A few different methods for the preparation of oligonucleotide N-alkylphosphoramidates were compared directly. One of these, involving the use of protected nucleoside phosphites as building blocks, provided the requisite N-alkylphosphoramidates via oxidation of the intermediate dinucleoside methyl phosphites with iodine in the presence of the appropriate alkylamine. This method was found to have several attractive features, including the use of building blocks identical with those employed for the synthesis of DNA and compatibility with procedures and instruments employed for the stepwise synthesis of oligonucleotides by solution and solid-phase methods. This procedure was used to make several di-, tri-, and tetranucleotide N-alkylphosphoramidates derived from deoxyadenosine and thymidine; alkyl substituents included N,N-dimethyl, N-butyl, N-octyl, N-dodecyl, and N-(5-aminopentyl). The aminoalkyl derivative of d(TpT) (24) was used to demonstrate the feasibility of introducing an intercalative agent to the alkylphosphoramidate moiety of such derivatives. The oligonucleotide N-alkylphosphoramidates were separated into their component diastereomers and characterized structurally by a number of techniques including circular dichroism, high-field 1H NMR spectroscopy, FAB mass spectrometry, and enzymatic digestion to authentic nucleosides and nucleotides. Physicochemical characterization of several di- and trinucleotide alkyl-phosphoramidates revealed that the adenine nucleotide analogues formed stable complexes with poly-(thymidylic acid). The stabilities of these complexes were found to increase with increasing chain length of the N-alkylphosphoramidate substituents. The finding that N-alkylphosphoramidate substituents can enhance the binding of certain oligonucleotides to their complementary polynucleotides suggests the existence of a novel source of polynucleotide affinity.

The unwinding of plasmid DNA by bleomycin A2 (BLM A2) was investigated by use of two-dimensional gel electrophoresis. It was found that Cu2+ ions greatly facilitated the unwinding of topoisomers of plasmid DNA by BLM A2 at concentrations where cupric ions alone had no effect on DNA supercoiling. The concentration of BLM A2 required for observable unwinding was reduced at least 100-fold in the presence of equimolar Cu2+. A plot of [Cu2+] vs extent of DNA unwinding in the presence of 10(-4) M BLM A2 gave a curve consistent with the action of cupric ions on BLM in an allosteric fashion, possibly rearranging the drug into a conformation that facilitates DNA unwinding. The participation of the metal center in enhancing DNA unwinding via direct ionic interaction with one or more negatively charged groups on the DNA duplex also seems possible. Further analysis of the structural factors required for BLM-mediated DNA unwinding was carried out with Cu2+ + BLM demethyl A2, the latter of which differs from BLM A2 only in that it lacks a methyl group, and associated positive charge, at the C-terminus. Cu(II).BLM demethyl A2 was found to be much less effective than Cu(II).BLM A2 as a DNA unwinding agent, emphasizing the strong dependence of this process on the presence of positively charged groups within the BLM molecule. These findings constitute the first direct evidence that the metal center of BLM can participate in DNA interaction, as well as in the previously recognized role of oxygen binding and activation.

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Molecules that interact with DNA under the influence of light can function by a variety of mechanisms.' These include some that alkylate DNA via photocycloaddition2 and others that form active oxygen species,3 contain a photoreactive metal enter,^ or function via electron transfer.5 Photochemical DNA-cleaving agents have been used to probe nucleic acid structure,4 as prosthetic groups for antisense oligonucleotides,6 as designed "photonu-~leases",~ and as photofootprinting agents.8Of particular interest is the DNA strand scission by photoactivated promazine derivatives, believed to involve three distinct mechanisms.9 When tested at 80 pM concentration, chlorpromazine was the most active of the derivatives studied, apparently due to a reactive intermediate resulting from C-Cl bond homolysis. Presently, we describe three chlorinated bithiazole derivatives (3-5) structurally related to bleomycin A5 (1) which mediate light dependent DNA cleavage at remarkably low concentrations.Preparation of bithiazoles 3-5 was accomplished starting from the N-t-Boc derivative of methyl 2'-(2-aminoethyl)-2,4'-bithiazole-4-carbox yla te; O conversion to the chlorinated bi thiazoles was then accomplished1 by lithiation

Electrospray ionization mass spectrometry (ESI-MS) has been used to characterize the covalent binding of different haptens to the enzyme glucose 6-phosphate dehydrogenase. The technique allows one to directly observe the relative amounts of each conjugated species present in a mixture, as well as the average hapten number. These measurements are useful for optimizing reaction conditions to yield a more precisely defined product for use in immunoassays. The results obtained show that ESI-MS with a quadrupole analyzer can be successfully used to analyze mixtures of derivatized proteins in the molecular weight range of 50-60 kDa, where the modifying hapten has a molecular weight as low as 130 Da.