The use of fluorescence anisotropy decay of poly d(A-T) ethidium bromide complex to estimate the unwinding angle of the double helix.

We measured the fluorescence decay under polarized light, of ethidium bromide bound to the poly d(A-T) isolated from Cancer Pagurus. The decay of the whole fluorescence is a single exponential function revealing a good homogeneity of the binding sites. The anisotropy decay due to energy transfers between the ethidium bromide molecules bound to a same poly d(A-T) molecule has been analysed, with a Monte Carlo calculation. We found the dye unwinds the poly d(A-T) duplex by an angle of 17 degrees plus or minus 2 degrees. This result is in agreement with the value previously found in the case of calf thymus DNA-ethidium bromide complex, although the base compositions of the two nucleic acids are different.     

Linear and circular dichroism of harmine and harmaline interacting with DNA

The interaction of the β-carboline derivatives harmine and harmaline with calf thymus DNA was studied using linear and circular dichroism techniques. Absorption linear dichroism in an electric field indicated that the transition moment (at 336 nm) of harmine lies at angle χ = 82° relative to the helix axis and that the same angle for harmaline (at 365 nm) is only 67°. The 82° angle found for harmine is compatible with the interpretation that the molecule is intercalated between two consecutive base pairs of the DNA. The c.d. results in the u.v. region for the DNA harmine complex support this interpretation, since the increase in the magnitude of all the DNA c.d. bands can also be explained by assuming an intercalation. Since a 67° angle was found for harmaline, an intercalation is in that case unlikely, the molecule is probably in a tilted position in one of the DNA grooves. However, harmaline can induce a conformational change in nucleic acids, as shown by the modification of the c.d. spectra of DNA and, especially, of poly[d(A-T)], the addition of harmaline to this polynucleotide gradually inducing its pre-melting at 4°C. This study shows that the hydrogenation of a double bond of the pyridine ring converting harmine to harmaline greatly alters the interactions of the molecule with DNA.     

The fluorescence anisotropy decay due to energy transfers occuring in the ethidium bromide-DNA complex. Determination of the deformation angle of the DNA helix

It has been shown in a preceding work that the fluorescence anisotropy decay of ethidium bromide-DNA complex is accelerated by energy migration between dyes bound to the same DNA molecule. In the present work, this result is confirmed. A quantitative analysis has been performed in the following way. The spectroscopic term of the transfer rate constant has been accurately reevaluated by quantum yield and spectral measurements. One assumes that the dye intercalates between two adjacent base pairs and that its distribution is random along the DNA molecule. One introduces the deformation angle δ of the DNA helix induced by the ethidium bromide intercalation. For several values of δ, the energy migration contribution to the anisotropy decay is computed by a Monte Carlo method. In multiplying these computed functions by the measured brownian anisotropy, one obtains the anisotropy decay curve. Comparison with the experimental data leads to the conclusion that the ethidium bromide molecule unwinds the DNA helix by an angle δ = ?16°. This result is m agreement with the work of other authors. We think that the method used here may provide accurate information on the spatial distribution of an array of chromophores bound to a rigid structure.     

The vibrational spectra and structure of poly(rA-rU)-poly(rA-rU)

Infrared and Raman spectra of aqueous poly(rA-rU)·poly(rA-rU), the double-helical complex containing strands of alternating riboadenylate and ribouridylate residues, display significant differences from one another and from corresponding spectra of poly(rA)·poly(rU), the double-helical complex of riboadenylate and ribouridylate homopolymers. Parallel studies on the copolymer and homopolymer complexes by cesium sulfate density gradient centrifugation, ultraviolet absorption spectroscopy, hydrogenion titration, 1-N oxidation of adenine residues by monoperphthalic acid and X-ray diffraction reveal, however, that the geometry of base pairing between adenine and uracil is closely similar in each complex and apparently of the Watson-Crick type. Therefore the differences observed between vibrational spectra of poly (rA-rU)·poly (rA-rU) and poly(rA)·poly(rU) are not due to different base-pairing schemes but may be attributed to differences in vibrational coupling between vertically stacked bases. Vibrational coupling may also account for the differences between infrared and Raman spectra of the same complex. Thus, the present results indicate that infrared and Raman frequencies of RNA in the region 1750–1550 cm^?1 should be dependent on the base sequence.     

X-ray crystallographic analysis of a ternary intercalation complex between proflavine and the dinucleoside monophosphates CpA and UpG

We report the crystal-structure analysis of a complex involving the drug proflavine and the two dinucleoside monophosphates cytidylyl-3′,5′-adenosine (CpA) and uridylyl-3′,5′-guanosine (UpG). The planar drug molecule is intercalated between C ?G and U ?A Watson-Crick base pairs, in a double-helical fragmentlike arrangement. Sugar conformations at the 3′-ends of the two strands are dissimilar. The backbone conformations fall within the ranges of values noted previously for dinucleoside intercalation complexes, and some correlations involving these are noted. The separation of the two strands and the basic twist angle of 16°, compared to other reported complexes, are indicative of sequence-dependent effects of the drug binding.     

Peritoneal resorption of ethidium bromide, free or linked to DNA in rodents]

Ethidium bromide, either free (EB) or bound to DNA (EB-DNA), is injected into the peritoneal cavity of adult rats or mice. EB is then detected by fluorescence microscopy in peritoneal cells and by spectrophotometry in the peritoneal fluid. EB-DNA persists for a longer period of time in the peritoneal cavity than free EB does.     

Interactions of molecules with nucleic acids. XII. Theoretical model for the interaction of a fragment of bleomycin with DNA

An intercalation model of a complex between DNA and a bleomycin fragment (BLMF), consisting of the bithiazole core and an amide and a protonated amino substituent, is presented. The model, which shows a preference for BLMF with the protonated amine in the minor groove and the acetyl terminal inserted into either the minor and major grooves, respectively, agrees with recently obtained nmr data. The selection of sites I and II, which have the smallest unwinding of the three theoretical intercalation sites, is consistent with the experimental unwinding angle of 12°. The bithiazole moiety stacks between two base pairs of the double helix, while the protonated substituent interacts ionically with the negatively charged regions of the backbone in the minor groove of the DNA. The protonated amine also forms an intramolecular hydrogen bond with the carbonyl oxygen of the amide group on the same substituent. Analysis of drug complexes with different base-pair sequences reveal four energetically defined groups. The relative energy of the dimer duplex complexes of BLMF correlates with bleomycin's observed base-sequence specificity upon cleavage. The most stable intercalation complexes form adjacent to the bases cleaved most readily. This correlation suggests a primary connection between intercalation and cleavage. A model cleavage site based on these preliminary theoretical calculations and the experimental observations is proposed. It consists of an intercalation site in a trimer duplex. Pyrimidine(p)purine sequences are the predominant sites for intercalation, and the base adjacent to the site at the (3′) end is cleaved.     

Intercalation of Zn(II) and Cu(II) complexes of the cyclic polyamine Neotrien into DNA: equilibria and kinetics

The equilibria and kinetics of the interaction of the Zn(II) and Cu(II) complexes of the macrocyclic polyamine 2,5,8,11-tetraaza[12]-[12](2,9)[1,10]-phenanthrolinophane (Neotrien) with calf thymus DNA have been investigated at pH=7.0 and T=25 degrees C by spectrophotometry, spectrofluorimetry and stopped-flow method. At low dye/polymer ratios both complexes bind to DNA according to the excluded site model. At high dye/polymer ratios the binding displays cooperative features. The logarithm of the binding constant depends linearly on -log[NaCl]. The kinetic results suggest the D + S <==> D, S <==> DS mechanism where the metal complexes (D) react with the DNA sites (S) leading to fast formation of an externally bound form (D,S) which, in turn, is converted into internally bound complex (DS) by intercalation. The binding constants, evaluated as ratios of rate constants, agree with those obtained from equilibrium binding experiments, thus confirming the validity of the proposed model. Fluorescence titrations, where the metal-Neotrien complexes were added to DNA previously saturated with ethidium bromide (EB), show that both complexes displace EB from the DNA cavities. The reverse process, i.e. the addition of excess ethidium to the DNA/metal Neotrien systems, leads to fluorescence recovery for DNA/ZnNeotrien but not for DNA/CuNeotrien. This observation suggests that the binding of CuNeotrien induces deep alterations in the DNA structure. Experiments with Poly(dA-dT)*Poly(dA-dT) and Poly(dG-dC)*Poly(dG-dC) reveal that CuNeotrien mainly affects the structure of the latter polynucleotide.     

High-sensitivity linear dichroism as a tool for equilibrium analysis in biochemistry. Stability constant of DNA--ethidiumbromide complex.

A stoichiometrical application of a sensitive method for linear dichroism (LD) detection is suggested for biochemical purposes. The complex formation between a binding site on a polynucleotide and a ligand may be studied with high precision if the following conditions are fulfilled: (1) The polymer can be given a fixed degree of orientation. (2) The site has a specific orientation with respect to the orientation axis of the polymer (e.g., intercalation). (3) The ligand has an anisotropic optical absorption property. The method was applied to studying the complex between DNA and ethidiumbromide, which was detected by LD with precision of +/- 0.5 X 10(-7) M in a 4 X 10(-4) M DNA solution, i.e., 0.1% occupation of the total site concentration can be detected. The complexation could be explained by a single type of site (n = 0.14 +/- 0.01 sites per nucleotide residue) and a stability constant K1 = (2.5 +/- 1) X 10(5) M-1 at 0.2 M ionic strength. From the specific LD an average angle 60 degrees was concluded between the helix axis and the long axis of the ethidiumbromide molecule. This value formally contradicts the Watson-Crick model or the intercalation model but may be explained by extension and deformation effects on the xhain by the flow.     

Interaction of tripeptides containing arginine and tyrosine (or phenylalanine) residues with synthetic polynucleotides and DNA of various origins

Model peptides--L-Arg-Gly-L-Arg, L-Arg-L-Tyr-L-Arg and L-Arg-L-Phe-L-Arg bind to different DNAs and synthetic polynucleotides and are found in the major groove of the double helix. Polynucleotide complexes containing L-Arg-Gly-L-Arg were studied in order to consider the influence of the arginine residues on the polynucleotide melting temperature. It was shown, that L-Arg-L-Tyr-L-Arg and L-Arg-L-Phe--L-Arg lowers the melting temperature in all polynucleotides studied. The dependence of the melting temperature of polynucleotide (DNA)--L-Arg-L-Tyr(L-Phe)-L-Arg complexes upon the polynucleotide GC-content has been detected. These effects reflect the intercalation of peptide tyrosyl (or phenylalanyl) residues into the double-stranded polynucleotide.     

Binding mode of 4',6-diamidino-2-phenylindole and ethidium to poly(dG).poly(dC).poly(dC)(+) triplex and poly(dG).poly(dC) duplex

Optical spectroscopic properties of 4',6-diamidino-2-phenylindole (DAPI) and ethidium bromide complexed with poly(dG).poly(dC).poly(dC)(+) triplex and poly(dG).poly(dC) duplex were compared in this study. When complexed with both duplex and triplex, ethidium is characterized by hypochromism and a red shift in the absorption spectrum, a complicate induced circular dichroism (CD) band in the polynucleotide absorption region, and a negative reduced linear dichroism signal in both polynucleotide and drug absorption regions. The spectral properties for both duplex- and triplex-bound ethidium are identical and both can be understood by the intercalation binding mode. In contrast, the absorption and CD spectra of DAPI complexed with triplex differ from those of the DAPI-duplex complex, although both complexes can be understood by the intercalation binding mode. Considering that the third strand runs along the major groove of the template duplex, we conclude that the DAPI molecule partially intercalates near the major groove of the duplex, where the third strand can affect its spectroscopic properties.     

Quaternary structure and proteolysis of the polynucleotide phosphorylase from C. perfringens]

This report describes structural studies on purified polynucleotide phosphorylase from C. perfringens. A method is described for the purification of the enzyme which yields a product equivalent in activity to the native polynucleotide phosphorylase from E. coli. These studies revealed a molecular heterogeneity arising from successive stages of proteolysis, to which this enzyme is especially sensitive; unusally, the enzyme is obtained as a mixture of variable proportions of the native and proteolysed forms. We found in all cases a trimeric basic structure composed of the native (alpha) or proteolysed (lapha) or proteolysed (alpha', alpha") catalytic sub-units, However, the enzyme is rather easily dissociated into its sub-units, a phenomenon which seems to accompany proteolysis (Table). Under the action of either endogenous proteases or trypsin, two enzymatic forms are obtained: their quaternary structures seem analogous, but they differ in their catalytic properties from each other and from the initial enzyme. With some care at each step of purification, the polynucleotide phosphorylase of E. coli can be obtained exclusively in its native form. The greater susceptibility to proteolysis of the enzyme from C. perfrigens and the relationship between such degradation and quaternary structure seem to be at the origin of the peculiar behavior of this polynucleotide phosphorylase.     

Interaction of carminomycin with DNA according to data of laser polarized fluorescence

Anti-tumour antibiotic carminomycin interaction with chicken erythrocyte DNA is studied in aqueous-salt solutions by the laser polarized fluorescence method. Fluorescence quenches almost equally effectively during the antibiotic absorption on native (nDNA) and denatured (dDNA) DNAs, but the polarization degree of residual fluorescence differs about two times. Carminomycin binding to dDNA is characterized by one interaction type with a large density of occupancy sites - one antibiotic molecule per base pair. Carminomycin forms two types of complexes with nDNA, differing significantly with binding constants. Strong binding, intercalation, is saturated at one carminomycin molecule per 3 base pairs independently on the solution ionic strength. The weaker, external, interaction is characterized by the binding constant being by two orders of magnitude lower than that for intercalation, and the external interaction contribution is negligible.     

抗菌肽BuforinⅡ衍生物与大肠杆菌基因组DNA的作用机制

【目的】研究抗菌肽BuforinⅡ的衍生物BF2-A/B与大肠杆菌基因组DNA的作用机制。【方法】琼脂糖电泳检测肽对DNA的断裂作用,凝胶阻滞实验研究肽与DNA的结合作用,圆二色谱考察结合肽后DNA结构的变化,荧光光谱分析肽与溴化乙锭竞争性嵌入DNA以及磷酸根对肽与DNA相互作用的影响。【结果】BF2-A/B不断裂基因组DNA而是结合DNA,使DNA双螺旋结构变得松散,削弱碱基对间的堆积作用,并取代EB,使EB-DNA复合体系荧光减弱。而PO43-的加入减弱了肽对DNA-EB荧光的淬灭作用。【结论】衍生肽与DNA的结合方式是先靠静电引力吸附到DNA磷酸基团上,随即插入双螺旋沟槽,嵌入碱基对间。BF2-B有更多的正电荷,更强的插入沟槽和嵌入碱基对的能力,使得其结合DNA的能力比BF2-A强。     

A structural model for the polyadenylic acid single helix.

In the crystal, the poly(A) fragment ApApA assumes a conformation with the 5′-terminal and middle adenosines in a single helical arrangement. From the atomic co-ordinates of these two nucleotides the structure of the poly(A) single helix was derived mathematically. The helix has a pitch height of 25.4 Å, nine nucleotides per turn and the normals to the adenine bases form an angle of 66 ° with the helix axis.     

The interaction of ellipticine derivatives with nucleic acids studied by optical and 1H-nmr spectroscopy: Effect of size of the heterocyclic ring system

The DNA interaction of derivatives of ellipticine with heterocyclic ring systems with three, four, or five rings and a dimethylaminoethyl side chain was studied. Optical spectroscopy of drug complexes with calf thymus DNA, poly [(dA-dT) · (dA-dT)], or poly [(dG-dC) · (dG-dC)] showed a 10 nm bathochromic shift of the light absorption bands of the pentacyclic and tetracyclic compounds upon binding to the nucleic acids, which indicates binding by intercalation. For the tricyclic compound a smaller shift of 1–3 nm was observed upon binding to the nucleic acids. Flow linear dichroism studies show that the geometry of all complexes is consistent with intercalation of the ring system, except for the DNA and poly [(dG-dC) · (dG-dC)] complexes of the tricyclic compound, where the average angle between the drug molecular plane and the DNA helix axis was found to be 65°. One-dimensional ¹H-nmr spectroscopy was used to study complexes between d(CGCGATCGCG)₂ and the tricyclic and pentacyclic compounds. The results on the pentacyclic compound show nonselective broadening due to intermediate chemical exchange of most oligonucleotide resonances upon drug binding. The imino proton resonances are in slow chemical exchange, and new resonances with upfield shifts approaching 1 ppm appear upon drug binding, which supports intercalative binding of the pentacyclic compound. The results on the tricyclic compound show more rapid binding kinetics and very selective broadening of resonances. The data suggest that the tricyclic compound is in an equilibrium between intercalation and minor groove binding, with a preference to bind close to the AT base pairs with the side chain residing in the minor groove. © 1994 John Wiley & Sons, Inc.     

Ligand-DNA interaction in a nanocage of reverse micelle

We have studied intercalation of ethidium bromide (EB) to genomic DNA encapsulated in a nanospace of an anionic AOT reverse micelle (RM). Circular dichroism (CD) study on the DNA in the RM reveals its condensed form. Here, we have used temporal decay-associated spectra (DAS) and time-resolved area normalized emission spectral (TRANES) techniques to investigate EB-binding to condensed DNA because the interference of emission from unbound EB in the RM makes conventional steady state and picosecond resolved fluorescence spectroscopic techniques challenging. The binding affinity of the ligand EB with the DNA in the RM is found to increase with the size of the RM, reflecting the effect of lessening of DNA condensation on the binding affinity. CD spectra of the DNA in the RM with various sizes indicate the structural change of the condensed DNA with reverse micellar size. DAS and TRANES techniques along with dynamic light scattering studies of the EB-DNA complex in the RM further reveal two kinds of binding modes of the ligand with the condensed DNA even in essentially monodispersed RMs. To investigate the role of RM on the ligand binding and secondary structure of the DNA, we have also studied complexation of EB with two synthetic self-complimentary oligonucleotides of sequences (CGCAAATTTGCG)2 and (CGCGCGCGCGCG)2 in the RM.     

Pulse fluorimetry study in polarized light of DNA-ethidium bromide complexes

In previous works, a quantitative analysis of the fluorescence anisotropy decay, based on a comparison of the experimental measurements with a Monte Carlo simulation of the excitation energy migration, has been shown to provide the value of the unwinding angle of the DNA helix, induced by an ethidium bromide (E.B.) molecule intercalation. In the present work some of the characteristics of the model used in the computation are reexamined: namely the influence of the direction of the E.B. electronic moment, and the influence of the dye distribution along the DNA helix are studied. The computations are compared with experimental results obtained with new experiments performed with calf thymus and micrococcus lysodeikticus DNA-E.B. complexes. It is found that the difference in base composition of these DNA does not influence the fluorescence properties of their E.B. complexes. Our study confirms the validity of the dye distribution obtained with the single adjacent excluded site principle. Reasonable values of the unwinding angle are obtained by assuming that the transition moment direction lies along the great axis of the E.B. molecule. The value of this unwinding angle is compared with other values proposed in the literature.     

Synthesis, crystal structure and DNA binding studies of a binuclear copper(II) complex with phenanthroline

A new binuclear copper(II) complex, [Cu2Phen2Cl4] (Phen=1,10-phenanthroline), has been synthesized and characterized. Single crystal X-ray diffraction results suggest that this complex structure belongs to monoclinic crystal system, Cc (no. 9) with the cell dimensions: a=9.849(2)A, b=17.833(4)A, c=13.374(3)A, beta=106.61(3) degrees , V=2251.0(8)A(3), Dc=1.8569 Mgm(-3), F(000)=1256.0, Z=4. One Cu(II) central atom situated in a distorted square planar geometry is four-coordinated. The other situated in a distorted square pyramidal geometry is five-coordinated. Only one bridging Cl atom exists in the complex. Spectroscopic studies, including electronic absorption and fluorescence spectra, conductivity measurements and parallel factor analysis (PARAFAC) of fluorescence excitation-emission three-way data array, were carried out on the DNA binding behavior of the complex. All the results suggested that the breakage of DNA secondary structure took place at low molar ratio of complex to DNA (0.3 at most) and intercalation into the base pair of DNA took place at high molar ratio. Additionally, the equilibrium concentration of EB-DNA and EB (EB: ethidium bromide) could be directly obtained by PARAFAC algorithm, proved to be a convincing method for studying the interaction of complexes with DNA.     

Effect of some drugs on excision repair in E. coli cells.

The intercalating dye ethidium bromide (EB), inhibits excision of pyrimidine dimers from UV-irradiated excision-proficient Escherichia coli B/r hcr+ cells. Inhibition is total at a 2.5 - 10(-4) M concentration 120 min after irradiation with a dose of 750 erg/mm2. The viability of irradiated cells diminishes in proportion to the EB concentration. Under wholly analogous conditions of cultivation and irradiation no inhibitory effect of KCN and caffeine (CFF) and only a slight effect of chloramphenicol (CAP) on dimer excision has been observed. The viability of cells is affected by these compounds but it does not appear to depend on the quantity of excised photoproducts. A change in the secondary structure of DNA induced by intercalation of EB appears to be the reason for the depression of excision of UV photoproducts.