Conformational properties of poly[d(G-T)].poly[d(C-A)] and poly[d(A-T)] in low- and high-salt solutions: NMR and laser Raman analysis

³¹P- and ¹H-nmr and laser Raman spectra have been obtained for poly[d(G-T)]·[d(C-A)] and poly[d(A-T)] as a function of both temperature and salt. The ³¹P spectrum of poly[d(G-T)]·[d(C-A)] appears as a quadruplet whose resonances undergo separation upon addition of CsCl to 5.5M. ¹H-nmr measurements are assigned and reported as a function of temperature and CsCl concentration. One dimensional nuclear Overhauser effect (NOE) difference spectra are also reported for poly[d(G-T)]·[d(C-A)] at low salt. NOE enhancements between the H8 protons of the purines and the C5 protons of the pyrimidines, (H and CH₃) and between the base and H-2′,2″ protons indicate a right-handed B-DNA conformation for this polymer. The NOE patterns for the TH3 and GH1 protons in H₂O indicate a Watson–Crick hydrogen-bonding scheme. At high CsCl concentrations there are upfield shifts for selected sugar protons and the AH2 proton. In addition, laser Raman spectra for poly[d(A-T)] and poly[d(G-T)]·[d(C-A)] indicate B-type conformations in low and high CsCl, with predominantly C2′-endo sugar conformations for both polymers. Also, changes in base-ring vibrations indicate that Cs⁺ binds to O2 of thymine and possibly N3 of adenine in poly[d(G-T)]·[d(C-A)] but not in poly[d(A-T)]. Further, ¹H measurements are reported for poly[d(A-T)] as a function of temperature in high CsCl concentrations. On going to high CsCl there are selective upfield shifts, with the most dramatic being observed for TH1′. At high temperature some of the protons undergo severe changes in linewidths. Those protons that undergo the largest upfield shifts also undergo the most dramatic changes in linewidths. In particular TH1′, TCH₃, AH1′, AH2, and TH6 all undergo large changes in linewidths, whereas AH8 and all the H-2′,2″ protons remain essentially constant. The maximum linewidth occurs at the same temperature for all protons (65°C). This transition does not occur for d(G-T)·d(C-A) at 65°C or at any other temperature studied. These changes are cooperative in nature and can be rationalized as a temperature-induced equilibrium between bound and unbound Cs⁺, with duplex and single-stranded DNA. NOE measurements for poly[d(A-T)] indicate that at high Cs⁺ the polymer is in a right-handed B-conformation. Assignments and NOE effects for the low-salt ¹H spectra of poly[d(A-T)] agree with those of Assa-Munt and Kearns [(1984) Biochemistry 23 , 791–796] and provide a basis for analysis of the high Cs⁺ spectra. These results indicate that both polymers adopt a B-type conformation in both low and high salt. However, a significant variation is the ability of the phosphate backbone to adopt a repeat dependent upon the base sequence. This feature is common to poly[d(G-T)]·[d(C-A)], poly[d(A-T)], and some other pyr–pur polymers [J. S. Cohen, J. B. Wouten & C. L Chatterjee (1981) Biochemistry 20 , 3049–3055] but not poly[d(G-C)].     

DNA binding of a spermine derivative: Spectroscopic study of anthracene-9-carbonyl-n1-spermine with poly[d(G-C)·(d(G-C))] and poly[d(A-T) · d(A-T)]

The binding of polyamines, including spermidine ( 1 ) and spermine ( 2 ), to poly[d(G-C) · d(G-C) ] was probed using spectroscopic studies of anthracene-9-carbonyl-N¹-spermine ( 3 ); data from normal absorption, linear dichroism (LD), and circular dichroism (CD) are reported. Ligand LD and CD for transitions located in the DNA region of the spectrum were used. The data show that 3 binds to DNA in a manner characteristic of both its amine and polycyclic aromatic parts. With poly [(dG-dC) · (dG-dC)], binding modes are occupied sequentially and different modes correspond to different structural perturbations of the DNA. The most stable binding mode for 3 with poly[d(G-C) · d(G-C)] has a site size of 6 ± 1 bases, and an equilibrium binding constant of (2.2 ± 1.1) × 10⁷ M^?1 with the anthracene moiety intercalated. It dominates the spectra from mixing ratios of approximately 133:1 until 6:1 DNA phosphate: 3 is reached. The analogous data for poly [d(A-T) · d(A-T)] between mixing ratios 36:1 and 7:1 indicates a site size of 8.3 ± 1.1 bases and an equilibrium binding constant of (6.6 ± 3.3) × 10⁵ M^?1. Thus, 3 binds preferentially to poly [d(G-C) · d(G-C)] at these concentrations. © 1994 John Wiley & Sons, Inc.     

Linear dichroism demonstrates that the bases in poly[d(AC)] · poly[d(GT)] and poly[d(AG)] · poly[d(CT)] are inclined from perpendicular to the helix axis

Flow linear dichroism is used to measure specific inclinations for each of the four bases in poly[d(AC)]·;poly[d(GT)] and poly[d(AG)]·poly[d(CT)] in both the B and A forms. For the B form in solution the bases are found to have a sizable inclination. Inclination is increased in the A form, as expected. In all cases the pyrimidines are more inclined than the purines. © 1993 John Wiley & Sons, Inc.     

Infrared dichroism of polynucleotides of repeated sequence. I. Poly(dA)·poly(dT) and poly[d(A-T)]·poly[d(A-T)]

Infrared dichroism measurements of oriented films of poly(dA)·poly(dT) and poly[d(A-T)]·poly[d(A-T)] have been made under the conditions of low salts content and high humidity for which the geometry is known. The angles which the transition moments make with the helix axis are compared with the orientations of the corresponding bonds. Except for the in-plane base model of poly[(A-T)]·poly[d(A-T)], there is no agreement. This may imply either that a model which assumes bonds and transition moments to be colinear is not acceptable or that x-ray data are inaccurate. These possibilities are discussed especially with respect to phosphate group orientation. An appendix gives the derivations of dichroic-ratio expressions for helical molecules of different symmetry types.     

Base tilt of poly[d(A)]-poly[d(T)] and poly[d(AT)]-poly[d(AT)] in solution determined by linear dichroism

We have measured the CD, isotropic absorption, and LD of poly[d(A)]–poly[d(T)] and poly[d(AT)]–poly[d(AT)] in the vacuum-uv spectral region. The reduced dichroism (LD divided by isotropic absorption) varied as a function of wavelength and was independent of shear gradient. Thus, the bases are not perpendicular to the helix axis in solution. Since the directions of the transition dipoles are known, the orientations of the bases in the polymers can be calculated from the reduced dichroism spectra. The results show that the base normals are tilted at angles greater than 25°, with respect to the helix axis, and thymine is tilted more than adenine for both polymers. The tilt axes of adenine and thymine are not parallel, indicating a large propeller twist. Space-filling models of poly[d(A)]–poly[d(T)] and poly[(AT)]–poly[d(AT)] are built based on our results, and the conformations of the two (A + T) polymers in solution are discussed.     

CD Spectral Comparisons of the Acid-Induced Structures of Poly[d(A)]Poly[r(A)], Poly[d(C)], and Poly[r(C)]

Abstract

CD spectra were used to compare the acid-induced structural transitions of poly[d(A)] and poly[d(C)] with those of poly[r(A)] and poly[r(C)], respectively. The types of base pairing were probably the same in the acid self-complexes of both A-containing polymers and in the acid self-complexes of both C-containing polymers. Similar base pairings were indicated by similarities in the difference CD spectra showing the changes during the first major acid- induced transitions of the polymers. Information from the CD spectra and pK_a values of the transitions suggested that the transitions for the RNA polymers involved similar structural changes. The two DNA polymers were markedly different. Single-stranded poly [d(A)] was in the most stacked structure and had the lowest pK^a for forming an acid self-complex. Single-stranded poly[d(C)] was in the least stacked structure and had the highest pK_a for forming a protonated duplex.     

Biological assays and noncovalent interactions of pyridine-2-carbaldehyde thiosemicarbazonecopper(II) drugs with [poly(dA–dT)]2, [poly(dG–dC)]2, and calf thymus DNA

The interaction of the Cu(II) drugs CuL(NO₃) and CuL′(NO₃) (HL is pyridine-2-carbaldehyde thiosemicarbazone and HL′ is pyridine-2-carbaldehyde 4N-methylthiosemicarbazone, in water named [CuL]⁺ and [CuL′]⁺) with [poly(dA–dT)]₂, [poly(dG–dC)]₂, and calf thymus (CT) DNA has been probed in aqueous solution at pH 6.0, I = 0.1 M, and T = 25 °C by absorbance, fluorescence, circular dichroism, and viscosity measurements. The results reveal that these drugs act as groove binders with [poly(dA–dT)]₂, with a site size n = 6–7, whereas they act as external binders with [poly(dG–dC)]₂ and/or CT-DNA, thus establishing overall electrostatic interaction with n = 1. The binding constants with [CuL′]⁺ were slightly larger than with [CuL]⁺. The title compounds display some cleavage activity in the presence of thiols, bringing about the rupture of the DNA strands by the reactive oxygen species formed by reoxidation of Cu(I) to Cu(II); this feature was not observed in the absence of thiols. Mutagenic assays performed both in the presence and in the absence of S9 mix, probed by the Ames test on TA 98, TA 100, and TA 102, were negative. Weak genotoxic activity was detected for [CuL]⁺ and [CuL′]⁺, with a significative dose–response effect for [CuL′]⁺, which was shown to be more cytotoxic in the Ames test and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide cell proliferation assays. Methylation of the terminal NH₂ group enhances the antiproliferative activity of the pyridine-2-carbaldehyde thiosemicarbazones.     

Psi compaction of poly[d(AT)].poly[d(AT)]

The compaction of poly[d(A–T)] · poly[d(A–T)] by Co(III) is accompanied by the formation of ψ(+)- and ψ(-)-structures. The chirality of the ψ-structure depends on the Co(III) concentration, ionic strength, temperature, pH, and the chain length of the polymer. The two forms can be readily interconverted by manipulating these factors. Phase diagrams have been constructed that demonstrate the regions of stability of the enantiomers as a function of two variables, while other factors are held constant. At critical points in the phase diagram the two forms are in such unstable equilibrium that mechanical motion will cause ψ(+) ? ψ(-) interconversion. The formation of both ψ(+)- and ψ(-)-structures by the action of Co(III) on poly[d(A–T)] · poly[d(A–T)] contrasts markedly with the behavior of poly[d(G–C)] · poly[d(G–C)] in similar circumstances by forming only the ψ(+)-structure and that of native DNA to produce no ψ at all. Thus the base sequence is important in determining the structure of chirally associated DNA molecules.     

Pressure dependence of the helix–coil transition temperature of poly[d(G-C)]

The Pressure Dependence of the Helix-Coil Transition Temperature (T_m) of Poly[d(G-C)] was studied as a function of sodium ion concentration in phosphate buffer. The molar volume change of the transition (ΔV) was calculated using the Clapeyron equation and calorimetrically determined enthalpies. The ΔV of the transition increased from +4.80 (±0.56) to +6.03 (±0.76) mL mol^?1 as the sodium ion concentration changed from 0.052 to 1.0M. The van't Hoff enthalpy of the transition calculated from the half-width of the differentiated transition displayed negligible pressure dependence: however, the value of this parameter decreased with increasing sodium ion concentration, indicating a decrease in the size of the cooperative unit. The volume change of the transition exhibits the largest magnitude of any double-stranded DNA polymer measured using this technique. For poly[d(G-C)] the magnitude of the change in ΔV with sodium ion concentration (0.94 ± 0.05 mL mol^?1) is approximately one-half that observed for either poly[d(A-T)] or poly (dA)·poly(dT). The ΔV values are interpreted as arising from changes in the hydration of the polymer due to the release of counterions and changes in the stacking of the bases of the coil form. As a consequence of solvent electrostriction, the release of counterions makes a net negative contribution to the total ΔV, implying that disruption of the slacking interactions contributes a positive volume change to the total ΔV. The larger magnitude of the ΔV compared with that of other double-stranded polymers may be due in part to the high helix-coil transition temperature of poly[d(G-C)], which will attenuate the contribution of electrostriction to the total volume change. The data in addition show that in the absence of other cellular components, the covalent structure of DNA is stabile under conditions of temperature and pressure more extreme than those experienced by any known organism. © 1995 John Wiley & Sons, Inc.     

Base tilt of B-form poly[d(G)]-poly[d(C)] and the B- and Z-conformations of poly[d(GC)]-poly[d(GC)] in solution

We have measured the CD, isotropic absorption, and linear dichroism (LD) in the vacuum-uv spectral region for the B-conformations of poly[d(G)]-poly[d(C)] and poly[d(GC)]-poly[d(GC)], and for the Z-conformation of poly[d(GC)]-poly[d(GC)] formed in 70% trifluoroethanol. The reduced dichroism (LD divided by isotropic absorption) for all conformations varied with wavelength, indicating that the bases are not perpendicular to the helix axis. Since the directions of the transition dipoles are known, the inclinations and axes of inclination of each base can be determined from the wavelength dependence of the reduced dichroism spectra. The results indicate that the base normals of the (G + C) polymers in the B- and Z-conformations are tilted at angles greater than 19° with respect to the helix axis. The guanine and cytosine bases have different inclinations, and the tilt axes are not parallel. Therefore, the bases for all the (G + C) polymer conformations studied are buckled and propeller twisted.     

CD of the synthetic RNA duplexes poly[r(A-T)] and poly[r(A-U)] in salt and ethanolic solutions.

Synthetic RNA poly[r(A-T)] has been synthesized and its CD spectral properties compared to those of poly[r(A-U)], poly[d(A-T)], and poly[d(A-U)] in various salt and ethanolic solutions. The CD spectra of poly[r(A-T)] in an aqueous buffer and of poly[d(A-T)] in 70.8% v/v ethanol are very similar, suggesting that they both adopt the same A conformation. On the other hand, the CD spectra of poly[r(A-T)] and of poly[r(A-U)] differ in aqueous, and even more so in ethanolic, solutions. We have recently observed a two-state salt-induced isomerization of poly[r(A-U)] into chiral condensates, perhaps of Z-RNA [M. Vorlícková, J. Kypr, and T. M. Jovin, (1988) Biopolymers 27, 351-354]. It is shown here that poly[r(A-T)] does not undergo this isomerization. Both the changes in secondary structure and tendency to aggregation are different for poly[r(A-T)] and poly[r(A-U)] in aqueous salt solutions. In most cases, the CD spectrum of poly[r(A-U)] shows little modification of its CD spectrum unless the polymer denatures or aggregates, whereas poly[r(A-T)] displays noncooperative alterations in its CD spectrum and a reduced tendency to aggregation. At high NaCl concentrations, poly[r(A-T)] and poly[r(A-U)] condense into psi(-) and psi(+) structures, respectively, indicating that the type of aggregation is dictated by the polynucleotide chemical structure and the corresponding differences in conformational properties.     

Stopped-flow kinetic analysis of the interaction of anthraquinone anticancer drugs with calf thymus DNA, poly[d(G-C)].poly[d(G-C)], and poly[d(A-T)].poly[d(A-T)]

The sodium dodecyl sulfate driven dissociation reactions of daunorubicin (1), mitoxantrone (2), ametantrone (3), and a related anthraquinone without hydroxyl groups on the ring or side chain (4) from calf thymus DNA, poly[d(G-C)]2, and poly[d(A-T)]2 have been investigated by stopped-flow kinetic methods. All four compounds exhibit biphasic dissociation reactions from their DNA complexes. Daunorubicin and mitoxantrone have similar dissociation rate constants that are lower than those for ametantrone and 4. The effect of temperature and ionic strength on both rate constants for each compound is similar. An analysis of the effects of salt on the two rate constants for daunorubicin and mitoxantrone suggests that both of these compounds bind to DNA through a mechanism that involves formation of an initial outside complex followed by intercalation. The daunorubicin dissociation results from both poly[d(G-C)]2 and poly[d(A-T)]2 can be fitted with a single exponential function, and the rate constants are quite close. The ametantrone and 4 polymer dissociation results can also be fitted with single exponential curves, but with these compounds the dissociation rate constants for the poly[d(G-C)]2 complexes are approximately 10 times lower than for the poly[d(A-T)]2 complexes. Mitoxantrone also has a much slower dissociation rate from poly[d(G-C)]2 than from poly[d(A-T)]2, but its dissociation from both polymers exhibits biphasic kinetics. Possible reasons for the biphasic behavior with the polymers, which is unique to mitoxantrone, are selective binding and dissociation from the alternating polymer intercalation sites and/or dual binding modes of the intercalator with both side chains in the same groove or with one side chain in each groove.     

Multivalent ions are necessary for poly[d(AC).d(GT)] to assume the Z form: a CD study.

In previous work, it was shown that poly [d(AC) · d(GT)] could be forced into the Z form by strong dehydrating conditions, provided EDTA was not present. Presumably multivalent impurities were also necessary for the transition. In order to gain control over the B to Z transition for this DNA, we carefully removed all divalent contaminants from the sample and asked the obvious question: What ions are necessary for the transition under dehydrating conditions? We systematically investigated the effect of various multivalent ions. The common contaminants Ca²⁺, Mg²⁺, and Fe³⁺ will not cause the transition, but Co²⁺ and Ni²⁺ facilitate the transition, undoubtedly because of their well-known propensity to bind to purine N7. Since the transition also depends on the synergistic dehydrating action of sodium perchlorate and ethanol, we include CD spectra for the independent variations of these two factors. In addition, vacuum-uv CD spectra for the A form and various B forms of poly [d (AC) · d (GT)] are presented for the first time.     

Far-infrared absorption of nucleotides and poly(I)·poly(C) RNA

We have measured the ir absorption of 5′CMP, 5′IMP, and poly(I)·poly(C) from ～25 to ～500 cm^?1. From a comparison of the data with the previously measured absorption of the corresponding nucleosides and bases we can identify several “lines” associated with the deformation of the ribose ring. Out-of-plane deformation of the bases contributes strongly to vibrations near 200 cm^?1. The same ribose vibrations observed in the nucleotides are found in poly(I)·poly(C). They sharpen with increasing water absorption. A study of the spectra of poly(I)·poly(C) as a function of the adsorbed water indicates that water does not contribute in a purely additive fashion to the polynucleotide spectrum but depends on the conformation of the helix. However, the only spectral feature that shifts drastically with conformation is near 45 cm^?1. Measurements at cryogenic temperatures indicate some sharpening of the spectrum of poly(I)·poly(C). Instead, no sharpening is observed in the spectrum of the nucleotides. Shear degradation of poly(I)·poly(C) produces significant spectral changes in the 200-cm^?1 region and sharpening of the features assigned to the low-frequency ribose-ring vibrations.     

Temperature dependence of the volumetric parameters of drug binding to poly[d(A-T)].Poly[d(A-T)] and Poly(dA).Poly(dT)

We report the temperature and salt dependence of the volume change (DeltaVb) associated with the binding of ethidium bromide and netropsin with poly(dA).poly(dT) and poly[d(A-T)].poly[d(A-T)]. The DeltaV(b) of binding of ethidium with poly(dA).poly(dT) was much more negative at temperatures approximately 70 degrees C than at 25 degrees C, whereas the difference is much smaller in the case of binding with poly[d(A-T)].poly[d(A-T)]. We also determined the volume change of DNA-drug interaction by comparing the volume change of melting of DNA duplex and DNA-drug complex. The DNA-drug complexes display helix-coil transition temperatures (Tm several degrees above those of the unbound polymers, e.g., the Tm of the netropsin complex with poly(dA)poly(dT) is 106 degrees C. The results for the binding of ethidium with poly[d(A-T)].poly[d(A-T)] were accurately described by scaled particle theory. However, this analysis did not yield results consistent with our data for ethidium binding with poly(dA).poly(dT). We hypothesize that heat-induced changes in conformation and hydration of this polymer are responsible for this behavior. The volumetric properties of poly(dA).poly(dT) become similar to those of poly[d(A-T)].poly[d(A-T)] at higher temperatures.     

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.     

Protonated polynucleotide structures. IX. Disproportionation of poly (G)-poly (C) in acid medium

The interaction between poly (G) and poly (C) was investigated in neutral and acid medium by optical methods. Three main points arise from this investigation. (1) The formation of poly (G)·poly (C) was complete only above an ionic strength of about 0.6M [Na⁺]. Lowering the ionic strength increased the amounts of free poly (G) and free poly (C) that could be detected. (2) When titrating towards acid pH values a transition took place which was characterized by potentiometry, mixing curves, and circular dichroism: a three-stranded poly (G)·poly (C)·poly (C⁺) complex was formed analogous to the transition observed for the acid titration of poly (I)·poly (C). (3) Even when the poly (G)·poly (C) complex was incompletely formed (at low ionic strength) in neutral medium all poly (C) entered the triple-stranded complex.     

Interaction of [Ru(bpy)2(dppz)] with human telomeric DNA: Preferential binding to G-quadruplexes over i-motif

Inspired by the enormous importance attributed to the structure and function of human telomeric DNA, we focus our attention on the interaction of [Ru(bpy)₂(dppz)]²⁺ with the guanine-rich single-strand oligomer 5′-AGGGTTAGGGTTAGGGTTAGGG-3′ (22AG) and the complementary cytosine-rich strand (22CT). In Na⁺ buffer, 22AG may adopt an antiparallel basket quadruplex, whereas, it favours a mixed parallel/antiparallel structure in K⁺ buffer. 22CT may self-associate at acidic pH into an i-motif. In this paper, the interaction between [Ru(bpy)₂(dppz)]²⁺ and each unusual DNA was evaluated. It was interesting that [Ru(bpy)₂(dppz)]²⁺ could promote the human telomeric repeat 22AG to fold into intramolecular antiparallel G-quadruplex without any other cations. What's more, [Ru(bpy)₂(dppz)]²⁺ was found to have a strong preference for binding to G-quadruplexes that were induced through either Na⁺ or K⁺, while weak binding to i-motif was observed. The results also indicated that [Ru(bpy)₂(dppz)]²⁺ could serve as a prominent molecular “light switch” for both G-quadruplexes, revealing a potential application of the title complex in luminescent signaling of G-quadruplex DNA.     

The interaction of Na ions with synthetic polynucleotides

The interaction of Na⁺ with poly A, poly U, poly A·poly U, and Poly A·2 poly U has been investigated by means of potentiometry, by means of potentiometry, by means of a linked-function analysis of its effect on the binding of Mg⁺⁺ ions, and of K⁺ by means of an analysis of its effect on the sedimentation coefficients of the polymers. The last method was found to be inapplicable. The results of the other two methods were found to be consistent, except in the case of poly A where the existence of base stacking, influenced by the binding of Mg⁺⁺, significantly affects the linked-function analysis. The results are also consistent with the effects of the concentration of Na⁺ ions on the thermally induced conformational transitions of poly A·poly U and poly A·2 poly U, and with the extents of “binding” of Na⁺ to DNA measured by equilibrium and by transport methods. The interaction of Na⁺ with polynucleotides appears to be physically quite specific, although its thermodynamic basis is not clear. The extent of binding of Na⁺, Ψ, was found to be independent of the total Na⁺ concentration but a quadratic function of the extent of Mg⁺⁺ binding, θ. In the absence of Mg⁺⁺, Ψ = 0.35–0.38 for poly U, 0.40 for poly A, 0.59 for poly A·poly U, and 0.66 for poly A·2 poly U.     

Raman spectroscopic measurements in self‐pressurized aqueous solutions above 100°C: The melting of poly(G) and poly(G) · poly(C)

We have studied by Raman spectroscopy the thermal behavior of associated polyguanylic acid [poly(G)] and polyguanylic–polycytidylic acid [poly(G) · poly(C)] in self‐pressurized aqueous solutions contained in sealed capillary tubes. The associated polynucleotides were found to be very resistant to heat, but evidence of thermal degradation was observed after melting of the helical structures. The cooperative melting transition of the four‐stranded complex of poly(G) was located at 141°C in 0.5M KCl, 135°C in 0.5M NaCl, 129°C in 0.5M LiCl, 123°C in 0.1M tetramethylammonium perchlorate, and 105°C in 0.1M tetraethylammonium bromide solutions. The transition was observed at 130°C in poly(G) · poly(C) (in 0.5M NaCl). The results in this case show that a four‐stranded poly(G) complex is formed following the melting of the double helix. © 1999 John Wiley & Sons, Inc. Biopoly 49: 21–28, 1999