Versatile strategy for oligonucleotide derivatization. Introduction of lanthanide(III) chelates to oligonucleotides.

[reaction: see text] Novel nucleosidic phosphoramidite blocks were synthesized by a Mitsunobu reaction between 2'-deoxy-5'-O-(4,4'-dimethoxytrityl)uridine and a primary alcohol containing a conjugate group in its structure (a protected functional group, an organic dye, or a precursor of a lanthanide(III) chelate) followed by phosphitylation. They were used in machine-assisted DNA synthesis in the standard manner. A slightly modified deprotection procedure was used for the preparation of oligonucleotide conjugates tethered to lanthanide(III) chelates. For the latter application one non-nucleosidic block was also synthesized.

Reactions of N,N-bis(2-chloroethyl)-p-aminophenylbutyric acid (chlorambucil) with 2'-deoxyguanosine.

N,N-Bis(2-chloroethyl)-p-aminophenylbutyric acid (chlorambucil, 1) was allowed to react in the presence of 2'-deoxyguanosine (16 mM) at physiological pH (cacodylic acid, 50% base), and the reactions were followed by HPLC/MS/MS techniques. Although the predominant reaction observed was chlorambucil hydrolysis, ca. 24% of 1 reacted with different heteroatoms of the nucleoside. As expected, the principal site of 2'-deoxyguanosine alkylation was N7. Alkylation of N7 caused spontaneous depurination, and N-(7-guaninylethyl)-N-hydroxyethyl-p-aminophenylbutyric acid (5) and the corresponding N7,N7-bis-adduct (6) were the major stable dGuo derivatives. Also several other adducts were detected and tentatively identified by means of MS/MS and UV. From them, the O(6-), N1-, N(2-), and O5'-derivatives can be biologically significant. Our results shed new light on DNA modifications caused by chlorambucil, which is an important chemotherapeutic drug and a known carcinogen.

Polymyxin permeabilization as a tool to investigate cytotoxicity of therapeutic aromatic alkylators in DNA repair-deficient Escherichia coli strains.

Chlorambucil (CLB; N,N-bis(2-chloroethyl)-p-aminophenylbutyric acid) and its biologically active beta-oxidation product phenylacetic acid mustard (PAM; N,N-bis(2-chloroethyl)-p-aminophenylacetic acid) are bifunctional aromatic alkylators. CLB is in wide clinical use as an anticancer drug and also as an immunosuppressant. The chemical structures indicate that CLB and PAM are mutagenic, teratogenic and carcinogenic, but the mode of action has remained obscure. We have investigated the biological effects of CLB and PAM with DNA repair-deficient Escherichia coli strains. In contrast to MNNG (N-methyl-N'-nitro-N-nitrosoguanine), CLB and PAM were not toxic to E. coli, but permeabilization of the outer membrane of the cells through use of polymyxin B nonapeptide (PMBN) rendered them susceptible to these compounds. The importance of DNA repair, shown by reversal of damage and attenuation of the toxicity of CLB and PAM, was indicated by the susceptibility of cells lacking O(6)-methylguanine-DNA methyltransferase I and II (ada ogt). Similarly, the protective role of base excision repair (BER) was substantiated by demonstration of an even more increased susceptibility to CLB and PAM of cells lacking 3-methyladenine-DNA glycosylase I and II (alkA1 tag-1). Cells deficient in mismatch repair (mutS) appeared to be slightly more sensitive than normal cells to CLB and PAM, although no such sensitivity to MNNG was observed. This implicates the role of mismatches in CLB- and PAM-related cytotoxicity. It is generally believed that bifunctional alkylating agents, like CLB and PAM, exert their cytotoxic action via DNA cross-linking. Our results with O(6)-methyltransferase- and 3-methyladenine-DNA glycosylase-deficient cells indicate that removal of the adducts prior to the formation of cross-links is an important mechanism maintaining cell viability. We conclude that PMBN permeabilization provides a valuable tool to investigate genetically engineered E. coli cells, whose outer membrane is not naturally permeable to mutagens or other interesting compounds.

Role of thiocyanate ion in detoxification of the anticancer agent chlorambucil.

N,N-Bis(2-chloroethyl)-p-aminophenylbutyric acid (chlorambucil, 1) is an orally administrated drug widely used in the chemotherapy of chronic lymphocytic leukemia. We have recently described a new metabolic path for the decomposition of 1 in human gastric juice based on its reactions with saliva-derived thiocyanate ion. We report here our quantitative data on the reactions of thiocyanate ion with CLB in various fluid matrixes at 37 degreesC. The rate of decomposition of 1 is zero-order with respect to SCN- concentration up to 100 mM. However, thiocyanate ion reacts ca. 18 300 times faster than water with the aziridinium ion derived from 1 at neutral and acidic pH. When the SCN- concentration was greater than 10 mM, practically no N,N-bis(2-hydroxyethyl)-p-aminophenylbutyric acid, 4, the product of chlorambucil hydrolysis, could be detected. Thiocyanate ion also effectively overcompensates for the rate retardation caused by Cl-; 10 mM SCN- is enough to decrease the effect of 0.5 M chloride ion to one-half. This is an important factor in human gastric juice where the chloride ion concentration is normally high.

Detoxification of an alkylating drug, N,N-bis(2-chloroethyl)-p-aminophenylbutyric acid (chlorambucil), in human gastric juice and saliva.

N,N-Bis(2-chloroethyl)-p-aminophenylbutyric acid (chlorambucil, 1) is an orally administered drug widely used in the chemotherapy of chronic lymphocytic leukemia. It is converted in gastric juice into three stable metabolites, which were characterized as N,N-bis(2-hydroxyethyl)-p-aminophenylbutyric acid (4), N-(2-hydroxyethyl)-N-[2-(thiocyano)ethyl]-p-aminophenylbutyric+ ++ acid (5), and N,N-bis[2-(thiocyano)ethyl]-p-aminophenylbutyric acid (6). 4 is the product of chloroambucil hydrolysis, while 5 and 6 are results of the reaction of 1 with saliva-derived thiocyanate ion. The destabilizing effect of low gastric oxonium ion concentration on 1 is also demonstrated.

Synthesis of carbon-3-substituted 1,5,9-triazacyclododecanes, RNA cleavage agents suitable for oligonucleotide tethering.

Two derivatives of 1,5,9-triazacyclododecane bearing an alkylamino tether group at carbon-3 (7 and 13) were synthesized. The first of them, 7, was prepared starting from diethyl 2-(2-cyanoethyl)malonate and the second one, 13, from glycerol. In both cases, the cyclization reaction was performed by allowing the corresponding ditosylates (5 and 12) to react with TBD. The guanidinium salts formed were reduced in situ to the orthoamides (6 and 12), acid-catalyzed hydrolysis of which yielded the title compounds. The suitability of the azacrowns prepared for oligonucleotide tethering is also demonstrated.

Kinetics of chlorambucil in vitro: effects of fluid matrix, human gastric juice, plasma proteins and red cells.

The mechanisms involved in the bioavailability of chlorambucil or 4-[p-(bis[2-hydroxyethyl]amino)phenyl]-butyric acid are poorly understood. The effects of different matrices on the disintegration of chlorambucil were investigated by HPLC, 1H NMR, 31P NMR, and mass spectrometry. Cellular incorporation and protein binding of the drug in vitro was assessed with [3H]-chlorambucil. Decomposition of chlorambucil and its major metabolite, phenylacetic acid mustard, to mono- and dihydroxy derivatives, was significantly faster in water than in PBS, (phosphate-buffered saline, pH 7.4). The hydrolysis of chlorambucil was as fast in plasma ultrafiltrate as in PBS; plasma proteins, preferentially albumin, prevented this disintegration. In phosphate-buffered media, two additional stabile hydrolysis products were found which were characterised as the mono- and bis-phosphates of 4-[p-(bis[2-hydroxyethyl]amino)phenyl]butyric acid, results of the reaction of nucleophilic buffer species with the aziridinium ion intermediates. Chlorambucil bound covalently to plasma proteins and was incorporated into red cells. These interactions are likely to have a significant role in vivo, reducing the bioavailability of the drug. High H+ concentration associated with high chloride concentration in human gastric juice had a stabilizing effect on chlorambucil. Incorporation of [3H]-chlorambucil into red cells was inhibited in a concentration-dependent fashion by whole human plasma as well as by albumin. We conclude that the chemico-biological interactions demonstrated in the present investigation provide explanations for the remarkable pharmacokinetic differences observed intra- and inter-individually in the clinical use of chlorambucil. The present information is important, when clinical or in vitro evaluation of efficacy and bioavailability of chlorambucil is considered.

Looped oligonucleotides form stable hybrid complexes with a single-stranded DNA.

Several new branched (1, 2), circular (9) and looped oligonucleotides (14-17) were synthesized. 3'-Deoxypsicothymidine was employed to create the site of branching when required. The circular and looped structures were obtained by oxidative disulfide bond formation between mercaptoalkyl tether groups. All the oligonucleotides prepared contained two T11 sequences, and the branched and looped oligomers an additional alternating CT sequence. The melting experiments revealed that the branched oligonucleotides form relatively weak hybrid (double/triple helix) complexes with the single-stranded oligodeoxyribonucleotide, showing a considerable destabilizing effect produced by the structure at the point of branching. The data obtained with looped oligonucleotides demonstrated considerable stabilization of the hybrid (double/triple helix) complexes with the complement. The data reported may be useful in attempting to design new antisense or antigene oligonucleotides capable of forming selective and stable bimolecular hybrid complexes with nucleic acids.

Synthesis and primer properties of oligonucleotides containing 3'-deoxypsicothymidine units, labeled with fluorescein at the 1'-position.

Several analogues of the standard M13 sequencing primer that contain up to five 3'-deoxypsicothymidines, or one or two such units labeled with fluorescein at the 1'-position, have been prepared. All these oligonucleotides have been shown to prime the DNA-polymerase-catalyzed synthesis of DNA.

Bisulfite ion-catalyzed transamination of cytosine residues with alpha, omega-alkanediamines: the effect of chain length on the reaction kinetics.

Pseudo-first-order rate constants for the bisulfite ion-catalyzed transamination of cytidine with 1,2-ethanediamine, 1,3-propanediamine, 1,4-butanediamine, and 1,6-hexanediamine have been determined. Hydrolytic deamination has been shown to compete with transamination under acidic conditions, but is of minor importance at pH > 5.3 when the total concentration of diamine is greater than 0.2 mol dm-3. The dependence of the transamination rate on pH and the concentration of diamine and bisulfite ion indicates that the major reaction involves nucleophilic attack of the diamine monocation on the N3 protonated bisulfite adduct of cytidine. The effect of the chain length of the diamine on the rate of transamination is discussed, and the results are compared with those obtained by reacting single-stranded DNA with the same diamines and labeling the transaminated product with a europium chelate.