlation between the antitumoral activity of these compounds against L1210 Leukemia cells and their in vitro reactivity towards DNA.

cis-Pt(NH3)2Cl2 and trans-Pt(NH3)2Cl2 inhibit DNA synthesis in cultured L1210 leukemia cells

A comparison of the inhibition of DNA synthesis by the two geometrical bidentate isomers cis- and trans-Pt(NH3)2Cl2 and by the monodentate [Pt(dien)Cl]Cl in a model used for screening potential antitumor compounds, the L1210 leukemia cells, is presented. The efficacy of penetration after a 2 hours Pt treatment is in the order trans (8) greater than cis (1) approximately dien (0.7). DNA replication is reduced to 50% of the control when 1.8 X 10(-4), 2.4 X 10(-4) and 80 X 10(-4) Pt atoms were bound per nucleotide for cis, trans and dien derivatives, respectively. If we admit that DNA is the pharmacological target of Pt antitumor compounds, these results suggest that a quantitative inhibition of DNA synthesis is certainly not correlated with antitumor activity.

Alteration in the nucleosome and chromatin structures upon interaction with platinum coordination complexes

The interaction of various platinum coordination complexes with nucleosomes and chromatin has been investigated by ultraviolet absorption spectrophotometry, circular and electric linear dichroism, and thermal denaturation, at low binding ratios (r less than 0.1-0.2). The general trend of the changes in these physicochemical properties is similar to that observed for the DNA-platinum complexes, which indicates that the same binding sites are involved in the platinum interaction with DNA and with its nucleoprotein complex. The cis-bidentate ligands, cis-dichlorodiammine, diaminocyclohexane and ethylenediamine platinum(II), showed a distinct behavior, with a more important destabilization of the DNA structure in the nucleoprotein than the trans-bidentate ligand, trans-dichlorodiammine-Pt(II), and monodentate ligand, diethylenetriamine-Pt(II). The drastic decrease of the negative electric dichroism in the 260 nm absorption band of the bases, observed with the five ligands, indicates a profound alteration of the DNA arrangement in chromatin and nucleosomes, attributed to a condensation of its superhelical structure. Some differences with previous observations on DNA complexes with the same platinum compounds indicate the possible formation of protein-DNA crosslinks in chromatin and nucleosomes. These could have some importance for the biological effects.

Denaturation level of DNA-Pt complexes evidenced by Tb3+ fluorescence enhancement and electric dichroism

The Tb3+ fluorescence is greatly enhanced, as a result of binding of various platinum coordination complexes to DNA, as compared to native DNA. The largest enhancement is observed for cis-Pt(NH3)2Cl2 but the fluorescence intensity does not however reach the level attained for thermally denatured DNA. Diethylenetriamine-Pt(II) produces very little increase of Tb3+ fluorescence. The electric dichroism in the DNA absorption band drastically decreases upon binding of the various Pt compounds investigated except diethylenetriamine-Pt. The results are discussed in terms of the various modes of binding of Pt derivatives to DNA, particularly in relation to the level of denaturation of the double helix.

Structures of the adducts formed between [Pt(dien)Cl]Cl and DNA in vitro

The products of the reaction between [Pt(dien)Cl]Cl and salmon sperm DNA have been purified and their structures determined. [Pt(dien)Cl]Cl binds at the N7 position of guanine for levels of fixation below 0.1 platinum per DNA base. Above this level of binding, [Pt(dien)Cl]Cl also reacts at the N7 position of adenine. 1,7-[Pt(dien)]2Ade was observed when more than 0.3 platinum per base were bound to the DNA. Platination at the N7 position of guanosine, unlike alkylation, stabilized the glycosyl linkage and did not lead to fission of the imidazole ring at high pH.