7-Aminoactinomycin D is a potent inhibitor of RNA polymerase and it has been demonstrated to bind to a single stranded DNA. Wadkins and Jovin showed that there is a 20 to 40 fold enhancement in the fluorescence of 7-aminoactinomycin D upon binding to certain single stranded DNA sequences. We report studies of the thermodynamics of the binding of the parent drug, actinomycin D, to single and double stranded DNA. A five-fold range of association constants is found for the different binding sequences that we have investigated. We will correlate these thermodynamic studies with measurements of the fluorescence enhancement, lifetime, and rotational correlation time of the drug bound to the various single and double stranded oligonucleotides.

Strong binding of the antitumor antibiotic actinomycin D to the sequence 5'-TGGGT-3' in double-stranded DNA was recently established by equilibrium binding studies (Bailey et al., 1993). Actinomycin D binding to this -TGGGT- containing sequence was shown to be comparable to that of an -XGCY- containing oligonucleotide (Ka approximately 10(6) M-1). Investigation of -TGGGT- as a high-affinity binding site for actinomycin D follows from our 1989 sequencing study (Rill et al., 1989) in which the photoaffinity analog of actinomycin D (7-azidoactinomycin D) was used to determine DNA base sequence specificities and neighboring base effects. The studies presented here examine the guanine requirements for actinomycin D binding to such nonclassical (non-dGpC) sites by varying the number of central guanine residues in a series of selected duplex oligonucleotides. The central -T(G)nT- motif varies from n equals 1 to 4. Actinomycin D binding to each of these undecamers is characterized and correlated with binding to oligonucleotides of identical length and similar sequences that contain classical dGpC binding sites. Binding affinities of actinomycin D to this series of oligonucleotide duplexes (10 degrees C) can be summarized as -TGGGT- > -TGGT- > TGGGGT- > -TGT. The kinetics of SDS-induced dissociation of actinomycin D from these oligonucleotides reveal single-exponential decays with duration dependent on the sequence at the binding site. With the exception of the -TGGGT- containing oligomer, dissociation times for the T(G)nT duplexes were drastically different and much shorter than times obtained for the dissociation of actinomycin D from oligonucleotides having classical dGpC sites.(ABSTRACT TRUNCATED AT 250 WORDS)

The influences of base sequence on the thermodynamic properties associated with the interaction of actinomycin D with DNA are examined. It has been previously established that GpC steps of double-helical DNAs are highly preferred binding sites for actinomycin D. In this study, a series of oligonucleotides was designed and synthesized to probe the effects of flanking base sequence (adjacent to the GpC step) and novel non-GpC binding sites on the binding of actinomycin D. The use of these oligonucleotides provides a direct method for quantitating sequence specificities and actinomycin D binding energetics. Effects of different 5' and 3' flanking nucleotides on the interactions of actinomycin with the core GpC binding sites were examined using UV-visible spectrophotometric methods, and changes in binding energetics were quantitated. These studies demonstrate strong actinomycin D binding affinities to both classical GpC and an atypical non-GpC site. Enthalpy and entropy components of the DNA binding energetics for the GpC binding sites are compared and correlated with those determined for actinomycin D binding to the high-affinity non-GpC site of an 11-mer containing TGGGT as the central sequence. This TGGGT site, first suggested to be a high-affinity sequence in our earlier photoaffinity labeling studies, exhibits binding of actinomycin D comparable in strength to that of traditional actinomycin D binding sites (i.e., GpC steps). From these studies, the overall affinity and specific thermodynamic contributions (delta H degree, delta S degree) to binding of actinomycin D are demonstrated to be highly influenced both by the sequence at the intercalation site and by neighboring bases which flank the intercalation site.

Arsenic doped silica glass (ASG) is a material which is well known to the electronics industry, due to its use in integrated circuit manufacture as a conformal covering for circuitry. We report here, for the first time, the use of ASG as a low loss waveguiding material. The guiding films were made by a CVD process, carried out between 400 and 450 °C. Three inch silica and thermal oxide coated silicon substrates were used. The thermal oxide layer was between 2 μm and 10 μm thick. Typical films which have been investigated were 1.5-2 μm thick and had a refractive index of about 1.51 at 632.8 nm, corresponding to an As2O3 content of approximately 10 mol%. They have also been patterned using standard photolithographic techniques. The properties of planar films and ridge waveguides will he discussed. We present results of loss measurements made by prism coupling into planar films and from end-fire launching into ridge guides. The scattered light was detected using a computer controlled camera system. Typically, we have measured a loss of 0.50 dBcm-1 with ±5% error for the lowest order TE mode in a planar film at 632.8 nm. The effects of reflow of the ASG on the measured loss of the guides will he illustrated. The potential for reducing this loss and the use of ASG as a passive waveguide material in integrated optics will also he discussed.