Conformational transitions of a synthetic DNA poly(dA-dU). poly(dA-dU) in concentrated solutions of caesium fluoride

Chiroptical properties of poly(dA-dU).poly(dA-dU) were studied in concentrated NaCl and CsF solutions to reveal the role of the alternating B conformation in the CsF-induced alternating B-X conformational transition of poly(dA-dT).poly(dA-dT). Poly(dA-dU).poly(dA-dU) has been chosen for this purpose because it has, instead of the alternating B conformation, a regular conformation like poly(dG-dC).poly(dG-dC) in low-salt solution. It was found that poly(dA-dU).poly(dA-dU) did not assume that Z form at high NaCl concentrations but exhibited extensive CsF-induced changes in the circular dichroism spectra like poly(dA-dT).poly(dA-dT). The changes of reflect two consecutive two-state conformational transitions of the polynucleotide, both taking place with fast kinetics and low cooperativity. The transition were interpreted as involving the regular and alternating B conformation at lower CsF concentrations and the alternating B and X conformation at higher CsF concentrations. A comparison of the behaviour of poly(dA-dU).poly(dA-dU) and poly(dA-dT).poly(dA-dT) in CsF solutions demonstrates that the thymine methyl groups promote the X form but are not crucial for its existence. On the other hand, the alternating B conformation appears to be the inevitable starting structure for DNA isomerization into the X form.     

RNA-like conformational properties of a synthetic DNA poly(dA-dU).poly(dA-dU)

Differences in the circular dichroism of poly(dA-dT).poly(dA-dT) and poly(dA-dU).poly(dA-dU) and in its temperature induced changes are reported. A comparison to the data obtained with DNA and RNA indicates that an absence of thymine methyl groups in the polynucleotide results in promoting its RNA-like conformational properties. However, poly(dA-dU).poly(dA-dU) is not an A-DNA type of double helix.     

Uracil in deoxyribonucleotide polymers reduces their template-primer activity for E. coli DNA polymerase I.

The physical and biochemical properties of two pairs of synthetic DNA template-primers were investigated. The copolymer poly(dA-dU) . poly(dA-dU) and the homopolymer duplex poly(dA). poly(dU) were characterized by a lower Tm and by a higher buoyant density value than the respective thymine polynucleotides poly(dA-dT) . poly(dA-dT) and poly(dA) . poly(dT). The polymerizing and the primer terminus adding reactions of a homogenous E. coli DNA polymerase I preparation, as measured by incorporation of [3H]dAMP into the acid-insoluble fraction, were significantly poorer with uracil-containing template-primers than with thymine templates. Moreover, the uracil-containing polynucleotides inhibited the polymerizing activity of DNA polymerase I to a greater extent than the thymine polynucleotides, when the enzymatic activity was investigated with a dATP/dTTP/dUTP-free incorporation system making use of poly(dI-dC) . poly(dI-dC) as the template-primer.     

Aliphatic substituents in place of thymine methyl promote zig-zag character of the poly(dA-dT)·poly(dA-dT) backbone

This work compared circular dichroism and phosphorus n.m.r. of poly(dA-dU)·poly(dA-dU), poly(dA-dT)·poly(dA-dT), poly(dA-ethyl⁵dU)·poly(dA-ethyl⁵dU), and poly(dA-butyl⁵dU)·poly(dA-butyl⁵dU) at low-salt and in concentrated caesium chloride and caesium fluoride solutions. It is demonstrated that growing bulk of the substituent increases the conformationl anomaly residing in the purine(3′–5′)pyrimidine steps while the backbone is less affected in the pyrimidine (3′–5′)purine steps. As the length of the substituent increases, conformation of the polynucleotides alters more dramatically at increasing concentrations of caesium cations. At high CsF concentrations, all the polynucleotides adopt a novel conformer which we call X-DNA and its formation is promoted by larger substituents. The X-DNA conformation of poly(dA-butyl⁵dU)·poly(dA-butyl⁵dU) gives two phosphorus n.m.r. resonances separated as much as in the case of the left-handed zig-zag Z-DNA double helix of poly(dG-dC)·poly(dG-dC) but X-DNA and Z-DNA differ qualitatively by an opposite dinucleotide repeat. Phosphorus n.m.r. spectra of poly(dA-dT)·poly(dA-dT) and poly(dA-butyl⁵dU)-poly(dA-butyl⁵dU) differ quantitatively at high CsF concentrations, which may reflect conformational variability of the X-DNA backbone. Poly(dA-butyl⁵dU)·poly(dA-butyl⁵dU), but not poly(dA-ethyl⁵dU)·poly(dA-ethyl⁵dU) and the related polynucleotides with shorter substituents in position 5 of uracil, exhibits one more reversible transition at very high caesium fluoride concentrations. It is accompanied by polynucleotide associations and has a slow kinetics. This transition may involve one more radical change in the double helix architecture from X-DNA into another conformation.     

Studies on binding of toromycin, an antitumor antibiotic, to DNA

Toromycin, an antitumor, bactericidal and antiviral compound, was found to bind to DNA in such a way as to interfere with the dissociation of double helix at an elevated temperature. The antibiotic did not introduce strand scission into DNA. Single-strand-specific nuclease S1-susceptibility of negatively supercoiled DNA was not influenced by its binding. The antibiotic was shown to bind to both of the alternating purine-pyrimidine copolymers, poly(dG-dC):poly(dG-dC) and poly(dA-dT):poly(dA-dT). The unique C-glycoside molecule of toromycin interacted with single-stranded DNA, but was found to have no affinity for RNA.     

Sequence-recognition and cleavage of DNA by a netropsin-phenazine-di-N-oxide conjugate

We report the synthesis, DNA-binding and cleaving properties, and cytotoxic activities of R-128, a hybrid molecule in which a bis-pyrrolecarboxamide-amidine element related to the antibiotic netropsin is covalently tethered to a phenazine-di-N-oxide chromophore. The affinity and mode of interaction of the conjugate with DNA were investigated by a combination of absorption spectroscopy, circular dichroism, and electric linear dichroism. This hybrid molecule binds to AT-rich sequences of DNA via a bimodal process involving minor groove binding of the netropsin moiety and intercalation of the phenazine moiety. The bidentate mode of binding was evidenced by linear dichroism using calf thymus DNA and poly(dA-dT).(dA-dT). In contrast, the drug fails to bind to poly(dG-dC).poly(dG-dC), because of the obstructive effect of the guanine 2-amino group exposed in the minor groove of this polynucleotide. DNase I footprinting studies indicated that the conjugate interacts preferentially with AT-rich sequences, but the cleavage of DNA in the presence of a reducing agent can occur at different sequences not restricted to the AT sites. The main cleavage sites were detected with a periodicity of about 10 base pairs corresponding to approximately one turn of the double helix. This suggests that the cleavage may be dictated by the structure of the double helix rather than the primary nucleotide sequence. The conjugate which is moderately toxic to cancer cells complements the tool box of reagents which can be utilized to produce DNA strand scission. The DNA cleaving properties of R-128 entreat further exploration into the use of phenazine-di-N-oxides as tools for investigating DNA structure.     

Conformational Variability of Poly(dA-dT)·Poly(dA-dT) and Some Other Deoxyribonucleic Acids Includes a Novel Type of Double Helix

Abstract

The article reviews data indicating that poly(dA-dT)?poly (dA-dT) is able of adopting three distinct double helical structures in solution, of which only the A form conforms to classical notions. The other two structures have dinucleotides as double helical repeats. At low salt concentrations poly(dA-dT)?poly(dA-dT) adopts a B-type alternating conformation which is exceptionally variable. Its architecture can gradually move in the limits demarcated by the CD spectra with inverted long wavelength CD bands and the ³¹P NMR spectra with a very low and a 0.6 ppm separation of two resonances. Contrary to Z-DNA, the ³¹P NMR spectrum of the limiting alternating B conformation of poly(dA-dT)?poly(dA-dT) is characterized by an upfield shift of one resonance. We attribute the exceptional conformational flexibility of the alternating B conformation to the unequal tendency of bases in the dA-dT and dT-dA steps to stack.

However, by assuming the limiting alternating B conformation, the variability of the synthetic DNA is not exhausted. Specific agents make it isomerize into another conformation by a fast, two-state mechanism, which is reflected by a further deepening of the negative long wavelength CD band and a downfield shift of the ³¹P NMR resonance of poly (dA-dT)?poly(dA-dT) that was constant in the course of the gradual alterations of the alternating B conformation. These changes are, however, qualitatively different from the way poly(dG-dC)?poly(dG-dC) behaves in the course of the B-Z isomerization. Poly(dG-dC) ?poly(dG-dC) displays purine-pyrimidine (dGpdC) resonance in the characteristic downfield position, while the downfield resonance of poly(dA-dT)?poly(dA-dT) belongs to the pyrimidine-purine (dTpdA) phosphodiester linkages. Consequently, phosphodiester linkages in the purine-pyrimidine steps play a similar role in the appearance of the Z form to the pyrimidine-purine phosphodiesters in the course of the isomerization of poly(dA-dT)?poly(dA-dT). This excludes that the high-salt structures of poly(dA-dT)?poly(dA-dT) and poly(dG-dC)?poly(dG-dC) are members of the same conformational family. We call the high-salt conformation of poly(dA-dT)?poly(dA-dT) X-DNA.

It furthermore follows from the review that synthetic molecules of DNA with alternating purine-pyrimidine sequences of bases can adopt either the Z form or the X form, or even both, depending on the environmental conditions. This introduces a new dimension into the DNA double helix conformational variability. The possible biological relevance of the X form is suggested by experiments with linear molecules of natural DNA. These indicate that Arich regions in natural DNAs can isomerize into the X form while the bulk of the molecule remains in the B form. The coexistence of both structures in a single DNA molecule may be understood in view of the favourable kinetic and thermodynamic properties with which the X form appears.     

Covalent binding of benzo[a]pyrenediol epoxides to polynucleotides

Spectroscopic studies on the trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene- (anti-BPDE-) modified synthetic polynucleotide solutions reveal interesting sequence-dependent stereoselective covalent binding of anti-BPDE to DNA. Absorption spectral results indicate that the G.C polymers are much more reactive than the A.T polymers toward this metabolite and the homopolymer suffers higher modification than its corresponding alternating polynucleotide. The covalently attached anti-BPDE exhibits only a 2-3-nm red shift in the guanine-containing polynucleotide and native DNA solutions as opposed to the 8-nm red shift in poly(G) and none in the A.T polymers. Distinct stereoselectivities are exhibited by poly(dG-dC).poly(dG-dC) vs. poly(dG).poly(dC) as suggested by the oppositely signed CD in the pyrene spectral region. Comparison with the syn-BPDE modified polynucleotides reveals some interesting differences with its anti diastereomer. Significant contributions from the intercalated syn-BPDE are apparent in the modified guanine-containing polynucleotides as indicated by the appearance of 10-nm red-shifted shoulders. In contrast to the strong dependence on polynucleotides for anti-BPDE, the rate of hydrolysis of syn-BPDE appears to be insensitive to their presence in the solution. anti-BPDE modification on the 50 microM hexaamminecobalt-induced Z-form poly(dG-dC).poly(dG-dC) is much less extensive than its corresponding B form, possibly the consequence of both structural and ionic strength factors. The spectral characteristics of anti-BPDE bonded to these two forms are distinctly different, with the Z form resembling more closely those of A.T polymers.(ABSTRACT TRUNCATED AT 250 WORDS)     

Molecular recognition of DNA by small molecules: AT base pair specific intercalative binding of cytotoxic plant alkaloid palmatine

The base dependent binding of the cytotoxic alkaloid palmatine to four synthetic polynucleotides, poly(dA).poly(dT), poly(dA-dT).poly(dA-dT), poly(dG).poly(dC) and poly(dG-dC).poly(dG-dC) was examined by competition dialysis, spectrophotometric, spectrofluorimetric, thermal melting, circular dichroic, viscometric and isothermal titration calorimetric (ITC) studies. Binding of the alkaloid to various polynucleotides was dependent upon sequences of base pairs. Binding data obtained from absorbance measurements according to neighbour exclusion model indicated that the intrinsic binding constants decreased in the order poly(dA).poly(dT)>poly(dA-dT).poly(dA-dT)>poly(dG-dC).poly(dG-dC)>poly(dG).poly(dC). This affinity was also revealed by the competition dialysis, increase of steady state fluorescence intensity, increase in fluorescence quantum yield, stabilization against thermal denaturation and perturbations in circular dichroic spectrum. Among the polynucleotides, poly(dA).poly(dT) showed positive cooperativity at binding values lower than r=0.05. Viscosity studies revealed that in the strong binding region, the increase of contour length of DNA depended strongly on the sequence of base pairs being higher for AT polymers and induction of unwinding-rewinding process of covalently closed superhelical DNA. Isothermal titration calorimetric data showed a single entropy driven binding event in the AT homo polymer while that with the hetero polymer involved two binding modes, an entropy driven strong binding followed by an enthalpy driven weak binding. These results unequivocally established that the alkaloid palmatine binds strongly to AT homo and hetero polymers by mechanism of intercalation.     

Conformational variability of poly(dA-dT).poly(dA-dT) and some other deoxyribonucleic acids includes a novel type of double helix

The article reviews data indicating that poly(dA-dT).poly(dA-dT) is able of adopting three distinct double helical structures in solution, of which only the A form conforms to classical notions. The other two structures have dinucleotides as double helical repeats. At low salt concentrations poly(dA-dT).poly(dA-dT) adopts a B-type alternating conformation which is exceptionally variable. Its architecture can gradually move in the limits demarcated by the CD spectra with inverted long wavelength CD bands and the 31P NMR spectra with a very low and a 0.6 ppm separation of two resonances. Contrary to Z-DNA, the 31P NMR spectrum of the limiting alternating B conformation of poly(dA-dT).poly(dA-dT) is characterized by an upfield shift of one resonance. We attribute the exceptional conformational flexibility of the alternating B conformation to the unequal tendency of bases in the dA-dT and dT-dA steps to stack. However, by assuming the limiting alternating B conformation, the variability of the synthetic DNA is not exhausted. Specific agents make it isomerize into another conformation by a fast, two-state mechanism, which is reflected by a further deepening of the negative long wavelength CD band and a downfield shift of the 31P NMR resonance of poly(dA-dT).poly(dA-dT) that was constant in the course of the gradual alterations of the alternating B conformation. These changes are, however, qualitatively different from the way poly(dG-dC).poly(dG-dC) behaves in the course of the B-Z isomerization. Poly(dG-dC).poly(dG-dC) displays purine-pyrimidine (dGpdC) resonance in the characteristic downfield position, while the downfield resonance of poly(dA-dT).poly(dA-dT) belongs to the pyrimidine-purine (dTpdA) phosphodiester linkages. Consequently, phosphodiester linkages in the purine-pyrimidine steps play a similar role in the appearance of the Z form to the pyrimidine-purine phosphodiesters in the course of the isomerization of poly(dA-dT).poly(dA-dT). This excludes that the high-salt structures of poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC) are members of the same conformational family. We call the high-salt conformation of poly(dA-dT).poly(dA-dT) X-DNA. It furthermore follows from the review that synthetic molecules of DNA with alternating purine-pyrimidine sequences of bases can adopt either the Z form or the X form, or even both, depending on the environmental conditions. This introduces a new dimension into the DNA double helix conformational variability. The possible biological relevance of the X form is suggested by experiments with linear molecules of natural DNA.(ABSTRACT TRUNCATED AT 400 WORDS)     

Sequence-dependent changes in the chiroptical properties of DNA upon interaction with dipyrandium

Interaction of dipyrandium with DNA and its dependence on the base sequence was studied using circular dichroism. It was found that calf thymus DNA and polynucleotide duplexes with alternating purine-pyrimidine sequences containing GC basepairs underwent similar alterations in the chiroptical properties upon binding of dipyrandium. The alterations suggest that these DNAs have similar B-type structures which may kink at the dipyrandium binding sites. On the other hand, poly(dA-dt)·poly(dA-dT) and especially poly(dA-dU)·poly(dA-dU) exhibit some features of A-type structure. Poly(dA-dT)·poly(dA-dT) changes its chiroptical properties little when complexed with dipyrandium, as if it contained some type of kinks as equilibrium structural elements.     

Interaction of nucleic acids with electrically charged surfaces: II. Conformational changes in double-helical polynucleotides

The influence of adsorption of double-stranded (ds) DNA, ds RNA and homopolymeric pairs at a mercury electrode on conformation of these polynucleotides was studied. Changes in the polarographic reducibility of polynucleotides, which were followed by means of normal pulse polarography and linear sweep peak voltammetry at the dropping mercury electrode were exploited to indicate conformational changes. It was found that, as a consequence of adsorption of ds polynucleotides on the negatively charged electrode conformational changes similar to denaturation take place in a narrow potential region around ?1.2 V (the region U). After sufficiently long time of the contact with the electrode (under our conditions about 10 s) these changes reach limiting values, which can approach total denaturation. Upon adsorption of ds polynucleotides on the electrode charged to more positive potentials than the region U either (1) no conformational changes occur or (2) only a small part of the polynucleotide (probably labile regions of the ds molecule) is very quickly denatured - the remainder of the molecule preserves its ds structure. Conformational changes of adsorbed ds polynucleotides are influenced by factors which change the stability of ds polynucleotides in solution. It is supposed that denaturation of ds polynucleotides in the region U might result from the strains connected with the repulsion of certain segments of the molecule anchored on the electrode from the negatively charged surface.     

Characterization of the binding of YO to [poly(dA-dT)]2 and [poly(dG-dC)]2, and of the fluorescent properties of YO and YOYO complexed with the polynucleotides and double-stranded DNA

The interaction between the fluorescent dye YO (oxazole yellow) and the alternating polynucleotides [poly(dA-dT)]₂[the duplex of alternating poly(dA-dT)]and [poly(dG-dC)]₂[the duplex of alternating poly(dG-dC)] has been studied with optical spectroscopic techniques including absorbance, flow linear dichroism, CD, and fluorescence measurements. The principal features of the spectra are very similar for the two polynucleotide solutions, showing that YO binds quite similarly to AT and GC base pairs. From a strongly negative reduced linear dichroism (LD^r) in the dye absorption band, an induced negative CD, and transfer of energy from the bases to bound YO, we conclude that at low mixing ratios YO is intercalated in both [poly(dA-dT)]₂ and [poly(dG-dC)]₂. At higher mixing ratios an external binding mode starts to contribute, evidenced from the appearance of an exciton CD. The conclusion that YO binds in a similar way to AT and GC base pairs should be valid also for the dimer YOYO since its YO units have been found to bind to double-stranded (dsDNA) in the same way as the YO monomer. The fluorescence properties of YO and YOYO complexed with DNA or the polynucleotides have been characterized by studying the dependence of fluorescence intensity on temperature, mixing ratio, and ionic strength. The fluorescence intensity and fluorescence lifetime of YO-DNA decrease strongly with increasing mixing ratio, whereas the fluorescence intensity of YOYO-DNA shows a weaker dependence, indicating that the quantum yield depends on the distance between the YO chromophores on the DNA chain. Further, the fluorescence intensity of YO depends on the base sequence; the quantum yield and fluorescence lifetime for YO complexed with [poly(dG-dC)]₂ are about twice as large as for YO complexed with [poly(dA-dT)]₂. Measurements of excitation spectra at different mixing ratios and different emission wavelengths indicate that the fluorescence of the externally bound chromophores is negligible compared to the intercalated ones. © 1995 John Wiley & Sons, Inc.     

Quinacrine: Spectroscopic properties and interactions with polynucleotides

The acridine dye quinacrine and its interactions with calf thymus DNA, poly(dA-dT) · poly (dA-dT), and poly (dG-dC) · poly(dG-dC) were studied by light absorption, linear dichroism, and fluorescence spectroscopy. The transition moments of quinacrine give rise to absorption bands polarized along the short axis (400–480-nm band), and the long axis (345-nm and 290-nm bands) of the molecule, respectively. Linear dichroism studies show that quinacrine intercalates into calf thymus DNA as well as into the polynucleotides, displaying fairly homogeneous binding to poly (dA-dT) · poly (dA-dT), but more than one type of intercalation site for calf thymus DNA and poly (dG-dC) · poly(dG-dC). Fluorescence spectroscopy shows that for free quinacrine the pK = 8.1 between the mono- and diprotonated states also remains unchanged in the excited state. Quinacrine bound to calf thymus DNA and polynucleotides exhibits light absorption typical for the intercalated diprotonated form. The fluorescence enhancement of quinacrine bound to poly (dA-dT) · poly(dA-dT) may be due to shielding from water interactions involving transient H-bond formation. The fluorescence quenching in poly(dG-dC) · poly(dG-dC) may be due to excited state electron transfer from guanine to quinacrine. © 1993 John Wiley & Sons, Inc.     

DNA sequence has an effect on the extent and kinds of alkylation of DNA by a potent carcinogen

A system has been developed to study the effects of base sequence (neighboring bases) upon the alkylation of guanine (G) and adenine (A) bases in DNA. The study was performed on the synthetic polydeoxyribonucleotides, poly(dG).poly(dC), poly(dG-dC).poly(dG-dC), poly(dA).poly(dT), poly(dA-dT).poly(dA-dT), poly(dA-dC).poly(dG-dT), poly(dA-dG).poly(dC-dT), as well as calf thymus DNA. Each polynucleotide was treated with N-[3H]methyl-N-nitrosourea (MNU), depurinated, and the freed alkylpurines separated by HPLC and quantitated by liquid scintillation counting. The amounts of 3-methylguanine (3-MG), 7-MG, and O6-MG relative to guanine, and 3-methyladenine (3-MA) and 1-MA plus 7-MA relative to adenine, and also the O6-MG/7-MG ratios were highly reproducible for a given polynucleotide. Significant differences were found in the amounts of each of the methylpurines formed when compared among the six synthetic polynucleotides and DNA. This evidence is interpreted as an effect upon alkylation which is ultimately dependent upon the base sequence. These findings may have significance in defining the specificity of chemical carcinogens in terms of the susceptability to modification of nucleotide sequences such as those found in certain oncogenes.     

Conformational peculiarities of polynucleotides with a nonrandom base sequence according to the 1H----3H exchange rate in C8H groups of purinic residues

We have determined the 1H----3H exchange rate constants between water and C8H groups of purinic residues of alternating polynucleotides poly(dA-dT).poly(dA-dT), poly(dG-dC).poly(dG-dC) and poly(dA-dC).poly(dG-dT) as well as homopolynucleotides poly(dA).poly(dT) and poly(dG).poly(dC) in aqueous solutions with high-salt concentrations (3 M NaCl and 4-6 M CsF), in water-ethanol (60%) solution and in 0.15 M NaCl at 25 degrees C. The rate constants for adenine (kA) and guanine (kG) of polynucleotides were compared with corresponding constants for E. coli DNA. dGMP nd dAMP at the same conditions. The relation between exchange rates and conformations of polynucleotides permits the study of their conformational peculiarities in solution. Of three alternating polynucleotides examined in 0.15 M NaCl the exchange retardation was observed only for poly(dA-dT).poly(dA-dT) as compared with that in B-DNA, which is in good agreement with the B-alternating "wrinkled" DNA model. The conformations of poly(dG-dC).poly(dG-dC) and poly(dA-dC).poly(dG-dT), according to the exchange data obtained are within the B form. For homopolynucleotides in 0.15 M NaCl, the KA value for poly(dA).poly(dT) is nearly the same as kA for B-DNA, which indicates the similarity of their conformations, whereas the kG value for poly(dG).poly(dC) is 1.7-fold lower in comparison with the kG value in B-DNA. This seems to be connected with the existence of B = A conformation equilibrium for poly(dG).poly(dC) in solution. The increase of NaCl concentration to 3 M results in a B----Z transition in the case of poly(dG-dC).poly(dG-dC) and in the shift of B = A equilibrium towards the A-form in the case of poly(dG).poly(dC) as is evidenced by alterations of their KG values. Poly(dA-dT).poly(dA-dT) in 6 M CsF and poly(dA-dC).poly(dG-dT) in 4.3 M CsF maintain their inherent conformations in 0.15 M NaCl in spite of the fact that they are characterised by the "X-type" CD-spectrum at these conditions. According to the exchange data the conformation of poly(dA).poly(dT) in 6 M CsF corresponds to the "heteronomous" DNA model or some other structure with lower accessibility of C8H groups of adenylic residues.     

Differential binding of the enantiomers of chloroquine and quinacrine to polynucleotides: Implications for stereoselective metabolism

Interaction of the antimalarial drugs quinacrine and chloroquine with DNA has been studied extensively in order to understand the origin of their biological activity. These studies have shown that they bind to DNA through an intercalative mode and show little sequence specificity. All previous experiments were carried out using the racemic form of these drugs. We have investigated the binding of the enantiomeric forms of quinacrine and chloroquine to synthetic polynucleotides poly (dA-dT) · poly(dA-dT) and poly (dG-dC) · poly(dG-dC), and found interesting differences in their binding parameters. Quinacrine enantiomers have a much higher binding affinity for the two polynucleotides compared to those of chloroquine. The negative enantiomers were found to have higher binding affinity than the positive ones. The binding constant for the binding of quinacrine (?) to poly(dG-dC) · poly(dG-dC) was found to be about 3 times that of quinacrine (+). The differences in these binding affinities were further confirmed by equilibrium dialysis of the complexes of the polynucleotides with the racemic form of the drugs, which resulted in the enrichment of the dialysate with the positive enantiomer. CD spectra of the enantiomers and their polynucleotide complexes are reported. Changes in the fluorescence properties of quinacrine in the presence of the two polynucleotides are also described. Biological implications of these findings are discussed. © 1993 John Wiley & Sons, Inc.     

The existence of unique B structures in polynucleotides with alternating purine-pyrimidine sequences

The infrared spectra of the sodium salts of calf-thymus DNA, poly(dA-dC).poly(dG-dT), poly(dA-dT) and poly(dG-dC) were measured for the samples as highly hydrated, nonoriented gels. The bands from the sugar-phosphate vibrational modes show that poly(dG-dC) assumes a B-family structure which is different from the B structures of the other samples. Poly(dG-dC) most likely assumes a wrinkled B structure. The other samples retain a smooth B structure. An alternating purine-pyrimidine sequence is not a sufficient condition for the formation of wrinkled B structure in a polynucleotide.     

Resonance Raman spectroscopy of polynucleotides

Resonance Raman Spectroscopy allows a selective study of the bases of DNA and therefore of the interactions of these bases with ligands. This technique is also sensitive to structural modifications. We show here that, first, the structures of native poly(dA-dT).poly(dA-dT) and poly(dA).poly(dT) are not the same and that, secondly, it is possible to characterize the B----Z transition of poly(dG-dC).poly(dG-dC). The study of the Raman hypochromism during the thermal denaturation of the polynucleotides reveals that the stacking of the adenines in poly(dA).poly(dT) is near that observed in poly(rA) but differs of this stacking in poly(dA-dT).poly(dA-dT). The enhancement of the intensity of the guanine line at 1193 cm-1 and of the cytosine lines at 780 cm-1, 1 242 cm-1 and 1268 cm-1 as well as the shift of the guanine line at low frequency should allow to characterize a small proportion of base pairs in Z form in any DNA.     

DNA-binding affinities and sequence selectivity of quaternary benzophenanthridine alkaloids sanguinarine, chelerythrine, and nitidine

A comparative study on the intercalating binding of sanguinarine, chelerythrine, and nitidine with CT DNA, poly(dG-dC).poly(dG-dC), poly(dA-dT).poly(dA-dT), and seven sequence-designed double-stranded oligodeoxynucleotides has been performed using fluorometric and spectrophotometric techniques, aiming at providing insights into their sequence selectivity for DNA-binding. The results show that both sanguinarine and nitidine bind preferentially to DNA containing alternating GC base pairs [d(TGCGCA)(2)], while chelerythrine exhibits quite distinct sequence selectivity from sanguinarine, which shows a high specificity for DNA containing contiguous GC base pairs [5'-TGGGGA-3'/3'-ACCCCT-5'].