Interaction between proflavine and chemically methylated deoxyribonucleic acid

Impact of linker between triazolyluracil and phenanthridine on recognition of DNA and RNA. Recognition of uracil-containing RNA

A phenanthridine-triazolyluracilyl multifunctional ligand, linked by a lysine–glycine peptide, binds to poly rA–poly rU with micromolar affinity and selective fluorescence response.

The size of the aryl linker between two polyaza-cyclophane moieties controls the binding selectivity to ds-RNA vs. ds-DNA

Aryl-linked (pyridine- vs. phenanthroline-) bis-polyaza pyridinophane scorpiands PYPOD and PHENPOD strongly bind to the double stranded DNA and RNA, whereby very intriguing RNA over DNA selectivity is finely tuned by aryl-linker length and aromatic surface. Moreover, PYPOD and PHENPOD dimer formation at high compound/polynucleotide ratios is highly sensitive to the fine interplay between the steric and binding properties of compound-dimers and the DNA minor groove/RNA major groove. That is demonstrated by significantly different induced CD spectra, which allow spectroscopic differentiation between various DNA/RNA secondary structures. A significantly higher (micromolar) antiproliferative effect of PYPOD and PHENPOD on human cell lines with respect to previously reported pyridine-based tripodal aliphatic polyamines is attributed to masked positive charges and increased hydrophobicity of novel compounds, resulting in more efficient membrane permeation and cellular uptake.

Guanidiniocarbonylpyrrole-aryl derivatives: structure tuning for spectrophotometric recognition of specific DNA and RNA sequences and for antiproliferative activity

We present a systematic study of different guanidiniocarbonylpyrrole-aryl derivatives designed to interact with DNA or RNA both through intercalation of an aromatic moiety into the base stack of the nucleotide and through groove binding of a guanidiniocarbonylpyrrole cation. We varied 1) the size of the aromatic ring (benzene, naphthalene, pyrene and acridine), 2) the length and flexibility of the linker connecting the two binding groups, and 3) the total number of positive charges present at different pH values. The compounds and their interactions with DNA and RNA were studied by UV/Vis, fluorescence and CD spectroscopy. Antiproliferative activities against human tumour cell lines were also determined. Our studies show that efficient interaction with, for example, DNA requires a significantly large aromatic ring (pyrene) connected through a flexible linker to the pyrrole moiety. However, a positive charge, as in 12, is also needed. Compound 12 allows for base-pair-selective recognition of ds-DNA at physiological pH values. The antiproliferative activities of these compounds correlate with their binding affinities towards DNA, suggesting that their biological effects are most probably due to DNA binding.

A novel bis-phenanthridine triamine with pH controlled binding to nucleotides and nucleic acids

The new bis-phenanthridine triamine is characterised by three pK(a) values: 3.65; 6.0 and >7.5. A significant difference in the protonation state of at pH = 5 (four positive charges) and at pH = 7 (less than two positive charges) accounts for the strong dependence of -nucleotide binding constants on nucleotide charge under acidic conditions, whereas at neutral pH all -nucleotide complexes are of comparable stability. All experimental data point at intercalation as the dominant binding mode of to polynucleotides. However, there is no indication of bis-intercalation of the two phenanthridine subunits in binding to double stranded polynucleotides, the respective complexes being most likely mono-intercalative. Thermal stabilisation of calf thymus DNA (ct-DNA) and poly A-poly U duplexes upon addition of is significantly higher at pH = 5 than at neutral conditions. This is not the case with poly dA-poly dT, indicating that the specific secondary structure of the latter, most likely the shape of the minor groove, plays a key role in complex stability. At pH = 5 acts as a fluorimetric probe for poly G (emission quenching) as opposed to other ss-polynucleotides (emission increase), while at neutral conditions this specificity is lost. One order of magnitude higher cytotoxicity of compared to its "monomer" can be accounted for by cooperative action of two phenanthridinium units and the charged triamine linker. The results presented here are of interest to the development of e.g. sequence-selective cytostatic drugs, and in particular for the possibility to control the drug activity properties over binding to DNA and/or RNA by variation of the pH of its surrounding.

Shielding of the D loop of ribosome-bound tRNA by elongation factor G

The topography of the complex of elongation factor G with post-translocative ribosomes has been studied in the Escherichia coli system using fluorescence spectroscopy. We find that a fluorophore attached to the D loop of tRNA is shielded from solvent access by the presence of the factor, and this effect is dependent on factor-promoted GTP hydrolysis. The shielding result suggests that (1) the factor could bind to the tRNA during translocation and (2) the tRNA binding site may be close to that of the factor. The alternative explanation, that the factor affects the conformation of the tRNA bound at a distant site, seems less likely.

Mechanism of ribosomal translocation. tRNA binds transiently to an exit site before leaving the ribosome during translocation

Escherichia coli ribosomes have a site (E) to which deacylated tRNA binds transiently before leaving the ribosome during translocation. The affinity of the site is Mg2+ dependent and low at physiological Mg2+ concentrations. Correct codon-anticodon interaction is unnecessary in this site. With these features, the E site cannot reduce frameshift errors through additional mRNA anchorage. Occupancy of the A site does not influence the tRNA binding in the E site, although a conformational change of elongation factor G, brought about by GTP hydrolysis, is necessary for efficient tRNA release. The tRNA can dissociate unhindered from the E site when the elongation factor is bound to the ribosome by fusidic acid. During elongation, the thermodynamically stable state is not attained, since E site occupation inhibits translocation. However, the E site can aid elongation by providing an intermediate state for tRNA dissociation, dispersing the process into more than one step.

Fluorescence relaxation of proflavin-deoxyribonucleic acid interaction. Kinetic properties of a base-specific reaction

The kinetics of proflavin binding to Micrococcus lysodeicticus deoxyribonucleic acid (DNA [(G-C) content 72%], to Bacillus megaterium DNA [(A-T) content 70%], and to the polydeoxyribonucleotides poly[d(G-C)] and poly[d(A-T)] was studied with fluorescence temperature-jump methods. Poly[d(A-T)] binds proflavin in a two-step reaction with a preequilibrium. Poly[d(G-C)] is characterized by a bimolecular reaction. The binding of acridines to natural DNAs is shown to be characterized by different types of sites whose properties depend on the base composition. The sites have considerable enthalpic differences which result in exchange of dye molecules between them when the temperature is changed. Also, on natural DNAs A-T base pairs are associated with a rapidly equilibrating external complex which is absent or much weaker for G-C base pairs.

Conformation of poly(dG-dC) . poly(dG-dC) modified by the carcinogens N-acetoxy-N-acetyl-2-aminofluorene and N-hydroxy-N-2-aminofluorene

Poly(dG-dC) . poly(dG-dC) was modified by reaction with N-acetoxy-N-acetyl-2-aminofluorene (N-AcO-AAF). Two samples with 6.6% and 8.5% modified bases were prepared. The modified bases are randomly distributed along the polymer chain, as deduced from competition experiments between antibodies against N-2-(guanosin-8-yl)-acetylaminofluorene, modified poly(dG-dC) . poly(dG-dC), and modified DNAs. Circular dichroism studies show that poly(dG-dC) . poly(dG-dC) modified by N-AcO-AAF is much more sensitive to the addition of alcohol than poly(dG-dC) . poly(dG-dC). In about 50% (vol/vol) alcohol, both polynucleotides have the same conformation, which is the Z form or a Z-like form. Moreover, in low salt and in the absence of alcohol, poly(dG-dC) . poly(dG-dC) modified by N-AcO-AAF is partially in the Z form. Poly(dG-dC) . poly(dG-dC) modified by N-hydroxy-N-2-aminofluorene can also adopt the Z form, but the transition is induced at a higher percentage than that of poly(dG-dC) . poly(dG-dC) modified by N-AcO-AAF. In low salt and in the absence of alcohol, no Z form was detected in poly(dG-dC) . poly(dG-dC) modified by N-hydroxy-N-2-aminofluorene.

The induced circular dichroism of proflavine intercalated to DNA. Dye-polymer exciton interactions

The circular dichroism induced in the visible absorption band of proflavine cation isolatedly intercalated to DNA was investigated in terms of the dye-DNA base pair exciton interaction. The remarkable ionic strength dependence of the induced CD magnitude was in good accord with the CD magnitude calculated on the basis of the dye-polymer Frenkel exciton interaction model and under the extent of helix deformation required for intercalation. In particular the application of the internal and modified intercalation models coupled with the deep trap approximation implied that the preference of the modified intercalation due to electrostatic interaction between the acridine-nitrogen atom and the DNA phosphate group is combined with relatively high ionic strength compared with the internal intercalation.

The role of the AT pairs in the acid denaturation of DNA

It has been determined previously that the protonation of the GC pairs induces a DNA conformation change which leads to a "metastable" structure. The role of the AT pairs, however, is no well known because the protonation does not modify their spectral properties. By means of an indirect method based on the binding of proflavine, it has been determined that the AT pairs are protonated before the acid-induced denaturation and that they seem to be unable to assume a conformation change when protonated. These results would indicate that the protonated AT pairs may be responsible for the induction of the acid denaturation and not the GC pairs as it was thought previously.

Base specificity in the inhibition of oncornavirus reverse transcriptase and cellular nucleic acid polymerases by antitumor drugs

Adriamycin, daunomycin, acridylmethanesulfonanilide, and alkoxybenzophenanthridine alkaloids (coralyne acetosulfate, fagaronine chloride, and nitidine chloride) inhibit template-directed nucleic acid polymerizing enzyme activities like reverse transcriptase, DNA polymerase, and RNA polymerase. Enzyme reactions with poly(dA-dT), poly(rA)-oligo(dT) and poly(dA)-oligo(dT) are more strongly inhibited by the drugs than those with poly(dC)-poly(dG) and poly(rC)-oligo(dG). These results suggest that the antitumor drugs inhibit nucleic acid polymerases by a specific interaction with A:T base pairs of the templates.

Effect of DNA base composition on the intercalation of proflavine. A kinetic study

The effect of DNA base composition on the kinetics of the association between DNA and proflavine has been investigated using the temperature jump relaxation method. It is found that, regardless of the G + C base composition the results fit a two step mechanism, the second of which exhibits characteristics of intercalation of proflavine into DNA. However, they two equilibrium constants corresponding to these steps, KI and KII, depend on the nature of the DNAs. The constant KI is found to be an order of magnitude greater for M. lysodeikticus DNA (72% G + C) than for calf thymus DNA (48% G + C). Increasing G-C content thus appears to favor the intermediate non-intercalated complex of proflavine with DNA. Methylation of M. lysodeikticus DNA with dimethyl sulfate, preferentially yielding N7 methyl guanine as the modified base, again leads to an apparent two step mechanism, with the value of KI unchanged with respect to untreated DNA, while the affinity of proflavine for the intercalated complex measured by the value of KII increases for methylated DNA.