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Biomedical subjects

G Dodin

Publications and source records attributed to G Dodin.

At least 19 recordsLinked to original sources
PubMed2000

Fourier and wavelet transform analysis, a tool for visualizing regular patterns in DNA sequences.

A correlation function that compares each base in a DNA sequence to its various neighbours and which is subsequently processed by Fourier and wavelet transforms has been developed. The procedure has been applied to sequences from the human chromosome 22, to nef genes from various HIV clones and to myosin heavy chain DNA. It permits to readily visualize regular features in DNA which are related to the stability of heteroduplexes formed upon strand slippage.

Animals↗
PubMed1999

Conformational variation of the central CG site in d(ATGACGTCAT)2 and d(GAAAACGTTTTC)2. An NMR, molecular modelling and 3D-homology investigation.

The determination of the solution structure of two self-complementary oligomers d(ATGACGTCAT)2 (CG10) and d(GAAAACGTTTTC)2 (CG12), both containing the 5'-pur-ACGT-pyr-3' sequence, is reported. The impact of the base context on the conformation of the central CpG site has been examined by a combined approach of: (a) 2D 1H-NMR and 31P-NMR; (b) molecular mechanics under experimental constraints; (c) back-calculations of NOESY spectra and iterative refinements of distances; and (d) 3D-homology search of the central tetrad ACGT within the complete oligonucleotides. A full NMR study of each fragment is achieved by means of standard 2D experiments: NOESY, 2D homonuclear Hartmann-Hahn spectroscopy, double-quantum-filtered COSY and heteronuclear 1H-31P correlation. Sugar phase angle, epsilon-zeta difference angle and NOE-derived distances are input as experimental constraints to generate molecular models by energy minimization with the help of jumna. The morass program is used to iteratively refine the structures obtained. The similarity of the two ACGTs within the whole oligonucleotides is investigated. Both the decamer and the dodecamer adopt a B-like DNA conformation. However, the helical parameters within this conformational type are significantly different in CG12 and CG10. The central CpG step conformation is not locked by its nearest environment (5'A and 3'T) as seen from the structural analysis of ACGT in the two molecules. In CG12, despite the presence of runs of A-T pairs, CpG presents a high twist of 43 degrees and a sugar phase at the guanine of about 180 degrees, previously observed in other ACGT-containing-oligomers. Conversely, ACGT in CG10 exhibits strong inclinations, positive rolls, a flat profile of sugar phase, twist and glycosidic angles, as a result of the nucleotide sequence extending beyond the tetrad. The structural specificity of CG10 and its flexibility (as reflected by its energy) are tentatively related to the process of recognition of the cyclic AMP response element by its cognate protein.

Base Sequence↗
PubMed1999

Impact of C5-cytosine methylation on the solution structure of d(GAAAACGTTTTC)2. An NMR and molecular modelling investigation.

The solution structures of d(GAAAACGTTTTC)2 and of its methylated derivative d(GAAAAMe5CGTTTTC)2 have been determined by NMR and molecular modelling in order to examine the impact of cytosine methylation on the central CpG conformation. Detailed 1H NMR and 31P NMR investigation of the two oligomers includes quantitative NOESY, 2D homonuclear Hartmann-Hahn spectroscopy, double-quantum-filtered COSY and heteronuclear 1H-31P correlation. Back-calculations of NOESY spectra and simulations of double-quantum-filtered COSY patterns were performed to gain accurate information on interproton distances and sugar phase angles. Molecular models under experimental constraints were generated by energy minimization by means of the molecular mechanics program JUMNA. The MORASS software was used to iteratively refine the structures obtained. After methylation, the oligomer still has a B-DNA conformation. However, there are differences in the structural parameters and the thermal stability as compared to the unmethylated molecule. Careful structural analysis shows that after methylation CpG departs from the usual conformation observed in other ACGT tetramers with different surroundings. Subtle displacements of bases, sugars and backbone imposed by the steric interaction of the two methyl groups inside the major groove are accompanied by severe pinching of the minor groove at the C-G residues.

5-Methylcytosine↗
PubMed1997

Induction of mitochondrial dysfunction and apoptosis in HeLa cells by bis-pyridinium oximes, a newly synthesized family of lipophilic biscations.

When tested on HeLa cells, bis-pyridinium oximes (BPO), a family of newly synthesized molecules whose charged pyridinium moieties are linked by a linear polymethylene chain of variable length (N = 3 to 12) have been shown to possess an inhibitory effect on cell growth and finally to provoke cell death. BPO-affected cells displayed reduced mitochondrial oxygen consumption and ATP stores and were blocked in the G1 phase of the cell cycle. Mitochondrial membrane potential, as assayed with the dye 3,3'-diexyloxacarbocyanine iodide [DiOC6(3)], increased in BPO-treated cells with time of exposure. Cell growth inhibition as well mitochondrial dysfunction were observed only with derivatives having a long polymethylene linking chain (N > or = 6). Furthermore, the concentration of the compound eliciting such effects was inversely related to the number of methylene groups in the linking chain. None of the BPO with N = 6 to 12 modified the mitochondrial DNA content, relative to the nuclear DNA content. In BPO (N = 8 and N = 12)-treated cells, chromatin fragmentation and internucleosomal DNA cleavage occurred massively, indicating that the death mode induced by these compounds is apoptosis. The possible pathway of action and the potential pharmacological interest of these compounds are discussed.

Adenosine Triphosphate↗
PubMed1993

The linking chain length in bridged aldehyde-substituted pyridinium dimers modulates a slow reversible binding that affects supercoiling of plasmid DNA.

Bridged aldehyde substituted pyridinium dimers bind to DNA. Binding induces retardation of the electrophoretic migration of circular plasmid due to relaxation of supercoiling. Binding to DNA is slow and reversible and depends on the length of linking chain, pH, ionic strength and temperature. It is postulated that release of topological stress results from the disruption of hydrogen bonding between complementary bases, a hypothesis consistent with facilitated attack of DNA by formaldehyde promoted by the bridged compounds.

Animals↗
PubMed1992

The binding of bridged bis-pyridinium oximes to DNA and its relevance to the induction of mitochondrial dysfunction in yeast.

Bis-pyridium oximes and methoximes from a newly synthesized series are weak DNA binders (K = 3.10(4) M-1 under physiological conditions). From the number of binding sites per phosphate, 0.25, the ionic strength dependence of the binding constant and the negative electric dichroism, it is concluded that monointercalation is the mode of association. In contrast to methoxy compounds, the oxime derivatives are able both to induce the mutated "petite" phenotype in yeast S. cerevisiae and to cause "in vitro" extensive condensation of single stranded DNA. This reaction is postulated to be relevant to the mutational process that leads to "peptide" cells. The absence of nuclear mutation is interpreted in terms of sequestration of the drug in mitochondria under the effect of the organelle inner membrane electrochemical potential.

Animals↗
PubMed1991

Mitochondrial uptake of bridged bis-methylpyridinium aldoximes and induction of the "petite" phenotype in yeast.

The 3,3'-[omega,omega'-alkanediylbis(oxy)]bis[2- (hydroxyimino)methyl]-1-methylpyridinium derivatives bearing a linking chain of 4, 5 and 6 methylene groups are accumulated in mitochondria with increasing efficiency under the effect of the electrical potential. Accumulation does not take place with derivatives carrying a 2 and 3 methylene-long linking chain. The uptake process is saturable. The efficiency of the various derivatives to induce the "petite" phenotype in yeast reflects the uptake rate observed with purified mitochondria.

DNA Damage↗
PubMed1991

Thermodynamics of drug-DNA interactions: entropy-driven intercalation and enthalpy-driven outside binding in the ellipticine series.

Viscosimetric and kinetic results allow one to characterize three modes of DNA binding in the ellipticine series: (1) Ellipticine and its 9 methoxy derivative, which present maximal DNA lengthening properties and bind DNA through a single step mechanism, can be considered as pure intercalators. (2) Ellipticinium derivatives and short-chain substituted oxazolopyridocarbazoles, which present intermediate DNA lengthening properties, bind DNA through a two-step mechanism, one being intercalation. (3) Long-chain substituted oxazolopyridocarbazole derivatives, which display the smallest DNA lengthening properties, bind DNA through a single-step mechanism, probably resulting from an outside binding mode. The viscosimetric and kinetic results are compared with the thermodynamic results obtained from the temperature dependence of the binding constants. It appears that drugs binding on the outside of the DNA double helix tend to have large enthalpy and small entropy contributions, whereas pure intercalating drugs have contributions from both enthalpy and entropy, with entropy dominating by about 2:1. Drugs showing two binding modes exhibit a continuum between the aforementioned extremes, with no breaks in behavior. From this comparison, a correlation between thermodynamic data and DNA binding modes is proposed. Possible molecular implications of both enthalpy and entropy to DNA binding free energy are discussed.

Buffers↗
PubMed1990

Ditercalinium, a nucleic acid binder, inhibits the respiratory chain of isolated mammalian mitochondria.

Ditercalinium (a 7H-pyridocarbazole dimer) has been designed to bisintercalate into double-stranded DNA with high affinity. In this paper we provide evidence for inhibitory interactions of ditercalinium with electron transport in isolated rat liver mitochondria. It is shown that ditercalinium probably inhibits the electron transfer between membrane cytochrome c and oxygen (cytochrome c oxidase activity) and the electron transfer between the matrix side of inner membrane (Complexes II and III) and membrane cytochrome c. The level of inhibition of the last oxidation step of the respiratory chain appears to be highly dependent on the drug/membrane diphosphatidylglycerol ratio. It is suggested that the mechanism of cytochrome c oxidase inhibition by ditercalinium could be due to the complexation with the diphosphatidylglycerol environment essential for its activity rather than to a drug-enzyme direct interaction. This hypothesis is strengthened by experiments with pure cytochrome oxidase. Therefore, the interaction of ditercalinium with diphosphatidylglycerol may be envisaged as one factor, among others, responsible for its hepatotoxicity.

Animals↗
PubMed1990

Binding of ellipticine to beta-lactoglobulin. A physico-chemical study of the specific interaction of an antitumor drug with a transport protein.

The unprotonated form of the anti-tumor alkaloid ellipticine binds to beta-lactoglobulins A and B from bovine milk with an affinity constant of 7 +/- 3 x 10(5) M-1. There is one binding site/dimeric protein molecule (the stable form at medium pH). The attachment site is not the beta-barrel nor the hydrophobic site identified as the retinol site in beta-lactoglobulin but a domain located at the interface of the two monomeric units where the ligand lies close to Trp61 of both polypeptide chains. The positive binding enthalpy observed in temperature-jump relaxation experiments is overcome by a strong entropy increase, tentatively thought to result from water release at the binding domain. Accordingly, desolvation is assumed to be the rate-determining step in the process of ellipticine binding.

Animals↗
PubMed1990

Acid-base properties of ellipticine bound to DNA, micelles and liposomes.

We have determined the acid-base properties of the alkaloid ellipticine, bound to DNA and to micelles and liposomes, taken as models for membranes, in the prospect of characterizing the actual structure of the bound ligand, this being relevant to the mode of action of the drug. The acid-base properties of ellipticine bound to sonicated calf thymus DNA and SDS micelles are similar as regards their pK values and their dependence on NaCl concentrations. This observation is satisfactorily understood in terms of sodium ion condensation around the negative phosphate and sulphate groups. The slope of pK vs log(Na+) is -1, a value predicted by Friedman theory. The pK of ellipticine bound to cationic (CTAB, DDTAB) or to neutral (Triton X100) micelles and to neutral liposomes (PC) is significantly lower than water (7.4), and, in contrast to the situation in DNA and SDS micelles, does not vary with addition of NaCl. Interestingly, this result is good evidence for ellipticine having a specific pK when bound to a hydrophobic structure. This view is likely to hold for ellipticine bound to DNA.

Alkaloids↗
PubMed1990

Kinetic and thermodynamic studies on drug-DNA interactions in the ellipticine series.

The temperature-jump (T-jump) method has been used to investigate the binding mechanism to calf-thymus DNA of ellipticine and some of its derivatives. The results show that the plant alkaloid, ellipticine, interacts with DNA at a unique intercalation site whereas most of its synthetic derivatives, such as ellipticinium, 9-hydroxy-ellipticinium and related alkyl-oxazolopyridocarbazoles recognize two distinct DNA sites. Parallel analysis of kinetic data and DNA lengthening abilities of these derivatives suggests that only one of these two DNA sites is an intercalation site. Owing to the determination of the genuine number of drug-DNA complexes (inferred from T-jump experiments) and with the results of thermodynamic investigations (Van't Hoff plots), further characterization of the molecular interactions involved in the binding process was proposed. Thus, the formation of the unique intercalation complex of ellipticine was found to be entropy driven whereas binding of drugs which recognize the second class of binding sites was essentially enthalpy driven. These different thermodynamic behaviors suggest that intercalation essentially results from hydrophobic solvent structure effects in contrast to the second binding mode which principally arises from hydrogen bonding interactions through DNA grooves.

Alkaloids↗
PubMed1989

The G.C base-pair preference of 2-N-methyl 9-hydroxyellipticinium.

Among the DNA-intercalating drugs in the ellipticinium series, 9-hydroxy derivatives elicit the highest antitumoral properties. In water these drugs display a very low fluorescence quantum yield. Replacement of H2O by D2O partially restores the fluorescence of the ellipticinium chromophore. The possibility that such a proton-exchange mechanism could be involved in a base-recognizing process at the DNA level (and therefore be responsible for some base preference) was examined by direct fluorescence titration in deuterated buffer and DNA/drug fluorescence energy transfer. These experimental approaches provide mutually consistent results showing that the 9-hydroxylated drug recognizes specific DNA sites that are not recognized by the non-hydroxylated drug. When compared to 2-N-methyl ellipticinium, the 2-N-methyl 9-hydroxyellipticinium presents: (1) higher binding constants for each DNA studied; (2) a base dependence of the fluorescence properties of the bound form (fluorescence increment upon DNA binding varying over 5-11); (3) a base dependence of its DNA affinity constants (1.1-3.3 x 10(6) M-1) and of its site size (exclusion parameters varying over 3.0-4.4); (4) a base dependence of its energy transfer from DNA bases. Analysis of the binding data suggests that the 9-hydroxyl group of 2-N-methyl ellipticinium is responsible for a G.C base-pair preference, the preferred binding site being a doublet sequence of two adjacent G.C which could be flanked either by a additional G.C base pair or by an A.T base pair.

Alkaloids↗
PubMed1989

Dynamics and thermodynamics of the counterion effect in a 7H-pyridocarbazole dimer (ditercalinium). Hypothesis of a nonbisintercalative binding mode to calf thymus DNA at high drug/base ratio.

Ditercalinium, a 7H-pyridocarbazole dimer designed to bisintercalate into DNA, forms tight ion pairs in water with inorganic and organic anions. The thermodynamics and kinetics of the acetate-ditercalinium pairing has been investigated by means of T-jump spectroscopy. The formation of the pair has a constant estimated to 1000 M-1 and proceeds via a fast two-step mechanism with a relaxation time of 12 microseconds (acetate pH 5) to 50 microseconds (cacodylate, pH 7.5) involving an intermediate solvent-separated ion pair. A strong association of ditercalinium to cardiolipid has been observed and is expected to be involved in the respiratory chain inhibition induced by ditercalinium (unpublished results). Direct estimates of the binding constants of the drug to calf thymus DNA were obtained by means of UV titrations at high drug/base ratio (greater than 0.17). The maximum number of binding sites per base both at pH 5 and pH 7.5 was found to be 0.22, a value consistent with monointercalation as expected from the prediction of Shafer's model for the interaction of bifunctional ligands to DNA. This work also supports the hypothesis that significant ionic binding may account for the ditercalinium/DNA interaction at high base/drug ratios (0.2).

Carbazoles↗
PubMed1988

Binding of ellipticine base and ellipticinium cation to calf-thymus DNA. A thermodynamic and kinetic study.

The acid-basic properties of ellipticine have been re-estimated. The apparent pK of protonation at 3 microM drug concentration is 7.4 +/- 0.1. The ellipticine free base (at pH 9, I = 25 mM) intercalates into calf-thymus DNA with an affinity constant of 3.3 +/- 0.2 X 10(5) M-1, and a number of binding sites per phosphate of 0.23. The ellipticinium cation (pH 5, I = 25 mM) binds also to DNA with a constant of 8.3 +/- 0.2 x 10(5) M-1 and at a number of binding sites (n = 0.19). It is postulated that the binding of the drug to DNA at pH 9 is driven by hydrophobic and/or dipolar effects. Even at pH 5, where ellipticine exists as a cation, it is thought that the hydrophobic interaction is the main contribution to binding. The neutral and cationic forms share common binding within DNA sites but yield to structurally different complexes. The free base has 0.04 additional specific binding sites per phosphate. As determined from temperature-jump experiments, the second-order rate constant of the binding of the free base (pH 9) is 3.4 x 10(7) M-1 s-1 and the residence time of the base within the DNA is 8 ms. The rate constant for the binding of the ellipticinium cation is 9.8 x 10(7) M-1 s-1 when it is assumed that drug attachment occurs via a pathway in which the formation of an intermediate ionic complex is not involved (competitive pathway).

Alkaloids↗
PubMed1988

Dynamics of drug-DNA interactions: a comparative temperature jump study of ellipticinium and 9-hydroxy ellipticinium.

The temperature-jump method has been used to compare the binding of 2-N methyl ellipticinium (NME) and 2-N methyl 9 hydroxy ellipticinium (NMHE) to three natural DNA's of different AT/GC composition. The relaxation signals, analyzed by the Padé-Laplace method, are characterized by two distinct relaxation times, tau 1 and tau 2, respectively in the 1-4 ms and 20-80 ms range. In the case of the NMHE/DNA interaction, the slower relaxation time tau 2 depends on the DNA composition, as follows: tau 2 (Micrococcus lysodeikticus) greater than tau 2 (Calf thymus) greater than tau 2 (Clostridium perfringens). Contrary to NMHE, NME which does not possess an OH group at the C-9 position, shows no relaxation time dependence upon DNA base composition. The observation of two relaxation times indicates that the binding equilibria are associated with at least two distinct drug/DNA complexes (probably arising from two distinct DNA binding sites). Three kinetic models, involving the formation of a weak intermediate ionic complex, are given to explain the binding reaction between these cationic drugs and the DNA. They allow the determination of the four rate constants associated with the two binding steps and lead to equilibrium association constants in agreement with those obtained from spectroscopic studies. The validity of the models is discussed and it is shown that the best kinetic scheme, for either NMHE or NME, could be that in which the ionic step is not a prerequiste to intercalation. The kinetic results show that the residence time of 9 hydroxy ellipticinium is markedly increased in GC rich DNA's and this could be related to the higher in vitro and in vivo cytotoxic properties of 9 hydroxy substituted ellipticines.

Alkaloids↗
PubMed1986

Heteroduplex stabilities in highly repetitive DNA. An hypothesis for the polymorphism of Plasmodium parasite antigenic response.

Codon repeats encountered in DNA sequences may formally lead to several double-stranded structures of similar stabilities. This is observed in the highly repetitive sequences of some Plasmodium antigens (S-antigen, CS proteins). It is postulated that gene recombination may occur via various heteroduplex molecules thus leading to antigenic polymorphism of Plasmodium parasites.

Animals↗