Interaction between proflavine and guanosine 5'-phosphate: importance of photoexcitation

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.

Mechanisms of quenching of the fluorescence of a benzo[a]pyrene tetraol metabolite model compound by 2'-deoxynucleosides

The hydrophobic interactions of bulky polycyclic aromatic hydrocarbons with nucleic acid bases and the formation of noncovalent complexes with DNA are important in the expressions of the mutagenic and carcinogenic potentials of this class of compounds. The fluorescence of the polycyclic aromatic residues can be employed as a probe of these interactions. In this work, the interactions of the (+)-trans stereoisomer of the tetraol 7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene (BPT), a hydrolysis product of a highly mutagenic and carcinogenic diol epoxide derivative of benzo[a]pyrene, were studied with 2'-deoxynucleosides in aqueous solution by fluorescence and UV spectroscopic techniques. Ground-state complexes between BPT and the purine derivatives 2'-deoxyguanosine (dG), 2'-deoxyadenosine (dA), and 2'-deoxyinosine (dI) are formed with association constants in the range of approximately 40-130 M(-1). Complex formation with the pyrimidine derivatives 2'-deoxythymidine (dT), 2'-deoxycytidine (dC), and 2'-deoxyuridine (dU) is significantly weaker. Whereas dG is a strong quencher of the fluorescence of BPT by both static and dynamic mechanisms (dynamic quenching rate constant k(DYN) = [2.5 +/- 0.4] x 10(9) M(-1)s(-1), which is close to the estimated diffusion-controlled value of approximately 5 x 10(9) M(-1)s(-1), both dA and dI are weak quenchers and form fluorescence-emitting complexes with BPT. The pyrimidine derivatives dC, dU, and dT are efficient dynamic fluorescence quenchers (k(DYN) approximately [1.5-3.0] x 10(9) M (-1)s(-1), with a small static quenching component due to complex formation evident only in the case of dT. None of the four nucleosides dG, dA, dC and dT are dynamic quenchers of BPT in the triplet excited state; the observed lower yields of triplets are attributed to the quenching of single excited states of BPT by 2'-deoxynucleosides without passing through the triplet manifold of BPT. Possible fluorescence quenching mechanisms involving photoinduced electron transfer are discussed. The strong quenching of the fluorescence of BPT by dG, dC and dT accounts for the low fluorescence yields of BPT-native DNA and of pyrene-DNA complexes.

The role of ground state complexation in the electron transfer quenching of methylene blue fluorescence by purine nucleotides

The effect of three purine nucleotides on the fluorescence of methylene blue in aqueous buffer has been investigated. Guanosine-5'-monophosphate (GMP) and xanthosine-5'-monophosphate cause fluorescence quenching while adenosine-5'-monophosphate causes a red shift in the fluorescence maximum. All three nucleotides form ground state complexes with the nucleotides as indicated by absorption spectroscopy. The fluorescence changes at nucleotide concentrations less than 30 mM are best described by a static mechanism involving the formation of non-fluorescent binary and ternary complexes in competition with dimerization of the dye. Quenching of the fluorescence decay (tau = 368 ps) at high GMP concentrations (10-100 mM) occurs at the rate of diffusion. The mechanism of fluorescence quenching may involve electron transfer within the singlet excited dye-nucleotide complex although published values of the oxidation potentials of various purine derivatives would suggest that all three nucleotides should cause quenching. Evidence for electron transfer was obtained from flash photolysis experiments in which 100 mM GMP was found to cause the appearance of a long lived transient species absorbing in the region expected for semimethylene blue.

Interactions of the dimethyldiazaperopyrenium dication with nucleic acids. 1. Binding to nucleic acid components and to single-stranded polynucleotides and photocleavage of single-stranded oligonucleotides

The binding of dimethyldiazaperopyrenium dication (1) with nucleosides, nucleotides, and single-stranded polynucleotides has been studied by photophysical methods. It has been shown that 1 may be a potential selective fluorescent probe for A- and/or T-rich polynucleotides. 1 efficiently cleaves oligonucleotides at guanine sites, under illumination with visible light, and therefore may be used as a sequence-specific artificial photonuclease.

Fluorescence decay studies of the DNA-3,6-diaminoacridine complexes

The interaction of several 3,6-diaminoacridines with DNAs of various base composition has been studied by steady-state and transient fluorescence measurements. The acridine dyes employed are of the following two classes: class I - proflavine, acriflavine and 10-benzyl proflavine; class II - acridine yellow, 10-methyl acridine yellow and benzoflavine. It is found that the fluorescence decay kinetics follows a single-exponential decay law for free dye and the poly[d(A-T)]-dye complex, while that of the dye bound to DNA obeys a two-exponential decay law. The long lifetime (tau 1) for each complex is almost the same as the lifetime for the poly[d(A-T)]-dye complex, and the amplitude alpha 1 decreases with increasing GC content of DNA. The fluorescence quantum yields (phi F) of dye upon binding to DNA decrease with increasing GC content; the phi F values for class I are nearly zero when bound to poly(dG) X poly(dC), but those for class II are not zero. This is in harmony with the finding that GMP almost completely quenches the fluorescence for class I, whereas a weak fluorescence arises from the GMP-dye complex for class II. The fluorescence spectra of the DNA-dye complexes gradually shift toward longer wavelengths with increasing GC content. In this connection, the fluorescence decay parameters show a dependence on the emission wavelength; alpha 1 decreases with an increase in the emission wavelength. In view of these results, it is proposed that the decay behavior of the DNA-dye complexes has its origin in the heterogeneity of the emitting sites; the long lifetime tau 1 results from the dye bound to AT-AT sites, while the short lifetime tau 2 is attributable to the dye bound in the vicinity of GC pairs. Since GC pairs almost completely quench the fluorescence for class I, partly intercalated or externally bound dye molecules may play an important role in the component tau 2.

Nanosecond fluorescence decay studies of the deoxyribonucleic acid-9-aminoacridine and deoxyribonucleic acid-9-amino-10-methylacridinium complexes

The binding interaction of the mutagenic dye 9-aminoacridine (9AA) with DNAs of various base composition has been studied by steady-state and transient fluorescence measurements. It was found that the fluorescence decays of 9AA and 9AA bound to poly[d(A-T)] which contains only one type of binding site are single exponential but that those of 9AA bound to DNA can be well described as a sum of three-exponential functions. The fluorescence quantum yields confirm that the AT base pair is responsible for the fluorescence of the bound 9AA, while the GC base pair almost completely quenches it. Nanosecond time-resolved spectroscopy indicates that the structure of the DNA-9AA complex is not substantially altered during the lifetime of the excited singlet state of the dye. Furthermore, the fact that the shapes or the maxima of the absorption and fluorescence spectra exhibit no dependence on the GC content of DNA indicates that the radiative lifetime of the bound 9AA is constant under a variety of circumstances. On the basis of these results, it is concluded that the emitting sites of 9AA on DNA are composed of at least three classes having different quantum yields: (I) tau1 = 2.0 +/- 0.3 ns, phi1 = 0.06 +/- 0.01, (II) tau2 = 12.3 +/- 0.7 ns, phi2 = 0.35 +/- 0.02, and (III) tau3 = 28.3 +/- 0.5 ns, phi3 = 0.81 +/- 0.02. Fluorescence decay behavior is also reported for the nonmutagenic dye 9-amino-10-methylacridinium (10Me-9AA) bound to DNA. The results of 10Me-9AA were found to be very similar to those of 9AA.