Dimeric bisbenzimidazoles inhibit the DNA methylation catalyzed by the murine Dnmt3a catalytic domain.

When located in the DNA minor groove, dimeric bisbenzimidazoles DB(n) effectively inhibited in vitro the Dnmt3a catalytic domain (IC50 5-77 µM). The lowest IC50 value was observed for compound DB(11) with an 11-unit methylene linker joining the bisbenzimidazole fragments. Increased time of incubation of DNA with DB(n) as well as the presence of AT-clusters in DNA enhances the inhibitory effect.

Kinetic and spectral parameters of interaction of Citrobacter freundii methionine γ-lyase with amino acids.

Kinetic parameters of Citrobacter freundii methionine γ-lyase were determined with substrates in γ-elimination reactions as well as the inhibition of the enzyme in the γ-elimination of L-methionine by amino acids with different structure. The data indicate an important contribution of the sulfur atom and methylene groups to the efficiency of binding of substrates and inhibitors. The rate constants of the enzyme-catalyzed exchange of C-α- and C-ß-protons with deuterium were determined, as well as the kinetic isotope effect of the deuterium label in the C-α-position of inhibitors on the rate of exchange of their ß-protons. Neither stereoselectivity in the ß-proton exchange nor noticeable α-isotope effect on the exchange rates of ß-protons was found. The ionic and tautomeric composition of the external Schiff base of methionine γ-lyase was determined. Spectral characteristics (absorption and circular dichroism spectra) of complexes with substrates and inhibitors were determined. The spectral and kinetic data indicate that deamination of aminocrotonate should be the rate-determining stage of the enzymatic reaction.

Minor groove dimeric bisbenzimidazoles inhibit in vitro DNA binding to eukaryotic DNA topoisomerase I.

The potential of six dimeric bisbenzimidazoles bound to scDNA to inhibit eukaryotic DNA topoisomerase (topo-I) was studied chemically; the tested compounds differed in linker structure and length. All the compounds inhibited topo-I, DB(7) being the most efficient; its inhibitory activity in vitro was 50-fold higher than that of camptothecin. It is noteworthy that inhibitory properties of nearly all the tested compounds increased many times if they were preincubated with scDNA for three days.

Hoechst 33258--poly(dG-dC).poly(dG-dC) complexes of three types.

It was found recently that Hoechst 33258, a dsDNA fluorescent dye used in cytological studies, is an efficient inhibitor of the interaction of TATA-box-binding protein with DNA, DNA topoisomerase I, and DNA helicases. In addition it proved to be a radioprotector. Biological activity of Hoechst 33258 may be associated with dsDNA complexes of not only monomeric, but also dimeric type. In this work, the Hoechst 33258 interaction with poly(dG-dC).poly(dG-dC) was studied using UV-vis and fluorescent spectroscopy, circular and flow-type linear dichroism. It was found that Hoechst 33258 formed with poly(dG-dC).poly(dG-dC) complexes of three types, namely, monomeric, dimeric, and, apparently, tetrameric, and their spectral properties were studied. Complexes of monomeric and dimeric types competed with distamycin A, a minor groove ligand, for binding to poly(dG-dC).poly(dG-dC). We proposed that Hoechst 33258 both monomers and dimers form complexes of the external type with poly(dG-dC).poly(dG-dC) from the side of the minor groove.

The Hoechst 33258 covalent dimer covers a total turn of the double-stranded DNA.

With the goal to design ligands recognizing extended regions on dsDNA, a covalent dimer of the fluorescent dye Hoechst 33258 [bis-HT(NMe)] composed of two dye molecules linked via the phenol oxygen atoms with a (CH2)3-N+ H(CH3)-(CH2)3 fragment was constructed using computer modeling and then synthesized. Its interactions with the double-stranded DNA (dsDNA) were studied by fluorescent and UV-Vis spectroscopy and circular (CD) and linear dichroism (LD). Based on variations in the affinity to the dsDNA, it was shown that complexes of three types are formed. The first type complexes result from binding of a bis-HT(NMe) monomer in the open conformation; in this case the ligand covers the total dsDNA turn and is located in the minor groove according to the positive value of CD at 370 nm. In addition, the ability to form bis-HT(NMe)-bridges between two dsDNA molecules, i.e., each of the two bis-HT(NMe) ends binds to two different dsDNA molecules, was demonstrated for the first type complexes. Spectral characteristics (maximal absorption at 362 nm, positive sign, and maximal value of CD at 370 nm) of the first type complexes conform to those of the specific Hoechst 33258 complex with poly[d(A-T)] x poly[d(A-T]. The second type complexes correspond to the bis-HT(NMe) sandwich (as an inter- or intramolecular) binding to dsDNA with stoichiometry > or = 5 bp. Thereby, a negative LD at 360 nm and the location of bis-HT(NMe) sandwiches in the minor groove of B form dsDNA seems contradictory. Spectral characteristics (maximal positive CD at 345 nm, a dramatic decrease in fluorescence intensity and the shift of its maximum to 490 nm) of these complexes favor a suggestion that this binding correlates to the formation of nonspecific dimeric Hoechst 33258 complex with dsDNA. The third type complexes are characterized by stoichiometry of one bis-HT(NMe) molecule per approximately 2 bp and the tendency to zero of LD values at 270 and 360 nm. We assume that in these complexes bis-HT(NMe) sandwich dimers are formed on dsDNA. The complexes of this type conform to the aggregation type complex of Hoechst 33258 with dsDNA. The ability of bis-HT(NMe) to cover the whole dsDNA turn or form bridges with two dsDNA upon the formation of the first type complexes essentially distinguishes it from Hoechst 33258, which can only occupy 5 bp and does not form such bridges. This specific property of bis-HT(NMe) may support new biological activities.

Thr-Val-Thr dansyl hydrazide: the first fluorescent tripeptide preferentially binding with at pairs in DNA.

In 1991-1993 we amended a DNA-protein recognition model advanced in 1975. Here we test our assumptions with a specially designed tripeptide L-Thr-L-Val-L-Thr-NH-NH-Dns (Dns is 5-dimethylaminonaphthalene-1-sulfonic acid residue). It is shown to dimerize in solution (as evidenced by the nonlinear concentration dependence of its fluorescence) and to bind with DNA mainly in beta-dimeric form (S-shaped adsorption isotherm obtained by equilibrium dialysis). The tripeptide is bound in the DNA minor groove (whence it can be displaced with distamycin A), and such complexes become able to associate into 'biduplex' structures (nonlinear dependence of the linear dichroism of bound peptide on DNA concentration). The peptide dimers clearly prefer the AT pairs [half-saturating peptide concentrations are (0.6-0.7) x 10(-4) M for poly(dA).poly(dT) but exceed (2.5-2.8) x10(-4) M for poly(dG).poly(dC)]. These results agree nicely with our earlier suggestions. Since Dns-tagged trivaline has been shown to prefer the GC pairs, we think it now becomes possible to design oligopeptides that would specifically bind to any predefined nucleotide sequence.

Mixed mode of ligand-DNA binding results in S-shaped binding curves.

S-shaped binding curves often characterize interactions of ligands with nucleic acid molecules as analyzed by different physico-chemical and biophysical techniques. S-shaped experimental binding curves are usually interpreted as indicative of the positive cooperative interactions between the bound ligand molecules. This paper demonstrates that S-shaped binding curves may occur as a result of the "mixed mode" of DNA binding by the same ligand molecule. Mixed mode of the ligand-DNA binding can occur, for example, due to 1) isomerization or dimerization of the ligands in solution or on the DNA lattice, 2) their ability to intercalate the DNA and to bind it within the minor groove in different orientations. DNA-ligand complexes are characterized by the length of the ligand binding site on the DNA lattice (so-called "multiple-contact" model). We show here that if two or more complexes with different lengths of the ligand binding sites could be produced by the same ligand, the dependence of the concentration of the complex with the shorter length of binding site on the total concentration of ligand should be S-shaped. Our theoretical model is confirmed by comparison of the calculated and experimental CD binding curves for bis-netropsin binding to poly(dA-dT) poly(dA-dT). Bis-netropsin forms two types of DNA complexes due to its ability to interact with the DNA as monomers and trimers. Experimental S-shaped bis-netropsin-DNA binding curve is shown to be in good correlation with those calculated on the basis of our theoretical model. The present work provides new insight into the analysis of ligand-DNA binding curves.

Atomic force and electron microscopy of high molecular weight circular DNA complexes with synthetic oligopeptide trivaline.

Intramolecular compact structures formed by high molecular weight circular superhelical DNA molecules due to interaction with synthetic oligopeptide trivaline (1) were studied by atomic force and electron microscopy. Three DNA preparations were used: plasmids pTbol, pRX10 and cosmid 27,877, with sizes 6,120 bp, 10,500 bp and 44,890 bp respectively. Plasmid pTbo1 and pRX10 preparations along with monomers contained significant amount of dimers and trimers. Main structures in all preparations observed were compact particles, which coincide in their appearance and compaction coefficient (3,5-3,7) with triple rings described earlier. The size and structure characteristics of triple rings and other compact particles on atomic force images in general coincide with those obtained by EM (2). AFM (3) images allow to get additional information about the ultrastructural organization and arrangement of DNA fibers within the compact structures. Along with triple rings in pTbol and pRX10-TVP complexes significant amount of compact structures were observed having the shape of two or three compact rings attached to each other by a region of compact fibre. Basing on the data of contour length measurements and the shape of the particles it was concluded that these structures were formed due to compaction of dimeric and trimeric circular DNA molecules. Structures consisting of several attached to each other triple rings were not found for pTbol, pRX10 monomers or cosmid preparations--TVP complexes where only single triple rings were observed. The conclusion is made that initiation of compact fibre formation within the circular molecules depends on the primary structure and for dimeric or trimeric circular molecules two or three compaction initiation points are present, located in each monomer unit within one circular DNA molecule. The nucleotide sequence dependent compaction mechanism providing independent compaction of portions of one circular molecule can be of interest for understanding of DNA compaction processes in vivo.

Concatemerization of tRNA molecules in the presence of trivaline derivative.

The interaction of tRNA with trivaline dansyl hydrazide trifluoroacetate (DHTV) has been studied. The shape of curves of fluorimetric titration of tRNA with DHTV and vice versa can be explained only by formation of DHTV dimers on tRNA molecules, and subsequent association of DHTV-saturated tRNA molecules with each other. The ability of tRNA molecules to form concatemers in solution in the presence of DHTV has been demonstrated by electron microscopy. Electron microscopy of the tRNA-DHTV complexes stained with uranyl acetate revealed flexible rods 6-7 nm thick and up to several micrometers long.

Circular superhelical DNA complexes with synthetic oligopeptide: unusual compact structures and influence of bent sequences on the results of compaction.

The organization of synthetic oligopeptide trivaline (1) complexes with four types of circular superhelical DNA preparations was studied by electron microscopy. The DNA molecules in the preparations investigated had different sizes ranging from 2.9 kb to 21.0 kb. Two plasmids contained bent DNA sequences from minicircles of kinetoplast DNA of Leishmania gymnodactili and Trypanosoma boissoni. The main structures in all preparations observed were circular compact particles which coincide in their appearance and compaction coefficient (3,5-3,7) with triple rings described earlier. But along with triple rings the new types of compact structures were observed having the shape of a ring with attached rod or the shape of two compact rings attached to each other by a region of compact fiber. The latter structures could be observed in significant quantities in case of DNA preparations longer than 10 kb. The conclusions can be made that due to TVP stimulated compaction of circular DNA molecules compact fibers containing both two or three DNA duplexes arranged side by side can be formed. It is shown that presence of bent DNA sequences stimulates the formation of structures containing more than one triple ring. It demonstrates the possibility of the primary DNA structure influence on the compaction process in case of the circular molecules. The new ways of circular DNA folding described can be of importance for understanding of DNA organization in different cell structures.

DNA quadruplexes assembled by simple peptide: effects of DNA homology and peptide removal.

Formation of heterologous (calf thymus dsDNA) and homologous (linearized pBR322 plasmid dsDNA) quadruplexes upon binding with the simple aliphatic tripeptide derivative (L-Val)3-N2H2-DNS.CF3COOH-DHTV) was examined by fluorimetry, flow linear (LD), circular dichroism (CD), and electron microscopy (EM). The morphology of the rod-like compact particles formed due to the association of dsDNA segments proved to be the same for both DNAs, whereas the stability of the compact DNA structure upon tripeptide removal from the complex with DNA differed substantially for homologous versus non-homologous dsDNA used. The increase in NaCl concentration in the solution up to 30 mM removes the peptide from both types of the complexes completely. At the same time at 20 mM NaCl calf thymus DNA quadruplexes readily dissociate, whereas the structures formed by plasmid DNA retain their morphology in the solution containing NaCl with concentrations up to 40 mM and are only partially disrupted at even higher NaCl concentration. These results provide an analogy between trivaline-DNA model complexes and RecA-DNA binding.

Trivaline molecular complexes with trinucleotides form in solution the extended, about 1000 A in length structures.

The fluorescence, flow linear dichroism and electron microscopy (EM) have shown the trivaline ability to interact in solution with certain molecules of trinucleotides. This interaction results in formation of extended structures up to several thousand angstroms in length. Such structures were observed for trivaline complexes with homopurine, homopyrimidine or random sequences of deoxyribo- and ribonucleotides, independently of the presence or absence of the terminal 5'-phosphate residue. A model of such a structural organization is proposed. An elementary structural unit consists of a trivaline beta-dimer and adsorbed trinucleotide. So, "dimeric" complex is formed. Two such "dimeric" complexes combine with each other by means of peptide-peptide contacts (as with beta-sandwich). So, "tetrameric" complex is formed. It has a dyad axis. Two such structural units combine with each other by means of Hoogsteen's hydrogen bonds. So, "octameric" complex is formed. It has three mutually perpendicular dyad axes. The "octameric" complexes appear to be able to combine with each other by means of stacking interactions, and to form the regular organized aggregates consisting of many dozens of elementary units. So, "stacking" structure is formed. The "octameric" complex is the symmetry translational unit of such a structure. The spatial position of the bases in all these structures is additionally fixed by the nucleo-peptide interactions. These aggregates have the appearance of extended structures on electron micrographs.

Homology in trivaline complex formation with dsDNA and ssRNA.

It has been shown by the equilibrium dialysis that at a polyU concentration above the "critical" one, the complete polymer saturation with trivaline reaches approximately 0.7 trivaline molecules per one phosphate group. i.e. at these conditions peptide dimer occupies on polyU a site of three bases (phosphates) in length. The trivaline complex with polyU at a concentration lower than the "critical" one does not reveal any noticeable fluorescence, but has rather significant positive linear dichroism at 265 and 330 nm. The trivaline-nucleic acids complex has a significant fluorescence at any dsDNA concentration while with polyU it is only so at a concentration above the "critical" one. Electron microscopy has shown that at a rather high concentration of dsDNA molecules in solution a "biduplex" structure undergoes an additional stage of compaction, during which the extended particles more than 30 nm in diameter are formed.

Trivaline 'catalyzes' 5'-pdGTT oligomerization in solution.

We have found that the 5'-pdGTT molecules at a concentration of 10(-4) M are oligomerized in solution in the presence of 10(-4) M tripeptide-(L-Val)3-NH-NH-DNS.CF3COOH and the condensation reagents (carbodiimide and imidazole). Oligonucleotides not less than 12 bases long were formed in the yield which was over 15%. It is known that in the absence of peptide 10(-2) M mono- or dinucleotides are required. Thus trivaline can be considered as one of the simplest enzymes. This oligomerization seems to be an essential way for the synthesis of long enough oligonucleotides of the random GC-sequence, which could be used at the earliest steps of evolution.

Structural organization of kinetoplast DNA and its compaction in the in vitro model system.

Electron microscopic studies of Leishmania gymnodactyli cells lysed at hypotonic conditions showed that the structures identified as kinetoplast DNA have the appearance of loose accumulations of crossed and sometimes branched rod-like structures 100 to 200 nm long and 20 nm thick. The compaction of isolated kinetoplast DNA (kpDNA) caused by interaction with synthetic tripeptide--dansylhydrazide trivaline--was also studied. The analysis of the structures arising at different steps of compaction showed that the minicircles are compacted forming rod-like structures where minicircle double-stranded DNA segments are closely associated side by side in a manner which was earlier described for initial compaction stages of "triple rings". These rod-like structures resemble in their appearance the structures found in lysed cell preparations obtained according to Miller's method. Branching of rod-like structures can be the consequence of minicircle catenation. In vitro compaction is completed with the formation of a compacted network, its diameter being 3 to 6 times smaller as compared with the initial one.

Electron microscopic and physico-chemical studies of DNA complexes with synthetic oligopeptides: binding specificity and DNA compact structures.

Binding to DNA of two synthetic peptides, Val-Thr-Thr-Val-Val-NH-NH-Dns and Thr-Val-Thr-Lys-Val-Gly-Thr-Lsy-Val-Gly-Thr-Val-Val-NH-NH-Dns (where Dns is a residue of 5-dimethylaminonaphthalene-1-sulfonic acid), has been studied by circular dichroism, electron microscopy and fluorescence methods. It has been found that these two peptides can self-associate in aqueous solution as follows from the fact that concentration-dependent changes are observed in the UV absorbance and fluorescence spectra. The two peptides can bind to DNA both in self-associated and monomeric forms. The pentapeptide in the beta-associated form binds more strongly to poly(dG).poly(dC) than to poly[d(A-C)].poly[d(G-T)] and poly(dA).poly(dT) whereas the tridecapeptide exhibits an opposite order of preferences binding more strongly to poly[d(A-C)].poly[d(G-T)] and poly(dA).poly(dT) than to poly(dG).poly(dC). Binding is a cooperative process which is accompanied by the DNA compaction at peptide/DNA base pair ratios greater than 1. At the initial stage of the compaction process, the coalescence of DNA segments covered by bound peptide molecules leads to the formation of DNA loops stabilized by the interaction between peptide molecules bound to different DNA segments. Further increase in the peptide/DNA ratio leads to the formation of rod-like structures each consisting of two or more double-stranded DNA segments. The final stage of the compaction process involves folding of fibrillar macromolecular complexes into a globular structure containing only one DNA molecule.

Triple rings: a new type of compact structure of circular DNA.

Complexes of circular superhelical pBR322 DNA with a synthetic tripeptide capable of beta-structure formation (dansylhydrazide trivaline) were studied at different peptide/DNA ratios by electron microscopy. It was shown on rotary-shadowed preparations that peptide binding induces intramolecular DNA condensation and compact ring-shaped particles are formed from fibres 120 A thick. The analysis of the morphology of the ring structures observed at various peptide/DNA ratios as well as contour length measurements enabled us to draw conclusions about the organization of the double-stranded DNA filaments in these structures. It was established that the fibres forming compact rings contain three double-stranded DNA segments closely associated due to DNA-peptide and peptide-peptide interactions. The mechanisms leading to the formation of the triple rings may be important in DNA condensation in vivo.

Torus-shaped particles formed due to intermolecular condensation of circular DNA upon interaction with synthetic tripeptide.

The morphology of complexes between relaxed circular plasmid pBR322 DNA and tripeptide L-Val-L-Val-L-Val-NH-NH-Dns (TVP) at different peptide/DNA ratios was studied by electron microscopy. The results show that interaction of TVP with circular DNA leads to the formation of perfect torus-shaped particles. The torus parameter measurements offer the possibility to conclude that DNA condensation observed is of intermolecular nature. On the basis of the analysis of the structures corresponding to the early stages of DNA compaction the model for intermolecular condensation of circular DNA into torus-shaped particles is proposed.