Uptake, cytofluorescence, and cytotoxicity of oxazolopyridocarbazoles (amino acid-ellipticine conjugates) in murine sarcoma cells.

The uptake, cytofluorescence, and cytotoxicity of elliptinium (NMHE) and a series of fluorescent oxazolopyridocarbazoles [amino acid-ellipticine conjugates (AA-NMHE)] were studied in murine sarcoma cells. For all these drugs, the uptake was rapid, directly proportional to the drug concentration, and unaffected by metabolic inhibitors which is consistent with a diffusion mechanism. By 4 h, the intracellular concentration of NMHE exceeded the external drug concentration by about 100 times; this suggests that the toxicity of NMHE is not, as previously assumed, limited by its transport across tumor cell membranes. Conjugation of NMHE with aliphatic amino acids increased the cellular uptake 5- to 7-fold. Cellular exposure to AA-NMHE conjugates resulted in the appearance of granular cytoplasmic fluorescence which was readily translocated to the nucleus upon continued exposure to fluorescent light. The cytotoxicity of the AA-NMHE conjugates (drug concentration required to reduce colony formation by 63% on the exponential part of the survival curve = 3-14 microM) was less than of NMHE (drug concentration required to reduce colony formation by 63% on the exponential part of the survival curve = 0.7 microM) as shown by colony formation following 4 h drug exposure. In contrast, the isoleucine-NMHE conjugate was the most cytotoxic compound (drug concentration required to reduce colony formation by 63% on the exponential part of the survival curve = 0.045 microM) when the drug exposure period was extended to 8 days. The general lower toxicity of the AA-NMHE conjugates is likely due to loss of the phenolic character of the NMHE moiety; therefore, attempts to link NMHE to amino acids remain attractive but will have to be done without affecting the 9-hydroxy group of NMHE.

Characterization of loose and tight dimer forms of avian leukosis virus RNA.

Retroviral genomes consist of two identical RNA molecules joined non-covalently near their 5'-ends. Recently, we showed that an imperfect autocomplementary sequence, located in the L3 domain, plays an essential role in avian sarcoma-leukosis virus (ASLV) RNA dimerization in vitro. This sequence can adopt a stem-loop structure and is involved in ASLV replication. Here, we found that in the absence of nucleocapsid protein, RNA transcripts of avian leukosis virus (ALV) were able to form two types of dimers in vitro that differ in their stability: a loose dimer, formed at a physiological temperature, and a tight dimer, formed at a high temperature. A mutational analysis was performed to define the features of these dimers. The results of this analysis unambiguously confirm that the two L3 stem-loops interact directly in both types of dimers. A loop-loop interaction is the main linkage in the loose dimer. In contrast, in the tight dimer, the stem and the loop of the L3 hairpin form an extended duplex. Surprisingly, we also found that the dimerization properties defined for our ALV strain (type SR-A) differ from those found in other ASLV strains.

Effect of dimerization on the conformation of the encapsidation Psi domain of Moloney murine leukemia virus RNA.

In Moloney murine leukemia virus, the encapsidation Psi element was shown to be necessary and sufficient to promote packaging of viral RNA, and to be required for dimerization. The conformation of the Psi domain (nucleotides 215 to 565) was investigated in solution by chemical probing. The four bases were monitored at one of their Watson-Crick positions with dimethylsulfate at cytosine N3 and adenosine N1, and with a carbodiimide derivative at guanosine N1 and uridine N3. Position N7 of adenine residues was probed with diethylpyrocarbonate. The analyses were conducted on in vitro transcribed fragments corresponding either to the isolated Psi domain or to the 5'-terminal 725 nucleotides. The RNA fragments were analyzed in their monomeric and dimeric forms. A secondary structure model was derived from probing data, computer prediction and sequence analysis of related murine retroviruses. One major result is that Psi forms an independent and highly structured domain. Dimerization induces an extensive reduction of reactivity in region 278 to 309 that can be interpreted as the result of intermolecular interactions and/or intramolecular conformational rearrangements. A second region (around position 215) was shown to display discrete reactivity changes upon dimerization. These two regions represent likely elements of dimerization. More unexpectedly, reactivity changes (essentially enhancement of reactivity) were also detected in another part of Psi (around position 480) not believed to contain elements of dimerization. These reactivity changes could be interpreted as dimerization-induced allosteric transitions.

Spontaneous dimerization of retroviral MoMuLV RNA.

The genome of the Moloney murine leukemia virus (MoMuLV) is composed of two identical RNA molecules joined at their 5' ends by the dimer linkage structure (DLS). Dimerization sequences are located within the PSI encapsidation domain. We present here an overview of the work we have performed on spontaneous dimerization of a MoMuLV RNA fragment encompassing the PSI domain in order to understand the mechanism by which retroviral RNA dimerization takes place. We present kinetical, thermodynamical and conformational evidence which leads to the conclusion that the PSI domain is a structurally independent domain and that conformational changes are triggered by the dimerization process. We conclude that at least one particular region (nucleotides 278-309) of the RNA is directly involved in the process while the conformation of some other regions is changed probably because of a long-range effect.

Subunit organization of chromatin from trypanosoma cruzi sensitive and resistant to ethidium bromide.

The chromatin from Trypanosoma cruzi has been analysed from a nuclear preparation after digestion with micrococcal nuclease. The DNA repeat length is found to be equivalent to 185 +/- 5 base pairs. The organization of chromatin in T. cruzi has been compared with that of sensitive trypanosomes treated with ethidium bromide and trypanosomes resistant to ethidium bromide. No differences were found.

A new series of ellipticine derivatives (1-(alkylamino)-9-methoxyellipticine). Synthesis, DNA binding, and biological properties.

A new series of ellipticine derivatives, 1-(alkylamino)-5,11-dimethyl-9-methoxy-6H-pyrido[4,3-b]carbazoles, were synthesized as potential DNA intercalating antitumor drugs. The structure of these compounds were confirmed by 1H NMR spectroscopy and mass spectrometry. These compounds are able to bind to DNA with an affinity of about 10(6) M-1, and their intercalating characteristics (lengthening and unwinding of DNA) depend upon the length of the chain in position 1. The cytotoxicities of these compounds on L1210 and NIH-3T3 cells are quite similar, and fluorescence techniques showed that the compounds are localized mainly in the cytoplasmic granules of the cells. One of these compounds appears to show a very high antitumor activity (equivalent to the more active known ellipticine analogues: 10-[[gamma-(diethylamino)propyl]amino]-6-methyl-5H- pyrido[3',4':4,5]pyrollo[2,3-g]isoquinoleine (BD40), 1-[[gamma-(diethylamino)propyl]amino]-9-methoxyellipticine (BD84) and 2-[beta-(diethylamino)ethyl]-9-hydroxyellipticinium chloride (DEAE).

Interaction of cis-diamminedichloroplatinum (II) to chromatin. Specificity of the drug distribution.

We have studied the interaction of the antitumoral drug, cis-diamminedichloroplatinum (II), cis-DDP, to chromatin. Degradation of chromatin-platinum complexes with micrococcal nuclease releases the platinum bound to the linker DNA. By comparing the percentage of platinum released throughout the digestion to the percentage of acid-soluble DNA we suggest that the linker DNA is the preferential target for this drug. This is mainly the case when the amount of bound platinum is low (r less than 0.03) and is less at higher drug concentrations. By comparing the rate constants corresponding to the reaction of cis-DDP to chromatin, DNA or core particle it appears that these constants are the same. This indicates that the bound platinum is located mainly at the DNA level. Our results are discussed with respect to the structure of chromatin and we conclude that this structure should play a role in the in vivo association of cis-DDP to DNA.

Interaction of an intercalating antitumoral agent: 9-hydroxy-2-methyl ellipticinium (NMHE) with chromatin.

In this work we study the effects of an intercalating antitumoral agent: 9-hydroxy-2-methyl ellipticinium (NMHE) on the structure of chromatin, using micrococcal nuclease and DNase 1 as structural probes. The binding of the drug to chromatin, either in vitro or in the nuclei, induces two structural changes of chromatin: (a) an unfolding of the overall structure which results in an activation of the rate of degradation of chromatin by micrococcal nuclease and (b) a disorganisation of the core particle structure leading to the unwrapping of the DNA from the histone core. Moreover, by studying the interaction of MMHE with nuclei labeled in the active regions of the genome through a nick-translation reaction, it appears that the drug is overconcentrated in these regions and does not induce any new structural changes. The interaction of NMHE with DNase 1-sensitive regions of chromatin indicates that these regions are already "open" or relaxed and represent a preferential target for the drug.

Interaction of cis-diamminedichloroplatinum(II) with sensitive and resistant L1210 cell lines. Drug binding to nuclei and DNA.

We used in parallel, to study the kinetics of cis-DDP cellular binding and distribution, a cL cell culture line established from L1210 murine leukemia ascites and its cLP derivative which acquired a 30-fold (ID50) resistance to cis-diamminedichloroplatinum(II). Cell cultures were incubated with 0.9 microgram/ml (3 microM) of the drug and after various incubation times up to 24 hr, the amount of platinum associated to whole cells, to isolated nuclei and to purified DNA was determined using atomic absorption spectrophotometry. For the first hours of incubation no significant difference in the rate of platinum association was observed between the two cell lines. After the first hours of incubation the amount of platinum associated to whole cells and to isolated nuclei was significantly higher in the drug sensitive cells. However, the rates of platinum association to the respective DNAs were quite similar in the two cell lines. Our study failed to demonstrate any significant quantitative modification of the overall drug-DNA association between the resistant and sensitive cell lines.

Dimer initiation sequence of HIV-1Lai genomic RNA: NMR solution structure of the extended duplex.

The genome of all retrovirus consists of two copies of genomic RNA which are noncovalently linked near their 5' end. A sequence localized immediately upstream from the splice donor site inside the HIV-1 psi-RNA region was identified as the domain responsible for the dimerization initiation. It was shown that a kissing complex and a stable dimer are both involved in the HIV-1Lai RNA dimerization process in vitro. The NCp7 protein activates the dimerization by converting a transient loop-loop complex into a more stable dimer. The structure of this transitory loop-loop complex was recently elucidated by Mujeeb et al. In work presented here, we use NMR spectroscopy to determine the stable extended dimer structure formed from a 23 nucleotides RNA fragment, part of the 35 nucleotides SL1 sequence. By heating to 90 degrees C, then slowly cooling this sequence, we were able to show that an extended dimer is formed. We present evidence for the three dimensional structure of this dimer. NMR data yields evidence for a zipper like motif A8A9.A16 existence. This motif enables the surrounding bases to be positioned more closely and permit the G7 and C17 bases to be paired. This is different to other related sequences where only the kissing complex is observed, we suggest that the zipper like motif AA.A could be an important stabilization factor of the extended duplex.

Effects of the 6-alkyl substitution of ellipticine on the uptake by NIH-3T3 cells and on the cytotoxicity.

New ellipticine derivatives of the 2-methyl ellipticinium (NME) series, i.e. 2,6-dimethylellipticinium (6-Me-NME) and 2-methyl-6-n-propylellipticinium (6-Pr-NME), have been studied as cytotoxic compounds. Their uptake by NIH-3T3 cells and efflux have been measured by a sensitive and specific high performance liquid chromatographic assay. These compounds are equitoxic if we compare their cytotoxicity by two methods: growth inhibition and cloning efficiency. However, they accumulate in NIH-3T3 cells at different steady state levels and the efflux rates are not similar. This raises the question of the mode of action of these drugs.

Relaxation of chromatin structure induced by ethidium binding. Involvement of the intercalation process.

In this paper we study the effects of the binding of ethidium on the structure of chromatin, using micrococcal nuclease as a structural probe. This binding induces two structural changes of chromatin either isolated or in the nuclei. (a) An unfolding of the overall structure which results in an activation of the rate of degradation by the nuclease. (b) A disorganisation of the core particle structure which has the effect of unwrapping the DNA from the histone core, this disruption can go on so far as to leave only 90 base pairs. By comparing the bindings of ethidium and tetramethylethidium, we conclude that the first type of structural change is due to an electrostatic effect and does not depend upon intercalation. On the other hand, the second one is due to the intercalation process and to the change of topological constraints on the DNA that such a process involves.

Poly(rA) binding of alpha-anomeric and beta-anomeric tetrathymidylates covalently linked to an intercalating oxazolopyridocarbazolium. Determination of the binding parameters.

We have investigated by means of absorbance measurements at 310 nm the binding of alpha-anomeric or beta-anomeric tetrathymidylates covalently substituted at their 3' end by an intercalating agent (oxazolopyridocarbazolium), to poly(rA). Taking into account the strong autoaggregation of the free ligands, we have derived the binding parameters corresponding to the [alpha] and the [beta] ligands. The affinity of the alpha-anomer for poly(rA) is higher than the affinity of the beta-anomer in accordance with the Tm studies conducted on such a system.

A kissing complex together with a stable dimer is involved in the HIV-1Lai RNA dimerization process in vitro.

Retroviruses contain a dimeric RNA consisting of two identical molecules of genomic RNA. The interaction between the two monomers is thought to occur near their 5'ends. We previously identified a region upstream from the splice donor site, comprising an autocomplementary sequence, responsible for the formation of dimeric HIV-1Lai RNA [Muriaux, D., Girard, P.-M., Bonnet-Mathonire, B., & Paoletti, J.(1995) J. Biol. Chem. 270,8209-8216]. This region appeared to be confined within a putative stem-loop structure. Here we report an in vitro model under conditions of low inioc strength. Two dimers of RNA 77-402 were identified as a function of temperature, and a significant difference was found in their thermostability. Dimer D55, formed at 55 degrees Celsius, is more stable than dimer D37, formed at 37 degrees C. RNase probing experiments confirm the involvement of a stem-loop structure in the dimerization process. In the monomer, the free G257-CGCGC262 sequence forms a loop in the 240-280 region of RNA 77-402, whereas this sequence is engaged in base pairing when D55 and D37 dimers are formed. Our results show that the loop-loop interaction of the autocomplementary G257CGCGC262 sequence, though hydrogen bonding, is responsible for the formation of dimer D37 and strongly suggest that D37 is a "kissing" complex. In contrast, in dimer D55, all the nucleotides of the two hairpin stems, 243-254/264-277, are involved in a complete interstrand interaction.

An unusually stable purine(purine-pyrimidine) short triplex. The third strand stabilizes double-stranded DNA.

Classical models for DNA triple helix formation assume the stabilization of these structures through the formation of Hoogsteen hydrogen bonds. This assumes that G-rich duplex DNA is more stable than triplex DNA. We report the results of co-migration assay, dimethyl sulfate footprint, and UV spectroscopic melting studies that reveal that at least in some cases of short (13-mer) purine(purine-pyrimidine) triplex the stability of double-stranded DNA is increased by the binding of the third strand. Under conditions which are usually considered as physiological (10 mM MgCl2, 150 mM Na+ or K+) and with a rate of heating/cooling of 1 degrees C/min, there is a good reversibility of the melting profiles which is consistent with a high rate of triplex formation. Other factors than Hoogsteen hydrogen bonds should therefore be involved in triplex stabilization. We suggest that oligonucleotides with similar properties could be efficient agents for artificial gene regulation.

The structure of chromatin: interaction of ethidium bromide with native and denatured chromatin.

The binding of ethidium bromide, as monitored by fluorescence enhancement, to chromatin prepared by nuclease digestion has been compared with the binding of the dye to sheared chromatin. The nuclease preparation (native chromatin) is characterized by a high affinity region of the Scatchard plot (r = 0-0.025, K1 = 1 X 10(6) M-1), a transition (r = 0.025-0.05), and a low affinity region (r = 0.05-0.12, K2 = 3 X 10(5) M-1). The final amount of ethidium bromide bound per base is 0.12 as compared with 0.20 for free DNA. Sheared chromatin has the two regions of high and low affinity (K1 = 2 X 10(6) M-1, K2 = 5 X 10(5) M-1) as originally shown by Angerer and Moudrianakis (1972), but the transition is much reduced or absent. Binding of the dye to native chromatin is independent of salt at concentrations ranging from 0.2 mM EDTA to 10 mM Tris-Cl, 10 mM NaCl, 0.2 mM EDTA, while sheared chromatin and DNA both bind ethidium bromide electrostatically as well as by intercalation at the low salt concentration, leading to extensive energy transfer. Thus the phosphate groups in native chromatin are unavailable to external cations even at very low salt. Polarization of fluorescence of ethidium bromide intercalated into native chromatin at low r is very high, indicating a highly rigid structure. As r approaches 0.02, there is a very rapid depolarization; at r = 0.03, the polarization is no greater than that of the dye intercalated into DNA. Depolarization is not due to energy transfer. The Scatchard plot derived for the bulk preparation of native chromatin is very similar to the one derived for the monomer nu body. These results indicate that the DNA in native chromatin is in a very rigid form, with its phosphate anions neutralized by structural components, not by free salt. Ethidium bromide intercalation appears partially to disrupt this structure, perhaps by unwinding, leading to slight changes in its properties.

Structural features associated with alpha- anomeric in oligo-alpha-thymidylates.

Comparison between gel electrophoresis migrations of oligo-alpha-thymidylates and oligo-beta-thymidylates indicates that the migration of alpha-oligonucleotides under native conditions is different from the migration of beta-oligonucleotides when the number of thymines, part of the sequence, is higher than 5. Such difference disappears when the gels are run under denaturing conditions. This, together with UV spectra, indicates that the structure of alpha-oligonucleotides is more organized than the structure of beta-oligonucleotides and that such an organisation appears for a length higher than 5 monomeric units.