Interaction of porphyrin-containing macrotetracyclic receptor molecule with single-stranded and double-stranded polynucleotides. A photophysical study

Calix[4]arene Polyamine Triazoles: Synthesis, Aggregation and DNA Binding

Artificial gene delivery systems are in great demand from both scientific and practical biomedical points of view. In this paper, we present the synthesis of a new click chemistry calix[4]arene precursor with free lower rim and new water-soluble calixarene triazoles with 12 amino-groups on the upper rim (one with free phenol hydroxyl groups and two another containing four butyl or tetradecyl fragments). Aggregation in the series of amino-triazole calixarenes of different lipophilicity (calixarene with free phenol hydroxyl groups or butyl and tetradecyl fragments on the lower rim) was studied using dynamic light scattering and fluorescent pyrene probe. It was found that calix[4]arene with a free lower rim, like alkyl-substituted butyl calix[4]arene, forms stable submicron aggregates 150-200 nm in size, while the more lipophilic tetradecyl -substituted calix[4]arene forms micellar aggregates19 nm in size. Using UV-Vis spectroscopy, fluorimetry and CD, it was shown that amino-triazole calix[4]arenes bind to calf thymus DNA by classical intercalation. According to DLS and TEM data, all studied macrocycles cause significant DNA compaction, forming stable nanoparticles 50-20 nm in size. Among all studied calix[4]arenes the most lipophilic tetradecyl one proved to be the best for both binding and compaction of DNA.

RNA and DNA complexes with hemin [Fe(III) heme] are efficient peroxidases and peroxygenases: how do they do it and what does it mean?

Guanine-rich RNAs and DNAs from chromosomal telomeres and elsewhere that fold into guanine quadruplexes (G-quadruplexes), are found to complex tightly with porphyrins such as N-methylmesoporphyrin IX (NMM) and hemin [Fe(III) heme]. By themselves, these DNAs and RNAs are found to be efficient catalysts for porphyrin metallation. When complexed with hemin, under physiological conditions, these nucleic acids display robust peroxidase (one-electron oxidation), as well as peroxygenase (two-electron oxidation, or oxygen transfer) activity. These surprising catalytic properties, that frequently match the catalytic performance of natural peroxidase and P450 monooxygenase enzymes, have been the subject of significant mechanistic analysis, as well as having found utility in a wide range of biosensing and other applications. This review summarizes recent insights into a surprising yet fundamental property of many RNAs and DNAs, a property with undoubted ramifications for cellular oxidative disease, de novo hemoenzyme design, and our understanding of the evolution of early biocatalytic systems.

In vitro selection of a photoresponsive RNA aptamer to hemin

A photoresponsive RNA aptamer to hemin was selected in vitro from a random sequence library of RNAs with azobenzene residues. The aptamer bound to hemin under visible light irradiation and was released by ultraviolet light.

A Water-Soluble, Octacationic Zinc Phthalocyanine as Molecular Probe for Nucleic Acid Secondary Structure

The interaction between CT-DNA and the zinc phthalocyanine ZnPc (1) was studied by UV/VIS and fluorescence titration, as well as by thermal denaturation. ZnPc was found to strongly bind to CT-DNA (K(app)=7.35 x 10(5) M(-1)) in a non-intercalative mode. The photosensitized cleavage of pBR322 DNA was found to efficiently proceed via singlet-oxygen ((1)O(2)) production. Further, ZnPc (1) caused site-specific scission of guanine (G) bases around the bulge of the hairpin oligonucleotides OD1-OD3, as clearly shown by gel-electrophoresis experiments.

Recognition of homo-polynucleotides containing adenine by a phenanthridinium bis-uracil conjugate in aqueous media

Among novel bis-nucleobase-phenanthridinium conjugates bis-uracil analogue stabilized significantly more effective poly-dA-poly-dT and poly-AH(+)-poly-AH(+) than adenine analogue and reference compound . For the alternating poly-dAdT-poly-dAdT however, the binding preference is lost, pointing to the importance of specific interactions of uracils of with homopolynucleotides containing consecutive adenines.

Intercalation of water-soluble bis-porphyrins into poly(dA)-poly(dT) double helix

The association constants (K) of nucleic acid monomers with a series of water-soluble bis-porphyrins (bisMC1, bisMC3, bisMC5, bisMC7, and bisMC11) in which two porphyrin units were linked by a methylene chain of various lengths were estimated spectrophotometrically. Among the bis-porphyrins, the K values are similar for each nucleic acid monomer, indicating that the bridging chain length does not affect the association of the bis-porphyrins with the nucleic acid monomers. The melting curves of poly(dA)-poly(dT) in the presence of bisMC3 or bisMC5 were found to be biphasic, suggesting that bisMC3 and bisMC5 are bound to poly(dA)-poly(dT) with a binding mode different from the groove binding exhibited by the corresponding porphyrin monomers. A negative-induced CD peak in the Soret region of bisMC3 and bisMC5 with poly(dA)-poly(dT) is observed and the visible spectral changes of bisMC3 and bisMC5 upon addition of poly(dA)-poly(dT) are accompanied by a large red shift of the Soret band (bisMC3: 21 nm, bisMC5: 23 nm) with substantial hypochromicity (bisMC3: 49%, bisMC5: 40%). Therefore, it is reasonable to conclude that both of the porphyrin units of bisMC3 and bisMC5 intercalate into poly(dA)-poly(dT). In contrast to poly(dA)-poly(dT), the melting curves of poly(dA.dT)(2) in the presence of the bis-porphyrins did not show such biphasic behavior. Together with the CD and visible absorption data, it is certain that these bis-porphyrins do not intercalate into poly(dA.dT)(2).

DNA-enhanced peroxidase activity of a DNA-aptamer-hemin complex

BACKGROUND

In vitro selection (SELEX) previously identified short single-stranded DNAs that specifically bound N-methylmesoporphyrin IX (NMM), a stable transition-state analogue for porphyrin-metallation reactions. Interestingly, iron(III)-protoporphyrin (hemin) was a good competitive inhibitor for the DNA-catalyzed metallation reaction, and appeared to bind strongly to the NMM-binding DNA aptamers. We investigated the peroxidase activity of the aptamer-hemin complexes to see if the DNA component of the complex, like the apoenzymes in protein peroxidases, could enhance the low intrinsic peroxidatic activity of hemin.

RESULTS

Two porphyrin-binding DNA aptamers bound hemin with submicromolar affinity. The aptamer-hemin complexes had significantly higher peroxidase activity than hemin alone, under physiological conditions. The Vobs of the PS2.M-hemin complex was 250 times greater than that of hemin alone, and significantly superior to a previously reported hemin-catalytic-antibody complex. Preliminary spectroscopic evidence suggests the coordination of the hemin iron in the complex changes, such that the complex more closely resembles horseradish peroxidase and other heme proteins rather than hemin.

CONCLUSIONS

A new class of catalytic activity for nucleic acids is reported. The aptamer-hemin complexes described are novel DNA enzymes and their study will help elucidate the structural and functional requirements of peroxidase enzymes in general and the ways that a nucleic acid 'apoenzyme' might work to enhance the intrinsic peroxidatic ability of hemin. These aptamer-hemin complexes could be regarded as prototypes for redox-catalyzing ribozymes in a primordial 'RNA world'.

Selective photocleavage of single-stranded nucleic acids by cyclobisintercaland molecules

Irradiation of mixtures of a single-stranded circular plasmid and of a double-stranded supercoiled DNA in presence of the cyclobisintercaland compounds 2 or 3 shows that these reagents effect the selective photocleavage of the single-stranded entity. Furthermore, 2 also cleaves tRNAasp preferentially at single-stranded domains.

Dimerization of tetracationic porphyrins: ionic strength dependence

Cationic porphyrins are under study in a number of contexts including their interaction with biological targets, as possible therapeutic agents and as building blocks for molecular devices such as molecular photodiodes and solar cells. Many cationic porphyrins dimerize readily in aqueous solution. Dimerization in turn can control the properties of the porphyrin as well as its binding to its target. The propensity of a porphyrin to dimerize in aqueous solution can be estimated by recording the optical spectrum of the solution as a function of the concentration of added salt. Analysis of the data in terms of the Debye-Hückel formalism gives an estimate of the extent of dimerization as a function of ionic strength. Data for TMPyP4 [meso-tetrakis(4-N-methylpyridinium)porphyrin] and its butyl and octyl homologs; TMAP [meso-tetrakis(4-N,N,N-trimethylanilinium)porphyrin]; T theta PP [meso-tetrakis[4-N-[(3-(trimethyl-ammonio)propyl)oxy]phenyl]porphyrin] and the ferrocenyl porphyrin P3Fc are discussed. Dimerization may affect binding of the cationic porphyrins to their targets, e.g., DNA.

A macrocyclic bis-acridine shifts the equilibrium from duplexes towards DNA hairpins

Nucleic acids can undergo dynamic conformational changes associated with the regulation of biological processes. A molecule presenting larger affinities for alternative structures relative to a duplex is expected to modify such conformational equilibria. We have previously reported that macrocyclic bis-acridine binds preferentially to single-stranded regions, especially DNA hairpins, due to steric effects. Here, we show, using gel electrophoresis, fluorescence and melting temperature experiments, that the macrocycle bis-acridine shifts an equilibrium from a duplex towards the corresponding hairpins. Competition experiments enlighten the higher affinity of the macrocycle for hairpins compared with double-stranded DNA. The macrocycle bis-acridine destabilizes a synthetic polynucleotide, by the formation of premelted areas. By extrapolation, the macrocycle bis-acridine should be able to disrupt, at least locally, genomic DNA duplexes and to stabilize unpaired areas, especially palindromic ones forming hairpins. Such macrocyclic compounds may have potential applications in the therapy of diseases involving hairpins.

Binding of meso-Tetrakis(N-methylpyridinium-4-yl)porphyrin to Double Helical RNA and DNA.RNA Hybrids

The binding properties of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (H(2)TMPyP) to RNA and DNA.RNA hybrid duplexes were studied by absorption and circular dichroism (CD) spectra. The duplexes studied were poly(rA).poly(rU), poly(rA).poly(dT), poly(rI).poly(rC), poly(rI).poly(dC), poly(rG).poly(rC), and poly(rG).poly(dC). The hypochromicity (about 40%) and the bathochromic shift (about 15 nm) of the porphyrin Soret absorption band upon binding were quite similar among the duplexes examined. The large bathochromic shift and hypochromicity suggested a significant perturbation in the porphyrin pi electrons upon binding. H(2)TMPyP was found to bind in a single step to poly(rI).poly(rC), poly(rG).poly(rC), and poly(rG).poly(dC) and in a multistep manner to poly(rA).poly(rU), poly(rA).poly(dT), and poly(rI).poly(dC). The induced CD spectra in the visible range suggested that the porphyrin preferred to bind to the RNA duplexes with self-stacking along the polymer surface and to the hybrids with intercalation, at least at higher duplex load. This implied a distinct conformational difference between the RNA duplexes and DNA.RNA hybrids, and a drug molecule is able to recognize the difference. The number of binding sites per base pairs (n), however, was very different among the RNA duplexes examined. We also found that the intensity of the bisignate-induced CD bands is proportional to the n value. This suggested that the transition moments on the neighboring porphyrins are interacting considerably with each other to produce intense induced CD peaks.

Interaction of water-soluble porphyrins with single- and double-stranded polyribonucleotides

CD and uv-visible absorption studies with several tetracationic water-soluble porphyrin derivatives show that some of these species can serve as probes to discriminate between A- and B-conformational forms of single-stranded polynucleotides. It is also observed that these porphyrins can participate in the formation of double helices by forming transient intermediate complexes en-route to duplex formation.