Translesional synthesis on DNA templates containing the 2'-deoxyribonolactone lesion.

A site-specifically modified oligonucleotide containing a single 2'-deoxyribonolactone lesion was used as a template for primer extension reactions catalyzed by M-MuLV reverse transcriptase (RT) and by the Klenow fragments of Escherichia coli DNA polymerase proficient (KF exo(+)) or deficient (KF exo(-)) in exonuclease activity. Analysis of the extension products in the presence of the four dNTPs or of a single dNTP showed that the M-MuLV RT was completely blocked and did not incorporate any dNMP opposite 2'-deoxyribonolactone. KF exo(-) preferentially incorporated nucleotides opposite the lesion following the frequency order dAMP > dGMP >> dTMP approximately dCMP and thus appeared to obey the 'A rule' for preferential incorporation as has been shown previously for the 2'-deoxyribose abasic site. In the sequence context examined, the primer extension by KF exo(-) appeared to be less efficient when dAMP was positioned opposite the lesion as compared with dTMP or dGMP. These two nucleotides promoted a more efficient polymerization accompanied by nucleotide deletion through misalignment incorporations. We therefore predict that the sequence context may strongly influence the translesional synthesis by KF exo(-) and thus the miscoding and mutational potential of the 2'-deoxyribonolactone in E.coli.

One-dimensional GIS-based model compared with a two-dimensional model in urban floods simulation.

A GIS-based one-dimensional flood simulation model is presented and applied to the centre of the city of Nîmes (Gard, France), for mapping flow depths or velocities in the streets network. The geometry of the one-dimensional elements is derived from the Digital Elevation Model (DEM). The flow is routed from one element to the next using the kinematic wave approximation. At the crossroads, the flows in the downstream branches are computed using a conceptual scheme. This scheme was previously designed to fit Y-shaped pipes junctions, and has been modified here to fit X-shaped crossroads. The results were compared with the results of a two-dimensional hydrodynamic model based on the full shallow water equations. The comparison shows that good agreements can be found in the steepest streets of the study zone, but differences may be important in the other streets. Some reasons that can explain the differences between the two models are given and some research possibilities are proposed.

Evaluation by women consulting in a family planning centre of their risk of HIV infection.

In order to assess women's self-perception of their risk of infection by HIV, research was performed among 654 women who had consulted in a family planning centre in the Paris region. Of the 452 (69%) women who took part in this research, 77% considered themselves as 'not at risk of carrying the AIDS virus', 11% as 'at risk' and 12% did not give a specific answer. The most important risk factors noted by the patient and the doctor were found to be the number of partners, the use of syringes and the non- or faulty use of condoms. Estimates of the risk of infection by physicians had a high correlation with those of the women, although there were wide differences between the opinions of the six doctors involved. In one case out of three the doctors were unable to decide whether or not their patient was at risk. The evident difficulties experienced by these physicians show an urgent need for the development of specific medical training programmes. The seroprevalence of 2.4% of HIV infection among the women studied, and 1.1% of those who consulted during the study period, confirm the importance of carrying out specific studies on women consulting in family planning centres.

Synthetic models of DNA complexes with antimalarial compounds. 2. The problem of guanine specificity in chloroquine binding.

Stacking interactions between the aminoquinoline ring of the antimalarial chloroquine and the purine bases have been studied by preparing and examining models in which the quinoline is linked to the base by a trimethylene chain. The degree of stacking of the models which reflects the strength of the interaction was quantitatively determined in water at different temperatures by hypochromism measurement in the uv. Adenine and guanine exhibit equal affinity for the quinoline nucleus as reflected by very close hypochromism values observed for the two models at all temperatures studied.

Synthetic models of deoxyribonucleic acid complexes with antimalarial compounds. 3. Forces involved in the stacking interaction between aminoquinoline and the nucleotide bases.

As an approach to the problem of the nature of the forces responsible for the stacking interactions between the aminoquinoline ring of the antimalarial chloroquine and the monomeric nucleotide bases, we have examined models in which the aromatic nucleus of the drug is linked to the nucleotide bases by a trimethylene chain. The degree of stacking of the models was determined in different conditions of solvent, pH, and temperature by hypochromism measurement in the UV. The results show that forces of the donor-acceptor type, due to the presence of a positive charge on the quinoline ring at neutral pH, do not bring an important contribution to the stacking interaction between the aminoquinoline and the nucleotide bases, while the influence of the solvent water is fundamental.

Search for DNA repair inhibitors: selective binding of nucleic bases-acridine conjugates to a DNA duplex containing an abasic site.

The abasic site is one of the most frequent DNA lesions generated by spontaneous or enzymatic cleavage of the N-glycosidic bond. The abasic site is also an intermediate in the nucleotide and base excision DNA repair. We examined molecules which recognize and cleave DNA at the abasic site with high efficiency. These molecules incorporate in their structure a nucleic base for abasic site recognition, an intercalator for DNA binding, and a polyamino linker for ionic interaction and DNA cleavage. Such compounds, by interfering with abasic sites in DNA, are also inhibitors of DNA repair. In order to better understand the parameters of the interaction, we carried out a UV thermal denaturation study of synthetic oligonucleotides containing the lesion both in the absence and in the presence of the drugs. A similar study was also carried out using the corresponding nonmodified oligonucleotide. The results indicate selective binding of the base-chain-intercalator conjugates to the abasic site containing oligonucleotides.

Abasic site recognition in DNA as a new strategy to potentiate the action of anticancer alkylating drugs?

Inhibition of abasic site repair in the cell seems an attractive strategy to potentiate the action of antitumor DNA alkylating drugs. Molecules that bind specifically and strongly to the abasic site are possible candidates to achieve such inhibition. We explored this strategy by preparing molecule 4 that incorporates (1) an aminoacridine intercalator for DNA binding, (2) an adenine moiety for abasic site recognition, and (3) a linker containing two guanidinium functions to increase binding to DNA without inducing cleavage at the base-sensitive abasic site. Compound 4 was compared to analogues containing secondary amines, i.e., 1. We report on synthesis of the new heterodimer 4. We show by physicochemical studies-including determination of association constants with calf-thymus DNA, T(m) measurements, and high-field NMR examination of the complexes formed with abasic DNA duplexes-that 4 binds specifically and more strongly to the abasic site than the analogues. Compound 4 does not cleave abasic plasmid DNA. Compound 4 shows apparent synergy with the anticancer bischloroethylnitrosourea (BCNU) in L1210 and A549 cell lines in vitro. It potentiates BCNU in the in vivo tests. The results favor the pertinence of the strategy.

Reversible photocycloaddition of a 4',5'-dihydropsoralen derivative with thymine.

The photocycloaddition reaction between a 4',5'-dihydropsoralen derivative and thymine was studied in solution using a synthetic bichromophoric model 8 in which the two rings are associated by a tetramethylene chain. In water this model molecule exhibits intramolecular ring-ring stacking interactions as evidenced by UV and NMR spectroscopies. Irradiation at 365 nm at usual concentrations (greater than or equal to 5.10(-4) M) leads exclusively to a regio- and stereo-selective dimerization reaction involving the 3,4 double bonds of the psoralen moities. Extreme dilutions (ca less than or equal to 2.10(-5) M) were necessary to observe the intramolecular reaction which results in the exclusive formation of a 3,4 cis-anti adduct. This reaction is completely reversed by irradiation at 254 nm. These results are discussed with regard to the behavior of the homologous models in which the furan part of the psoralen ring is not hydrogenated. These latter compounds also lead exclusively to a 3,4 cis-anti adduct. It appears that saturation of the furan ring increases strongly the quantum yield of the photoaddition at 365 nm (0.01----0.18) and that the triplet excited state of the 4',5'-dihydropsoralen is involved in the photoaddition.

Molecular modelling study of DNA-Troeger's bases interactions.

The two enantiomeric forms: 1R,5R (R) and 1S,5S (S) of the Troeger's base analog, 9,19-methano-9,10,19,20-tetrahydrodiacridino-[b,f]-[1,5]- diazocine which possess a C2 axis of symmetry, are susceptible to interact differently with DNA. This paper reports the results of molecular modelling calculations on B DNA-Troeger's base complexes. Two interaction modes have been examined: intercalation and binding in the grooves. Into the limits of accuracy of such a kind of calculations, some tendencies seem to appear. In the intercalation mode, the R and S enantiomers exhibit a selectivity for alternating dinucleotidic sequences and the minor groove is enantioselective for S. Binding in the major groove is selective for S with G-C sequences, and in the minor groove the stereoselectivity appears for R with A-T sequences. The S-(dG-dC)5.(dG-dC)5 complex in the major groove seems to be the most favoured.

Aminothiols linked to quinoline and acridine chromophores efficiently decrease 7,8-dihydro-8-oxo-2'-deoxyguanosine formation in gamma-irradiated DNA.

In a search for more active radioprotective compounds, we have prepared and examined a series of model molecules in which the radioprotective beta-aminothiol unit (free or derivatized as acetate or phosphorothioate) is tethered to the DNA-binding chromophores quinoline and acridine through links of variable length. The modifying activity of these 'hybrid' molecules was estimated by measuring the formation of 8-oxo-2'-deoxyguanosine (8-oxodGuo) in double-strand DNA upon exposure to gamma-rays in oxygen-free solution in the presence of the drugs. We show that all hybrid molecules protect the guanine moiety from oxidation more efficiently than the parent beta-aminothiol units. The degree of protection is the highest for the molecules in which the thiol is linked to the strong binding intercalator acridine through a long polyaminochain.

Identification of 4-acetoxyaminoquinoline from the hydrolysis of 1-acetoxy-4-acetoxyimino-1,4-dihydroquinoline, in vitro and in vivo properties.

4-Acetoxyaminoquinoline (Ac-4-HAQ) (1) was identified as a hydrolysis product of 1-acetoxy-4-acetoxyimino-1,4-dihydroquinoline (diAc-4-HAQO). The reaction allowing the obtention of (1) obeys to a reduction mechanism implying the N1-O cleavage. The carcinogenic properties of (1) observed by Sato et al. (Japan J. Exp. Med., 40 (1970) 475) in mice were studied in rats with the in vivo system we used previously with 4-nitroquinoline-1-oxide (4-NQO) and 4-hydroxyaminoquinoline-1-oxide (4-HAQO). In rats (1) does not covalently bind DNA. It was, therefore, possible to propose an interpretation of the results obtained by Enomoto et al. (Proc. Soc. Exp. Biol. Med., 136 (1971) 1206) who injected diAc-4-HAQO s.c. to mice and rats. Compound 1 could be responsible for the carcinogenic effects observed through the following pathway: (1) should be formed by hydrolysis of diAc-4-HAQO and reactivated by an enzymatic system to N-oxide derivative, the 4-acetoxyaminoquinoline-1-oxide (Ac-4-HAQO), which constitutes an ultimate carcinogen model of 4-NQO.

Fluorescent labelling of oligodeoxyribonucleotides by the oxyamino-aldehyde coupling reaction.

We describe the reaction of oligonucleotides containing an aldehydic group at the 5'-end or inside the sequence with an oxyamino label. The reaction was found to be highly selective and represents an efficient method for derivatization of oligonucleotides.

Labeling during cleavage of nucleic acids for their detection on DNA chips.

A new and efficient strategy for labeling of nucleic acids prior to their hybridization on high density DNA chip has been developed. Our approach which combines the fragmentation and the labeling is based on the reactivity of the terminal phosphates of cleaved DNA and RNA fragments with a reporter molecule bearing aryldiazomethane group.

Use of an aminooxy linker for the functionalization of oligodeoxyribonucleotides.

We describe the preparation of oligonucleotides containing a 5'-linker bearing an aminooxy group. Use of the trityl protecting group for the aminooxy moiety allows purification of the modified oligonucleotide by reverse phase HPLC and cleavage in mild acidic conditions. Derivatization with an aldehydic reporter group is efficient and rapid.

Interaction of a spin-labeled adenine-acridine conjugate with a DNA duplex containing an abasic site model.

The abasic site is a common lesion in DNA that is also formed as an intermediate in the base excision repair of damaged bases. We have previously reported the adenine-acridine conjugate 1 that was designed to bind to the abasic site and interfere with the repair process. High-field NMR had shown that 1 forms specific complexes with a DNA duplex containing an apurinic abasic site model. We report here the dynamics of the interaction of the nitroxide-labeled analogue 3 of the conjugate 1 with the same apurinic oligonucleotide and with the parent unmodified duplex. Identical study of the labeled acridine subunit 5 used as a reference is also reported. In the presence of the apurinic duplex and depending on the concentrations and drug ratios, three species are observed: the radical "free in solution", the "intercalation" complex characterized by its similarity to that observed in the presence of the parent unmodified duplex, and the "abasic-site-specific" complex which is the sole species visible at low drug ratios. The experimental data reinforced by molecular modeling of the complex and theoretical calculation of correlation times suggest (i) the most immobilized form corresponds to that observed by NMR and (ii) complexation of the drug is little or not modified by the spin-label. We also show that the abasic site constitutes a binding site for the propylaminoacridine intercalator 5.

Formation of a cyclic adenine adduct with a 4-nitroquinoline N-oxide metabolite model.

Pentacyclic adducts are obtained in the reaction of adenine derivatives with the diacetyl ester of 4-hydroxyamino quinoline oxide, the postulated metabolite of the potent carcinogen, 4-nitroquinoline N-oxide (4-NQO).

Enantiospecific recognition of DNA sequences by a proflavine Tröger base.

The DNA interaction of a chiral Tröger base derived from proflavine was investigated by DNA melting temperature measurements and complementary biochemical assays. DNase I footprinting experiments demonstrate that the binding of the proflavine-based Tröger base is both enantio- and sequence-specific. The (+)-isomer poorly interacts with DNA in a non-sequence-selective fashion. In sharp contrast, the corresponding (-)-isomer recognizes preferentially certain DNA sequences containing both A. T and G. C base pairs, such as the motifs 5'-GTT. AAC and 5'-ATGA. TCAT. This is the first experimental demonstration that acridine-type Tröger bases can be used for enantiospecific recognition of DNA sequences.