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

Hydration effects of Ni(2+) binding to synthetic polynucleotides with regularly alternating purine-pyrimidine sequences

High precision ultrasonic and densimetric techniques have been used to study the interaction of Ni(2+)ions with right-handed poly[d(G-C)].poly[d(G-C)], poly-[d(A-C)].poly[d(G-T)] and poly[d(A-T)].poly[d(A-T)] in 5 mM CsCl, 0.2 mM HEPES, pH 7.5 at 20 degrees C. From these measurements the changes in the apparent molar volume and the apparent molar adiabatic compressibility due to the interaction have been obtained. The volume effects of the binding, calculated per mole of Ni(2+)ions, range from 11.7 to 23.9 cm(3)mol(-1)and the compressibility effects range from 19.3 x 10(-4)to 43.1 x 10(-4)cm(3)mol(-1)bar(-1). These data are interpreted in terms of dehydration of the polynucleotides and Ni(2+)ions, i.e. the release of water molecules from the hydration shells of the molecules. An increase in G+C content gives an increase in volume and compressibility effects, indicating a rise in the extent of dehydration. The dehydration effects of Ni(2+)binding to poly[d(G-C)].poly[d(G-C)] are approximately twice those of poly[d(A-T)].poly[d(A-T)]. The volume and compressibility effects of Ni(2+)-EDTA complex formation have also been measured and used as a model system for quantitative estimation. These values revealed that Ni(2+)ions can coordinate two atomic groups of poly[d(G-C)]. poly[d(G-C)], while in the case of the Ni(2+)-poly[d(A-T)]. poly[d(A-T)] complex volume and compressibility effects correspond to one direct or two indirect (through water) contacts.

Characterization of low-salt and high-salt conformation of poly(dI-dC) by hydrogen-deuterium exchange kinetics: a classical Raman spectroscopy study

Poly(dI-dC) in H2O and D2O solution can undergo different equilibrium geometries which strongly depend on the salt nature and concentration. These structures were studied by classical Raman spectroscopy in order to monitor a hydrogen-deuterium exchange kinetics in 8-CH group in inosine. Spectral and isotopic exchange rate changes depending on NaCl concentration were observed and interpreted on the basis of previously obtained results from resonance and classical Raman spectroscopy studies of poly(dI-dC) and hydrogen-deuterium exchange measurements of different conformations of nucleic acids. It is shown that: i) the Raman spectrum of low-salt poly(dI-dC) corresponds to the right-handed polymer with characteristic bands for B conformation, but the value of the retardation factor of isotopic exchange suggests that this form is not a pure canonical B form and that it contains some portion of the A form, ii) the Raman spectrum of the high-salt poly(dI-dC) corresponds to the right-handed polymer with characteristic bands for both the A and B conformations, iii) the retardation factor of hydrogen deuterium exchange for the high-salt form of poly(dI-dC) is essentially higher than in the low-salt form which indicates a dominant presence of the A form in the high-salt conformation of poly(dI-dC). This leads to the conclusion that the high-salt conformation of poly(dI-dC) is a mixture of A and B forms with the predominant A form.

Reversal of the Z- to B-conformation of poly(dA-dT) center dot poly(dA-dT) induced by netropsin and distamycin A

Poly(dA-dT) center dot poly(dA-dT) which adopts the Z-form at 5 M NaCl in presence of 95 mM Ni2+ions is reversed to the B-conformation by the nonintercalating drugs netropsin (Nt) and distamycin A (Dst). The drug-induced reversal from the Z-to B-form of poly(dA-dT) center dot poly(dA-dT) is evidenced by CD spectral changes at characteristic wavelengths around 295 nm and 248 nm. The drug-induced conformational transition is accompanied by a slow kinetic process. The results suggest the preference of these AT-specific drugs for the B-form and the inability of Nt and Dst to form a stable complex with the Z-form of poly(dA-dT) center dot poly(dA-dT).

B-Z transition of synthetic oligonucleotides containing non-Z forming elements

Ten oligonucleotides of the length 8-12 base pairs have been synthesized, which contain, in addition to the obligatory sequences CG/CG, sequences not favorable for the transition to the Z conformation (A.T pairs, GG/CC or AA/TT sequences). Conformational transitions of these oligonucleotides in high concentrations of NaClO4 in the absence and in the presence of Ni2+ were investigated using CD spectroscopy. The B-Z transition is affected by the length and sequence of the oligonucleotide. Increasing the NaClO4 concentration alone the transition of only one of the oligonucleotides studied. (CGCGCGTGCACGCGCG)2, can be induced. Other oligonucleotides remain in the B conformation or only partial transition to the Z conformation can be observed. Most other oligonucleotides can be converted into the Z conformation at intermediate concentrations of NaClO4 (2.0-3.2 M) by an addition of Ni2+ ions. In some cases, however, Ni2+ can destabilize the double stranded structure of the sample. We have studied the effect of the presence of A.T pairs in the G.C containing oligonucleotides and the effect of the presence of pu-pu/pyr-pyr sequences. The presence of the latter sequences in the Z form implicates the formation of a Z-Z'junction which makes the transition quite difficult. Despite the fact that some oligonucleotides contained several structural elements not favorable for the transition, we did not find any sequence which would completely block the ability of the oligonucleotide to adopt the Z conformation.

Association of poly(CA).poly(TG) DNA fragments into four-stranded complexes bound by HMG1 and 2

The tandemly repeated DNA sequence poly(CA).poly(TG) is found in tracts up to 60 base pairs long, dispersed at thousands of sites throughout the genomes of eukaryotes. Double-stranded DNA fragments containing such sequences associated spontaneously with each other in vitro, in the absence of protein, forming stable four-stranded structures that were detected by gel electrophoresis and electron microscopy. These structures were recognized specifically by the nuclear nonhistone high mobility group (HMG) proteins 1 and 2 as evidenced by gel retardation. Such sequence-specific complexes might be involved in vivo in recombination or other processes requiring specific association of two double-stranded DNA molecules.

A and Z canonical conformations in d(CnGCGn) crystals characterized by microFTIR and microRaman spectroscopies

Two crystals d(C2GCG2) and d(C5GCG5) have been studied under microscope by Fourier transform ir spectroscopy and Raman spectroscopy. The x-ray diffraction study of the latter crystal had shown that the d(C5GCG5) sequence is the first DNA dodecamer known to adopt a canonical A conformation [N. Verdaguer, J. Aymami, D. Fernandez-Forner, I. Fita, M. Coll, T. Huynh-Dinh, J. Igolen, and J. A. Subirana (1991) Journal of Molecular Biology, Vol. 221, pp. 623-635]. Characteristic ir marker bands and Raman marker peaks of the A conformation have thus been obtained and are compared with previously proposed assignments correlated to fiber diffraction x-ray results obtained on polymers. The d(C2GCG2) sequence crystal had previously been studied in an intermediate form between B and Z [L. Urpi, J. P. Ridoux, J. Liquier, N. Verdagner, I. Fita, J. A. Subirana, F. Iglesias, T. Huynh-Dinh, J. Igolen, and E. Taillandier (1989) Nucleic Acids Research, Vol. 17, pp. 6669-6679]. In this paper we present results obtained from a crystal with this oligonucleotide in Z conformation. The effect of the crystallization conditions on the geometry of the obtained oligomer helix is discussed. The influence of the addition, to the central tetramer CGCG, of dCn stretches (at the 5' end) and dGn stretches (at the 3' end) of different lengths, on the conformational flexibility of the nucleic acid, is considered.

Ultraviolet resonance Raman marker bands of the right to left helix structure transitions in DNA and polynucleotide model compounds

The right to left helix structural transition in purine-pyrimidine alternating copolymers has been extensively studied by vibrational spectroscopies, amongst many other experimental approaches. Here, the use of resonance Raman spectroscopy in the ultraviolet region (223-, 257- and 281 nm excitation wavelengths) to monitor such structural changes is reviewed in the light of new results obtained on poly(dA-dC).poly(dG-dT) on one hand, and the previous results obtained on poly(dG-dC)2, poly(dA-dT)2 and natural DNA (Chicken erythrocytes) on the other. It is now possible to define B----Z transition marker bands involving the proper bases, which show a similar behaviour on structural transition whatever the composition of alternating purine-pyrimidine sequences: the 1580- and 1487 cm-1 lines of the purines, the 1486- and 1294 cm-1 lines of the pyrimidines are good markers in the vibrational spectra recorded at various UV excitation wavelengths.

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 systemically 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.

Changes in poly[d(T-G).d(C-A)] chirality due to Hg(II)-binding: circular dichroism (CD) studies

The conformation of poly[d(T-G).d(C-A)] in aqueous solution (0.1 M NaClO4, 5 mM cacodylic acid buffer, pH 6.9) was studied by circular dichroism (CD) spectroscopy in the ultraviolet. The conformation of the polynucleotide, as reflected by its chiroptical signature, changes in a highly cooperative fashion in the presence of Hg(ClO4)2. The CD changes signal transitions first from the B to a modified B-state (B*), or to a non-B structure termed X, and finally to a form that is presumably Z. The alterations are totally reversible subsequent to the removal of mercury with the help of a suitable complexing agent such as sodium cyanide, indicating that mercuration does not disrupt Watson-Crick hydrogen bonding to any extent.

Local supercoil-stabilized DNA structures

The DNA double helix exhibits local sequence-dependent polymorphism at the level of the single base pair and dinucleotide step. Curvature of the DNA molecule occurs in DNA regions with a specific type of nucleotide sequence periodicities. Negative supercoiling induces in vitro local nucleotide sequence-dependent DNA structures such as cruciforms, left-handed DNA, multistranded structures, etc. Techniques based on chemical probes have been proposed that make it possible to study DNA local structures in cells. Recent results suggest that the local DNA structures observed in vitro exist in the cell, but their occurrence and structural details are dependent on the DNA superhelical density in the cell and can be related to some cellular processes.

CD evidence that the alternating purine-pyrimidine sequence poly[d(A-C).d(G-T)], but not poly[d(A-T).d(A-T)], undergoes an acid-induced transition to a modified secondary conformation

Circular dichroism and UV absorption data showed that poly[d(A-C).d(G-T)] (at 0.01M Na+ (phosphate), 20 degrees C) underwent two reversible conformational transitions upon lowering of the pH. The first transition was complete at about pH 3.9 and resulted in an acid form of the polymer that was most likely a modified, protonated duplex. The second transition occurred between pH 3.9 and 3.4 and consisted of the denaturation of this protonated duplex to the single strands. UV absorption and CD data also showed that the separated poly[d(A-C)] strand formed two acid-induced self-complexes with pKa values of 6.1 and 4.7 (at 0.01M Na+). However, neither one of these poly[d(A-C)] self-complexes was part of the acid-induced rearrangements of the duplex poly[d(A-C).d(G-T)]. Acid titration of the separated poly[d(G-T)] strand, under similar conditions, did not show the formation of any protonated poly[d(G-T)] self-complexes. In contrast to poly[d(A-C).d(G-T)], poly[d(A-T).d(A-T)] underwent only one acid-induced transition, which consisted of the denaturation of the duplex to the single strands, as the pH was lowered from 7 to 3.

Interpretation of DNA vibrational spectra by normal coordinate analysis

1. In the following article we undertake a brief review of the most prominent DNA vibrational markers as observed experimentally by Raman and i.r. spectroscopies on polynucleotides and explain how a simplified valence force field can account for the evolution of the DNA vibrational spectra. 2. Our discussion made as a review of our previous investigations on the interpretation of DNA vibration modes, is based on some of the most characteristic and structure dependent DNA vibrational markers.

The Z-conformation of poly(dA-dT).poly(dA-dT) in solution as studied by ultraviolet resonance Raman spectroscopy

Poly(dA-dT).poly(dA-dT) structures in aqueous solutions with high NaCl concentrations and in the presence of Ni2+ ions have been studied with resonance Raman spectroscopy (RRS). In low water activity the effects of added 95 mM NiCl2 in solution stabilize the syn geometry of the purines and reorganize the water distribution via local interactions of Ni-water charged complexes with the adenine N7 position. It is shown that RRS provides good marker bands for a left-handed helix: i) a purine ring breathing mode around 630 cm-1 coupled to the deoxyribose vibration in the syn geometry, ii) a 1300-1340 cm-1 region characterizing local chemical interactions of the Ni2+ ions with the adenine N7 position, iii) lines at about 1483- and 1582 cm-1 correlated to the anti/syn reorientation of the adenine residues on B-Z structure transition, iv) marker bands of the thymidine carbonyl group couplings at 1680- and 1733 cm-1 due to the disposition of the thymidine residues in the Z helix specific geometry. Hence poly(dA-dT).poly(dA-dT) can adopt a Z form in solution. The Z form observed in alternate purine-pyrimidine sequences does not require G-C base pairs.

Existence of the C structure in poly(dA-dC).poly(dG-dT)

We show that the lithium salt of calf-thymus DNA can assume the C structure in nonoriented, hydrated gels. The transitions between the B and C structures showed little hysteresis and none of the metastable structural states which occur in oriented gels. Therefore crystal-lattice forces are not needed to stabilize the C structure. The occurrence of the alternative structures of the Li, Na and K salts of poly(dA-dC).poly(dG-dT) was measured as a function of hydration for nonoriented gels. Poly(dA-dC).poly(dG-dT).Li exists in the B structure at high hydrations and in the C structure at moderate hydrations with no A or Z structure at any hydration tested. The Na salt of poly(dA-dC).poly(dG-dT) exists in the B structure at high hydration, as mixtures of B and C at moderate hydrations and in the A structure at lower hydrations. The potassium salt behaves similarly except that mixtures of the C and A structures exist at lower hydrations. ZnCl2 and NaNO3, which promote the Z structure in duplex poly(dG-dC), promote the C structure in poly(dA-dC).poly(dG-dT). Information contained in the sequence of base pairs and not specific ionic interactions appear to determine the stability of the alternative structures of polynucleotides as hydration is changed.

Conformations in crystals and solutions of d(CACGTG), d(CCGCGG) and d(GGCGCC) studied by vibrational spectroscopy

Crystals of self complementary DNA hexamers d(CACGTG), d(CCGCGG) and d(GGCGCC) were grown by vapour diffusion technique and studied by microRaman and microIR spectroscopies. The oligonucleotides were studied in parallel in solution by vibrational spectroscopy. A B- greater than Z transition was detected by Raman spectroscopy during the crystallization process for d(CACGTG). Vibrational spectroscopy shows that the d(GGCGCC) crystals adopt a B geometry. On the contrary the d(CCGCGG) sequence which is shown to be able to undergo in solution or in films quite easily the B- greater than Z transition, remains trapped in crystals in a geometry which may correspond to an intermediate conformation often proposed in models of the B- greater than Z transition. The crystals used in this study were characterized by X-ray diffraction. The unit cell and space group have been determined.

The concentration dependence of the right to left conformational transition in natural DNA identified by Raman spectroscopy

The classical and resonance Raman spectra of DNA from Chicken Erythrocytes have been obtained for different DNA concentrations in solution with low and high ionic strengths. The classical Raman spectra of 30 mg/ml DNA solutions were measured in varying the sodium chloride concentration from 0.1 to 4.5 M NaCl. An increase in the salt content of the solution leads to spectral changes in the 600-700 cm-1 region, indicating a C2' endo/anti to C3' endo/syn conformational transition of the purine residues. Other changes around 840 cm-1, due to the antisymmetrical stretching vibration of the PO2 group, are also detected: they were characteristic for the B----Z transition in model systems such as poly(dG-dC).poly(dG-dC). The resonance Raman spectra of low (1 mg/ml) and high (30 mg/ml) concentrated DNA solutions were obtained with low (0.1 M) and high (4.5 M) NaCl contents, in using a 284 nm excitation wavelength. No change was observed in the intensities and band positions in the low and high salt solutions of low concentrated DNA. Thus it is assumed that the DNA structure remains unchanged whatever the salt concentration for low concentrated DNA. In contrast, great modifications of the intensities and positions of some lines were found in the spectra of high DNA concentration solution when the NaCl content is increased up to 4.5 M: these changes resemble to some extent those observed in the study of B----Z transition of several polynucleotide model compounds. It is assumed that the right-handed to left-handed conformational transition may occur in certain sections of natural DNA, likely containing alternating purine-pyrimidine sequences, when the DNA concentration is sufficiently important.

Interpretation of DNA vibration modes: IV--A single-helical approach to assign the phosphate-backbone contribution to the vibrational spectra in A and B conformations

A calculated approach based on the Higgs method for assigning the vibration modes of an infinite helicoidal polymeric chain has been performed on the basis of a reliable valence force field. The calculated results allowed the phosphate-backbone marker modes of the A and B forms, to be interpreted. In the dynamic models used, the bases have been omitted and no interchain interaction was considered. The calculation can also interprete quite satisfactorily the characteristic Raman peaks and infrared bands in the 1250-700 cm-1 spectral region arising from the sugar or sugar-phosphate association and reproduce their evolution upon the B----A DNA conformational transition. They clearly show that the phosphate-backbone modes in the above mentioned spectral region constitute the optical branches of the phonon dispersion curves with no detectable variation in the first Brillouin-zone.

Particular behavior of the adenine and guanine ring-breathing modes upon the DNA conformational transitions

Harmonic dynamics calculations performed on the deoxyguanosine (dG) and deoxyadenosine (dA) residues, based on a reliable force field, show that the breathing motions of both guanine and adenine residues are involved in two different vibration modes (750-500 cm-1 spectral region). The calculated results reveal a strong coupling of these modes with the sugar pucker motions. This effect has been verified for the dG residue by the Raman spectra of polyd(G-C). As far as the dA residue is concerned, the particular behavior of the adenine residue breathing mode predicted by these calculations, has been confirmed by Raman spectra of polyd(A-T) undergoing a B----Z conformational transition.