A left-handed (Z) conformation of poly(dA-dC).poly(dG-dT) induced by polyamines.

Blocks of potential Z-DNA forming alternating purine-pyrimidine (APP) sequences are widely dispersed in native DNAs. We have studied the effects of naturally occurring polyamines on the conformation of a synthetic APP sequence, poly(dA-dC).poly(dG-dT) by circular dichroism spectroscopy. In the presence of micromolar concentrations of spermidine (125 microM) and spermine (16 microM), this polymer undergoes B to Z transition in low ionic strength (2 mM Na+) buffers. The concentration of polyamines required for B to Z transition increases with Na+ in the buffer and a straight line is obtained on plotting ln[Na+] vs. ln [spermidine 3+]. However, at concentrations of polyamines higher than those necessary to induce B to Z transition, Z-DNA converts to psi-DNA, an ordered, twisted, tight packing arrangement of the double helix. These results suggest a pathway for the transient formation of Z-DNA segments in vivo by interaction of the ubiquitous polyamines with naturally occurring blocks of APP sequences.     

Circular dichroism of polynucleotides: Interactions of NiCl2 with poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC) in a water-in-oil microemulsion

The thermal behavior of the synthetic, high molecular weight, double stranded polynucleotides poly(dA-dT).poly(dA-dT) [polyAT] and poly(dG-dC).poly(dG-dC) [polyGC] solubilized in the aqueous core of the quaternary water-in-oil cationic microemulsion CTAB|n-pentanol|n-hexane|water in the presence of increasing amounts of NiCl(2) at several constant ionic strength values (NaCl) has been studied by means of circular dichroism and electronic absorption spectroscopies. In the microemulsive medium, both polynucleotides show temperature-induced modifications that markedly vary with both Ni(II) concentration and ionic strength. An increase of temperature causes denaturation of the polyAT duplex at low nickel concentrations, while more complex CD spectral modifications are observed at higher nickel concentrations and ionic strengths. By contrast, thermal denaturation is never observed for polyGC. At low Ni(II) concentrations, the increase of temperature induces conformational transitions from B-DNA to Z-DNA form, or, more precisely, to left-handed helical structures. In some cases, at higher nickel concentrations, the CD spectra suggest the presence of Z'-type forms of the polynucleotide.     

Immunological and spectroscopic studies of poly(dG-dC).poly(dG-dC) modified by cis-diamminedichloroplatinum(II)

The conformational changes induced by the binding of cis-diamminedichloroplatinum(II) to poly(dG-dC).poly(dG-dC) have been studied by reaction with specific antibodies, by circular dichroism and 31P nuclear magnetic resonance. Polyclonal and monoclonal antibodies to Z-DNA bind to platinated poly(dG-dC).poly(dG-dC) at low and high ionic strength. Antibodies elicited in rabbits immunized with the platinated polynucleotide bind to double stranded polynucleotides known to adopt the Z-conformation. At low and high ionic strength the circular dichroism spectrum of platinated poly(dG-dC).poly(dG- dC) does not resemble that of poly(dG-dC).poly(dG-dC) (B or Z conformation). At low ionic strength, the characteristic 31P nuclear magnetic resonance spectrum of the Z-form is not detected. It appears only at high ionic strength, as a component of a more complex spectrum.     

Influence of tetraalkyl ammonium ions on the structure of poly (rG-dC).poly (rG-dC): unexpected transitions among the Z, A and B conformations.

The conformation of the double-stranded, mixed ribodeoxyribo polynucleotide, poly (rG-dC).poly (rG-dC), has been examined in the presence of tetraalkyl ammonium ions. Tetramethyl ammonium ion stabilizes the "low salt" Z conformation (1) of the polymer from submillimolar to molar concentrations of the counterion. In the presence of tetraethyl and tetrapropyl ammonium ions the polymer exists in the low salt Z form up to 2 mM concentration of the counterions and then flips to the right hand helical A form. With tetrabutyl ammonium counterions the polymer is in an A conformation at low ion concentrations and converts to a B form at concentrations greater than thirty millimolar. These results are interpreted in terms of electrostatic and solvent interactions of the polynucleotide.     

Spectrophotometric and kinetic studies of the binding of Ni, Co, and Mg to poly(dG-dC) · poly(dG-dC). Determination of the stoichiometry of the Ni-induced B → Z transition

Data are reported for the binding of Ni²⁺, Co²⁺, and Mg²⁺ to the B-form of double-stranded poly(dG-dC) at ionic strength conditions I = 0.001 M, 0.01 M, and 0.1 M. The apparent binding constants for Ni²⁺ and Co²⁺ are about the same and are 2- to 3-fold higher than those for Mg²⁺. Kinetic studies indicate that Mg²⁺ binds to the polynucleotide mainly (or solely) as a mobile cloud (electrostatically, outer-sphere), whereas the transition metal ions undergo site binding (inner-sphere coordination) with poly(dG-dC). The kinetic data suggest that an Ni²⁺ ion coordinates to more than one binding site at the polynucleotide, presumably to G-N₇ and a phosphate group.

At low ionic strength conditions the addition of Ni²⁺ induces a B → Z conformational transition in poly(dG-dC). As demonstrated by UV absorption and CD spectroscopy, the transition occurs at I = 0.001 M already when 3 × 10⁻⁵ – 7 × 10⁻⁵ M of Ni²⁺ are added to 8 × 10⁻⁵ M (in monomeric units) of poly(dG-dC), and at I = 0.01 M between 2.5 × 10⁻⁴ and 4.5 × 10⁻⁴ M of Ni²⁺. Using murexide as an indicator of the concentration of free Ni²⁺ ions, the amount of Ni²⁺ which is bound to the polynucleotide could be determined. At I = 0.001 M it was established that the B → Z transition begins when 1 Ni²⁺ is bound coordinatively per four base pairs, and the transition is complete when 1 Ni²⁺ is bound coordinatively per three base pairs. It is this coordinated Ni²⁺ which induces the B → Z transition.     

Studies of bivalent copper ion binding to poly C

Ultraviolet differential spectra of single-stranded poly C, taken in the presence of Cu2+ ions, are studied at various ionic strengths and temperatures. Coordinational and conformational components of these spectra are obtained. The Cu2+ ion coordination site on the polynucleotide bases is found to be N(3) and possibly O(2). The direction of the poly C absorption band shift due to ion binding and conformational transitions is established. At low ionic strengths of the solution Cu2+ ions cause the helical parts of poly C to melt. At high ones the formation of double-stranded parts was observed in addition to the above effect. The calculated concentration dependences of ion-poly C bases association constants show that binding is cooperative at any ionic strength.     

Toroidal condensation of Z DNA and identification of an intermediate in the B to Z transition of poly(dG-m5dC) X poly(dG-m5dC)

Using a combination of spectroscopic techniques, quasi-elastic laser light scattering (QLS), and electron microscopy (EM), we have been able to show that the B to Z transition of poly(dG-m5dC) X poly(dG-m5dC) is accompanied by extensive condensation of the DNA in both low and high ionic strength buffers. At low concentrations of NaCl (2 mM Na+), an intermediate rodlike form, which exhibits a circular dichroism (CD) spectrum characteristic of an equimolar mixture of B and Z forms, is observed. This is produced by the orderly self-association of about four molecules of the polymer after prolonged incubation of a concentrated solution at 4 degrees C. On addition of 5 microM Co(NH3)63+, the CD spectrum of the intermediate changes to that of the Z form, which is visualized as a dense population of discrete toroids on an EM grid stained with uranyl acetate. On the other hand, addition of NaCl to a solution of poly(dG-m5dC) X poly(dG-m5dC) in the absence of any multivalent ion condenses the polymer to toroidal structures at the midpoint (0.75 M NaCl) of the B to Z transition. Further addition of NaCl unfolds these toroids to rodlike structures, which show characteristic Z-form CD spectra. These results show that Z DNA can take up a variety of tertiary structural forms and indicate that its inverted CD spectrum is due to its left-handed helical sense rather than to differential scattering artifacts.     

Reactivity and binding of benzo(a)pyrene diol epoxide to poly(dG-dC).(dG-dC) and poly(dG-m5dC).(dG-m5dC) in the B and Z forms

The physical and covalent binding of the carcinogen benzo(a)pyrene-7,8-diol-9,10-oxide (BaPDE) to poly(dG-dC).(dG-dC) and poly(dG-m5dC).(dG-m5dC) in the B and Z forms were studied utilizing absorbance, fluorescence and linear dichroism techniques. In the case of poly(dG-dC).(dG-dC) the decrease in the covalent binding of BaPDE with increasing NaCl concentration (0.1-4 M) as the B form is transformed to the Z form is attributed to the effects of high ionic strengths on the reactivity and physical binding of BaPDE to the polynucleotides; these effects tend to obscure differences in reactivities with the B and Z forms of the nucleic acids. In the case of poly(dG-m5dC).(dG-m5dC) the B-to-Z transition is induced at low ionic strength (2 mM NaCl + 10 microM Co(NH3)6Cl3) and the covalent binding is found to be 2-3-times lower to the Z form than to the B form. Physical binding of BaPDE by intercalation, which precedes the covalent binding reaction, is significantly lower in the Z form than in the B form, thus accounting, in part, for the lower covalent binding. The linear dichroism characteristics of BaPDE covalently bound to the Z and B forms of poly(dG-m5dC).(dG-m5dC) are consistent with nonintercalative, probably external conformations of the aromatic pyrenyl residues.     

Chain flexibility and hydrodynamics of the B and Z forms of poly(dG-dC).poly(dG-dC).

The solution properties of the B and Z forms of poly(dG-dC).poly(dG-dC) have been measured by static and dynamic laser light scattering. The radius of gyration, persistence length, translational and segmental diffusion coefficients, and the Rouse-Zimm parameters have been evaluated. The persistence length of the Z form determined at 3 M NaCl is about 200 nm compared to 84 and 61 nm respectively for the B forms of poly(dG-dC).poly(dG-dC), and calf thymus DNA, both determined at 0.1 M NaCl. The data on persistence length, diffusion coefficients and the Rouse-Zimm parameters indicate a large increase in the chain stiffness of Z DNA compared to the B form. These results are opposite to the ionic strength effects on random sequence native DNAs, for which the flexibility increases with ionic strength and levels off at about 1 M NaCl.     

A twenty-two-fold increase in the relative affinity of estrogen receptor to poly (dA-dC).poly (dG-dT) in the presence of polyamines.

We studied the relative efficacy of polyamines to facilitate the binding of estrogen receptor to poly(dA-dC).poly(dG-dT). In the absence of polyamines, 1,400 micrograms/ml of this polynucleotide eluted 50% of bound estrogen receptor from DNA-cellulose. In contrast, 50% estrogen receptor was eluted by 65 micrograms/ml of poly(dA-dC).poly(dG-dT) complexed with 150 microM spermidine. Putrescine and spermine also enhanced the ability of poly(dA-dC).poly(dG-dT) to elute estrogen receptor, but the magnitude of the effect was not as high as that of spermidine. Control experiments with calf thymus DNA and poly(dA-dT).poly(dA-dT) showed 6- and 3-fold increase, respectively in their affinity for estrogen receptor in the presence of spermidine. The dramatic increase in the affinity of poly(dA-dC).poly(dG-dT) for estrogen receptor in the presence of polyamines might be a result of the conversion of the polynucleotide to the left-handed Z-DNA form. These results show that polyamines are capable of participating in estrogenic regulation of gene expression by altering the affinity of the receptor for specific DNA sequences.     

Divalent cations are not required for the stability of the low-salt Z-DNA conformation in poly(dG-ethyl5dC)

It is demonstrated that poly(dG-ethyl5dC) adopts Z form in low-salt solution like poly(dG-methyl5dC). Its existence is, however, not contingent on the presence of divalent cations in the polynucleotide solution. The Z form is transformed into B form below room temperature. The arising B form cannot be transformed back into Z form by millimolar MgCl2 concentrations. On the contrary, the addition of MgCl2 at room temperature converts the low-salt Z form of poly(dG-ethyl5dC) into B form. It follows from the results that Z form is a stable DNA conformation not only at high but even at low ionic strengths.     

Interaction of the alternating double stranded copolymer poly(dA-dT) x poly(dA-dT) with NiCl(2) and CdCl(2): solution behavior

The thermal denaturation of the synthetic high molecular weight double stranded polynucleotide poly(dA-dT) x poly(dA-dT) has been studied in aqueous buffered solution (Tris 1.0 mM; pH 7.8+/-0.2) in the presence of increasing concentrations of either Ni(2+) (borderline cation) or Cd(2+) (soft cation) at four different constant ionic strength values (NaCl), making use of UV and circular dichroism (CD) spectroscopies. The experimental results show that the B-type double helix of the polymer is stabilized against thermal denaturation in the presence of both cations at low concentrations, relative to the systems where only NaCl is present, in the same conditions of ionic strength and pH. The effect is more pronounced for Ni(2+) than for Cd(2+). At higher concentrations, both cations start to destabilize the double helix, with Cd cations inducing larger variations of T(m). In many cases, when denaturation starts, interstrand cross-linking occurs with formation of aggregates that precipitate.     

Polyamines favor DNA triplex formation at neutral pH

The stability of triplex DNA was investigated in the presence of the polyamines spermine and spermidine by four different techniques. First, thermal-denaturation analysis of poly[d(TC)].poly[d(GA)] showed that at low ionic strength and pH 7, 3 microM spermine was sufficient to cause dismutation of all of the duplex to the triplex conformation. A 10-fold higher concentration of spermidine produced a similar effect. Second, the kinetics of the dismutation were measured at pH 5 in 0.2 M NaCl. The addition of 500 microM spermine increased the rate by at least 2-fold. Third, in 0.2 M NaCl, the mid-point of the duplex-to-triplex dismutation occurred at a pH of 5.8, but this was increased by nearly one pH unit in the presence of 500 microM spermine. Fourth, intermolecular triplexes can also form in plasmids that contain purine.pyrimidine inserts by the addition of a single-stranded pyrimidine. This was readily demonstrated at pH 7.2 and 25 mM ionic strength in the presence of 100 microM spermine or spermidine. In 0.2 M NaCl, however, 1 mM polyamine is required. Since, in the eucaryotic nucleus, the polyamine concentration is in the millimolar range, then appropriate purine-pyrimidine DNA sequences may favor the triplex conformation in vivo.     

Differential promotion and suppression of Z leads to B transitions in poly[d(G-C)] by histone subclasses,polyamino acids and polyamines.

The right-handed (B) conformation of poly[d(G-C)] in 7.5 mM sodium cacodylate and 25% ethylene glycol can be readily converted to the left-handed (Z) conformation by the addition of 250 microM MnCl2 and this transition can be reversed by chelation of the Mn ions with EDTA or by addition of NaCl. This ability to obtain such reversible transitions in solvent and solute conditions which allow DNA-protein interactions and their assessment by c.d. permitted an analysis of the effect of purified histones, polyamino acids, protamine and polyamines on these transitions. Individual core histones H3, H4, H2a and H2b or protamine stabilised the Mn-induced Z form and prevented the transition to B DNA normally observed after chelation with EDTA or on dialysis to physiological salt concentrations. A similar suppression of Z leads to B transition was also achieved with poly-L-arginine (but not with poly-L-lysine). In contrast, histones H1 and H5 promoted the Z leads to B transition. Polyamines (spermine and spermidine) converted the B form to another right-handed (A) form which transformed to the Z form after the addition of EDTA and this Z form was restored to the B conformation on the addition of NaCl. These results suggest that sequence-dependent variations in the conformation of natural DNA may be modulated by interaction with histones and other basic cellular components and may provide a conformational basis for nucleosome formation and possibly for the control of gene expression.     

Interaction of poly(I)·poly(C) with trans-dichloro-diammine-platinum (II)

The covalent binding of trans-Pt (NH₃)₂Cl₂ to the double-stranded poly(I)·poly(C) follows three types of reactions, depending on r_b and the concentration of polynucleotide in the reaction mixture. At r_b ? 0.1, the principal reaction is coordination to poly(I), giving rise to some destabilization of the double strand, as shown by uv and CD spectra, and a decrease in T_m values, giving rise to free loops of poly(C). At higher r_b and low polynucleotide concentration, the free cytidine bases react with platinum bound on the complementary strand to form intramolecular (interstrand) crosslinks that restabilize the double-stranded structure. At high r_b and high polynucleotide concentration, while the above reaction still occurs, the predominant one is the formation of intermolecular crosslinks. Under no conditions has strand separation been observed.     

Z form of poly d(A-C).poly d(G-T) in solution studied by Raman spectroscopy.

Poly d(A-C).poly d(G-T) structures have been studied in solution by Raman spectroscopy, in presence of Na+, Mn2+ and Ni2+ counterions. Increase of the Na+ concentration or addition of Mn2+ ions up to 1M MnCl2 does not modify the B geometry of the polynucleotide. On the contrary, in conditions of low water activity (4M NaCl), the presence of small amounts of nickel ions (65 mM) induces a left-handed geometry of the DNA. The shift of the guanine line located at 682 cm-1 in B form to 622 cm-1 reflects unambiguously the C2'-endo/anti-greater than C3'-endo/syn reorientation of the deoxyribose-purine entities. Moreover modifications in the phosphate backbone lines indicate that the polymer is in a Z conformation. New or displaced lines corresponding to adenosine vibrations are correlated with the left-handed structure. An interaction of the Ni2+ ions specifically with the N7 site of purines, combined with a low water activity is necessary to promote the B-greater than Z transition.     

Left-handed helical structure of poly[d(A-C)].poly[d(G-T)] studied by infrared spectroscopy

Infrared spectroscopic studies demonstrate the ability of poly[d(A-C)].poly[d(G-T)] to adopt a Z-type conformation. The Z form of the unmodified polynucleotide is induced by Ni2+ counterions and not by Na+. The B----Z equilibrium is shifted at room temperature, in the presence of 1 Ni2+/nucleotide, by an increase in the concentration of poly[d(A-C)].poly[d(G-T)]. The importance of specific binding of Ni2+ ions on the N7 site of purines in the stabilization of the Z form is also discussed.     

Identification of a new electronic transition in the Z form of poly(dG-dC)·poly(dG-dc) by infrared absorption and resonance Raman spectroscopy

Infrared absorption and resonance Raman spectroscopy (RRS) are used to study poly(dG-dC)·poly(dG-dC) in two different forms: the right-handed B form at low ionic strength and the left-handed Z form at high ionic strength. The existence of a new electronic absorption band in the 290–300-nm region is evidenced by uv RRS studies of the Z form at different wavelengths of excitation. Infrared absorption spectra prove that this new electronic band is polarized perpendicularly to the cytosine plane. The possibility of a nπ* character of this transition moment is discussed.     

Hexammineruthenium (III) chloride: a highly efficient promoter of the B-DNA to Z-DNA transition of poly-(dG-m5dC).poly(dG-m5dC) and poly(dG-dC).poly(dG-dC)

The effects of Ru(NH3)(3+)6 on the conformation of poly(dG-m5dC).poly(dG-m5dC) and poly(dG-dC).poly(dG-dC) were studied by circular dichroism (CD) spectroscopy. Ru(NH3)(3+)6 at very low concentrations provokes the Z-DNA conformation in both polynucleotides. In the presence of 50 mM NaCl, the concentration of Ru(NH3)(3+)6 at the midpoint of B to Z transition of poly(dG-m5dC).poly(dG-m5dC) is 4 microM compared to 5 microM for Co(NH3)(3+)6. The half-lives of B to Z transition of poly(dG-m5dC).poly(dG-m5dC) in the presence of 10 microM Ru(NH3)(3+)6 and Co(NHG3)(3+)6 are at 23 and 30 min, respectively. The concentration of Ru(NH3)(3+)6 at the midpoint of B to Z transition of poly(dG-dC).poly(dG-dC) is 50 microM. These results demonstrate that Ru(NH3)(3+)6 is a highly efficient trivalent cation for the induction of B to Z transition in poly(dG-m5dC).poly(dG-m5dC) and poly(dG-dC).poly(dG-dC). In contrast, Ru(NH3)(3+)6 has no significant effect on the conformation of calf thymus DNA, poly(dA-dT).poly(dA-dT) and poly(dA-dC).poly(dG-dT).     

Conformational effects of histones H1 on DNA structure. Comparative study between H1-1, H1(0), H5 and sperm holothuria phi 0

Interactions of mammalian histones, H1-1 and H1(0), phi 0 from holothuria sperm and H5 with poly(dA-dT), poly(dG-dC) and poly(dG-me5dC) were measured by a nitrocellulose filter binding assay and circular dichroism. All of the proteins bound to every one of the polymers, but differed in the extent of binding, which depended on the polynucleotide/protein ratios and ionic strength. The order of retention of all polymers was phi 0 greater than H1-1 greater than H1(0). The binding of H1(0) to poly(dG-me5dC) was remarkably sensitive to ionic strength. The proteins caused changes in the spectral features of the polynucleotides, but differed in the type and extent of the change. Complexes prepared with H1-1 and H1(0) with all polymers showed a strongly negative psi spectrum. Complexes of poly(dA-dT) and phi 0, at a protein/polynucleotide ratio of 0.4, displayed a distinctive spectrum, giving the appearance of a Z-like DNA spectrum, at low ionic strength. At higher ionic strength the complexes showed a psi spectrum. Complexes of poly(dG-me5dC) in the Z or B conformation with phi 0 showed spectral features characteristic of a mixture of a Z-like and a psi spectrum. In contrast, H5 reduced the Z-DNA spectral features in the presence of Mg, and produced an inversion of the B spectrum up to a polynucleotide/protein ratio of 0.24. These findings demonstrate the ability of different proteins to produce changes in the conformation of DNA. This may reflect the ability of chromatin to undergo differential condensation, depending on both the base composition of DNA and the type of H1 histone bound to it.