Role of actinomycin pentapeptides in actinomycin-deoxyribonucleic acid binding and kinetics

Interaction of actinomycin D with promoter element of c-met and its inhibitory effect on the expression of c-Met

c-Met, the tyrosine kinase receptor for hepatocyte growth factor plays a pivotal role in normal cellular signaling and overexpression of c-Met protein is reported in several human cancers. Thus, transcriptional regulation of c-met appears to be an attractive target for chemotherapy. Therefore, we selected a 24mer GC rich sequence (24R) from the c-met promoter located at -142 to -119 from transcription start site and studied its interaction with anticancer drug, Actinomycin D. Spectroscopic analysis demonstrated a strong complexation between ActD and 24RY as shown by: (i) a high binding constant, K of 4-5 x 10(5) M(-1) with DeltaDeltaG of -47 +/- 1.5 Kcalmol(-1); (ii) marked increase by +10 degrees C in melting temperature of 24RY; and (iii) significant changes in circular dichroic spectra of both ActD and 24RY. Molecular modeling revealed the preference of ActD to the Sp1 binding site, GGCGGG, in 24RY. Expression of the c-Met was checked in HepG2 cells, a human hepatocellular carcinoma cell line by using western blotting and immunocytochemistry. Downregulation of c-Met expression by as much as 50% was observed in the presence of 20ng/ml (IC(50)) of ActD. Taking into account of the binding studies also, we feel that the down regulation of c-Met perhaps involves binding of ActD to the promoter site of c-met. Therefore, c-met could be a challenging and promising target for therapeutic strategies in combating cancer.

Visualising the kinetics of dissociation of actinomycin from individual sites in mixed sequence DNA by DNase I footprinting

We have investigated the kinetics of dissociation of actinomycin D from DNA by a variation of the footprinting technique. Complexes of actinomycin with a radiolabelled DNA fragment (tyrT) were dissociated by addition of a large excess of unlabelled calf thymus DNA and the mixture subjected to DNase I footprinting at subsequent intervals. The rates at which the footprints disappeared varied between the different binding sites. The dissociation was temperature dependent with average time constants of 30 s, 10 mins and 2 hours at temperatures of 37 degrees C, 20 degrees C and 4 degrees C respectively. The dissociation from a DNA fragment containing the synthetic insert T9GCA9 was significantly faster, with a half-life of about 1 min at 20 degrees C. In contrast, the dissociation of distamycin was too fast to measure (< 5 s) even at 4 degrees C.

Reassessment of structural characteristics of the d(CGCG)2:actinomycin D complex from complete 1H and 31P NMR

Complexes formed between Actinomycin D (ActD) and the tetranucleotides d(AGCT)2 and d(CGCG)2 were studied in detail by one and two-dimensional 1H and 31P NMR. The 31P two dimensional chemical exchange experiment, at room temperature on saturated complexes (1:1), showed unambiguously that the asymmetrical phenoxazone ring binds to the unique GC site under the two possible orientations in the d(AGCT)2 tetranucleotide but adopts a single orientation in the d(CGCG)2 tetranucleotide. For the d(CGCG)2:Act D saturated complex, complete assignments of all protons and phosphorus signals of the two-nucleotide strands, as well as of the two cyclic pentapeptide chains has allowed us to study in details the conformational features of the complex from NOE and coupling constants analysis. The tetranucleotide remains in a right-handed duplex, but the sugar puckers are modified for residues at the intercalation site. A uniform C2' endo pucker is observed for residues on the strand facing the quinoid side of the phenoxazone ring while a C2' endo-C3-endo equilibrium about 60% of C2' endo is proposed for the two residues on the strand facing the benzenoid side of the phenoxazone ring. In contrast to previous studies on ActD-DNA interactions, we have been able to measure the 3J phosphorus-proton coupling constants at the intercalation site but also adjacent to it, showing that 31P chemical shifts are not simply related to the backbone conformation. Molecular mechanics calculations, using empirical distances deduced from NOE effects as restrained distances during minimizations, led to a model differing mainly from those previously published by orientation of the N methyl groups of both N-Methyl-Valines.

Collisional activation decomposition of actinomycins using tandem mass spectrometry

The collisional activation (xenon) decomposition of actinomycin V, dactinomycin, 7-nitrodactinomycin, 7-aminodactinomycin, and a mixture of dactinomycin, actinomycin C1 and actinomycin C2 was studied using a triple-quadrupole mass spectrometer with fast atom bombardment (xenon) ionization. Fragmentation pathways of the structurally significant ions were rationalized by assuming an initial McLafferty rearrangement at the ester linkage between the methylvaline and the threonine of both rings to form linear pentapeptides, followed by fragmentation in either pentapeptide yielding typical sequence ions and sequence cleavages from both rings.

Sequence-specific assignments and their use in NMR studies of DNA structure

There has been a surge of recent interest, reflected by a sharp increase in the number of publications, in the area of high-resolution nuclear magnetic resonance (NMR) studies of DNA. The goal of many of these studies is to monitor the structure of biologically important DNA sequences directly in solution; the impetus for such studies was the realization, from early single-crystal X-ray structures, that nearest-neighbor context effects are a major determinant of local structure in short double-helical DNAs (Dickerson & Drew, 1981; Dickerson, 1983). Thus, instead of the previously assumed regular averaged structure of the double helix derived from fibre diffraction analysis, the more interesting concept emerged that specific sequence-dependent distortions from ‘classical’ DNA structure might be responsible for the recognition of such sequences by a variety of ligands such as repressors, polymerases, drugs, etc.

Kinetic evidence for redistribution of actinomycin molecules between potential DNA-binding sites

The kinetics of interaction between actinomycin D and DNA have been measured by stopped-flow and detergent-dissociation methods. The results are consistent with a model in which the antibiotic initially binds to many sequences on the heterogeneous DNA lattice and subsequently 'shuffles' between the available sites until a thermodynamically determined optimal state of binding is attained. The amplitudes of the two slowest components in the reaction with calf thymus DNA do not vary in parallel as the total level of antibiotic binding is increased; they appear to reflect directly the redistribution of antibiotic molecules along the DNA lattice. The dissociation profile is shown to depend upon the time for which the antibiotic and DNA are premixed, so that for short mixing times a higher proportion of the decay is represented by faster-dissociating species. The rate of appearance of the slowest-dissociating species correlates well with the slowest optical change in the association reaction. Stopped-flow experiments indicate that the antibiotic first binds to sites on natural DNA with an average association constant of 4 X 10(3) M-1 and that it subsequently migrates to sites with higher affinity. Similar experiments performed with poly(dG-dC) are less easily interpreted and seem to indicate that conformational changes or cooperative effects can also occur.

Aqueous solution structure of an intercalated actinomycin D-dATGCAT complex by two-dimensional and one-dimensional proton NMR

Two-dimensional NOESY and COSY 1H NMR techniques have been employed to determine the conformation of the complex formed by actinomycin D and the hexanucleoside pentaphosphate dATGCAT. One-dimensional NOE experiments in H2O confirmed the intact nature of the oligonucleotide double helix within the complex. The drug chromophore was intercalated between the GC base pairs, with the pentapeptide lactones nestled in the minor groove. No significant conformational change of the pentapeptide lactones between bound and free drug was observed.

31P NMR and viscometric studies of the interaction of meso-tetra(4-N-methylpyridyl) porphine and its Ni(II) and Zn(II) derivatives with DNA

The interactions of meso-tetra(4-N-methylpyridyl) porphine (TMPyP) and its Zn(II) and Ni(II) derivatives with DNA have been investigated by 31P NMR and viscometric titrations. TMPyP and its Ni derivative increase the viscosity of linear DNA, cause unwinding and reverse coiling of superhelical DNA, and induce a separate downfield peak in the 31P NMR spectrum of DNA. The Zn derivative slightly decreases the viscosity of linear DNA, does not unwind superhelical DNA, and does not give a downfield NMR peak. The main DNA 31P NMR signal is shifted slightly upfield on either the addition of TMPyP or the Ni compound. These results indicate that TMPyP and the Ni(II), but not the Zn(II), derivative bind to DNA by intercalation.