[Binding of actinomycin C 3 to mono, di, and oligonucleotides]

Kinetic studies of drug-dinucleotide complexes

Three classes of kinetic behavior are observed in the complexes of actinomycin or ethidium with deoxydinucleotides. First, the initial dinucleotide binding to form a 1:1 complex is a rapid bimolecular process, whose rate could be measured for combination of actinomycin with d(pTpG) d(pGpT), d(pGpA), d(pGpG) d(pCpGpG), and d(pCpG) andfor combination of ethidium with d(pGpC). Second, with one exception, all reactions in which a second dinucleotide is added to form a 2:1 dinucleotide-drug complex are limited by a first-order step at high concentration. This class includes the combination of actinomycin with all dinucleotides tested except d(pGpC), and the reaction of ethidium with nucleotides of complementary sequence pyrimidine-purine, such as d(pCpG). The final class is the special case of d(pGpC) interacting to form a 2:1 complex with actinomycin. Third-order kinetics is observed, with no evidence for a first-order, rate-limiting step.

NMR studies of the structure and stability of the 1 : 2 actinomycin D-d-pG-C complex in aqueous solution

We describe NMR studies at superconducting fields which characterize aspects of the structure and stability of the 1 : 2 actinomycin-d-pG-C complex in solution as monitored at the Watson-Crick base pairs and backbone phosphate groups. Two guanine N1H resonances (12.17 and 11.66 ppm) are observed in the 360 MHz proton NMR spectra of the complex in water at -4 degrees C. These slowly exchangeable resonances, which demonstrate the presence of two Watson-Crick G + C base pairs in the complex, broaden in a sequential manner with increasing temperature. The terminal and internucleotide phosphates of both d-pG-C molecules are observable in the 145.7 MHz 31P spectra of the 1 : 2 actinomycin-d-pG-C complex at 0 degrees C. The internucleotide phosphate resonance at 1.905 ppm broadens prior to that at 2.385 ppm with increasing temperature, consistent with a sequential breakage of the G + C base pairs in the complex. The lifetime of the complex (4.5 +/- 0.5 X 10(-4) s, 33 degrees C) was deduced from the variation of the d-pG-D internucleotide 31P resonance line width on gradual addition of the antibiotic in solution.

The interaction of actinomycin C3 and actinomine with DNA. A small-angle x-ray scattering study

Small-angle X-ray scattering was applied to solutions of calf thymus DNA and calf thymus DNA complexed with various amounts of actinomycin C3 or actinomine in phosphate-saline buffer at pH 6.9 and I equals 0.2. From the measurements of DNA in the absence of dye, two cross-section radii of gyration of R-c equals 0.875 plus or minus 0.015 nm and R-c2 equals 0.81 plus or minus 0.02 nm, and a mass per unit length of M/l equals 1906 plus or minus 43 daltons/nm resulted. The investigation of DNA complexed with dye revealed a decrease of the cross-section radii of gyration as compared to those for the DNA in the absence of dye and a relatively low increase of the mass per unit length on binding of actinomycin and a slight decrease of M/l on binding of actinomine. The latter results are interpreted on the basis of a length increase of the DNA double helix by 0.47 plus or minus 0.03 nm per actinomycin molecule and by 0.355 plus or minus 0.03 nm per actinomine molecule bound. The results for R-c and R-c2 obtained for the various samples of complexed DNA were extrapolated to the limiting binding ratio where each dye molecule is associated with a minimum of six nucleotide pairs. According to this extrapolation, the cross-section radii of gyration of such a complex would amount to (R-c)b equals 0.805 plus or minus 0.015 nm and (R-c2)b equals 0.76 plus or minus 0.015 nm for the complex with actinomycin, and to (R-c)b equals 0.77 plus or minus 0.015 nm and (R-c2)b equals 0.75 plus or minus 0.01 nm for the actinomine complex. On the basis of a core and shell model for solvated DNA, these results can be understood as to indicate a decrease of the radial dimensions of both the core and the shell when the dye is bound. The experimental results are compared with theoretical data calculated from the atomic coordinates of the detailed intercalation model for the actinomycin - DNA complex as recently proposed by Sobell and Jain. The model proves to be consistent fairly well with our data on the length increase of the double helix, but it appears to be unable to explain the experimentally observed decrease of R-c2 on binding of dye.