Poly(d2NH2A-dT): two-dimensional NMR shows a B to A conversion in high salt

Poly(d2NH2A-dT) forms a structure in high salt that is clearly distinct from the B form present in low salt. Two-dimensional nuclear Overhauser effect (2D NOE) NMR spectra establish that the conformation of the high-salt form is not Z. Correlations of observed cross peaks in the 2D NOE spectra and estimated interproton distances of the common DNA conformations are consistent only with an A form or closely related structure. This interpretation is also consistent with the negative circular dichroic band observed in the high-salt form of poly(d2NH2A-dT) and in A-form ribohomopolymer helices containing 2NH2A.     

Characterization of intermediate conformational states in the B↔Z transitions of poly(dG?dC) · poly(dG?dC)

Time-dependent uv absorption and CD spectrum changes in salt-induced conformational B → Z and Z → B transitions of poly(dG? dC) · poly(dG? dC) were measured. This polynucleotide does not convert directly from a right-handed double-helical B form to a left-handed double-helical Z form, but goes through an intermediate, B* form, with the B → B* transition proceeding nearly instantaneously, and then transforms gradually to the Z form. Uv absorption spectra of these B and B* forms are nearly identical, but their CD spectra are quite different. The CD spectrum of the B* form is identical with that obtained for DNA in high salt solutions and is similar to a spectrum which for some time was thought to be a C form. These B and B* forms have the same number of base pairs per turn [Sprecher, C.A., Baase, W.A. & Johnson, Jr., W.C. (1979) Biopolymers 18 , 1009–1019]. Kinetic measurements showed that uv absorption and CD intensities at fixed wavelengths do not change in a simple exponential curve. However, both the uv absorption spectrum change in the B → Z transition and the CD spectrum change in the B* → Z transition, respectively, have isosbestic points. In the B → Z transition, no hyperchromicity can be observed. These results suggest that this B* form unfolding or premelting process is a rate-determining step in the B* → Z transition and makes it easy for the unfolded or premelted polynucleotide to almost immediately fold into the Z form. The double helix does not dissociate into single strands and transforms from the B* form to the Z form point-by-point along the chain in a soliton-like manner of with a small amount of open states in which the bases are unpaired. Also, in the Z → B transition, the polynucleotide does not convert directly from the Z to the B form, but goes through a B*-like form. In this transition, the uv-absorption spectra also have an isosbestic point. The reaction velocity in the Z → B transition is much faster than that in the B → Z transition. Possibly, the positive CD band between 265 and 310 nm in the B form comes from a n-π* transition due to an interaction of the bases with sugarphosphate groups.     

Conformational Transitions of Poly(dl-dC) in Aqueous Solution as Studied by Ultraviolet Resonance Raman Spectroscopy

Abstract

Poly(dI-dC) in aqueous solution can undergo different equilibrium geometries, which strongly depend on salt nature and concentrations. These equilibrium structures have been monitored by resonance Raman spectroscopy (RRS) measurements in the ultraviolet region, i. e. by using 257 and 281 nm laser excitation wavelengths which favor the resonance enhancement of the Raman contributions from inosine and cytosine residues of poly(dI-dC), respectively. Spectral changes depending on the NaCl concentration and on the presence of Ni²⁺ ions have been observed and interpreted in comparison with RRS results previously obtained for other alternating purine-pyrimidine polydeoxyribonucleotides, i.e. poly(dG-dC), poly(dA- dT) and poly(dA-dC). poly(dG-dT), which also showed B to Z conformational transitions in varying the salt concentrations. It is shown here that: i) the base stacking geometries are nearly the same in the high-salt form (5 M NaCl) of poly(dl-dC) as in the low-salt form (0.1M NaCl) of the polymer, ii) however, the high-salt structure yields important differences from a B-helix (obtained in low-salt solution) as regards the nucleoside conformations (sugar puckering and base-sugar orientation), and: iii) the addition of 9 mM NiCl₂ in the high-salt (5 M NaCl) solution of poly(dI-dC) induces the Z-conformation of the polymer.     

Influence of a Mechanical Tension on the B-C and B-C Conformational Transitions in DNA Fibres

Abstract

In the present fibre X-ray study we attempt to quantify the effect of a mechanical tension on the conformations, and transitions between the structural forms of DNA A simple experimental device has been realized in order to apply precise mechanical forces on DNA fibres during X-ray exposure. It is shown that, as the applied tension is increased, the B→A transition can be prevented as well as with a decrease of the sodium salt content A kind of distorted B form is then observed the helical parameters of which change with the relative humidity. On the contrary, the mechanical tension does not prevent the B→C transition; it only slows down the form change and improves the X-ray patterns up to a relative humidity of 0%.     

Inclusion of ionic interactions in force field calculations of charged biomolecules--DNA structural transitions

The potential of mean force (PMF) approach for treating polyion-diffuse ionic cloud interactions [D. M. Soumpasis (1984) Proceedings of the National Academy of Sciences USA 81, 5116-5120] has been combined with the AMBER force field describing intramolecular interactions. The resultant generalized AMBER-PMF force field enables one to treat the conformational stabilities and structural transitions of charged biomolecules in aqueous electrolytes more realistically. For example, we have used it to calculate the relative stabilities of the B and Z conformations of d(C-G)6, and the B and heteronomous (H) conformations of dA12.dT12, as a function of salt concentration. In the case of d(C-G)6, the predicted B-ZI transition occurs at 2.4M and is essentially driven by the phosphate-diffuse ionic cloud interactions alone as suggested by the results of earlier PMF calculations. The ZII conformer is less stable than the B form under all conditions. It is found that the helical parameters of the refined B and Z structures change with salt concentration. For example, the helical rise of B-DNA increases about 10% and the twist angle decreases by the same amount above 1M NaCl. In the range of 0.01-0.3M NaCl, the H form of dA12.dT12 is found to be more stable than the B form and its stability increases with increasing salt concentration. The computed greater relative stability of the H conformation is likely due to noninclusion of the free energy contribution from the spine of hydration, a feature presumed to stabilize the B form of this sequence.     

Left-handed Z-DNA helices in polymers, restriction fragments, and recombinant plasmids

Studies on DNA polymers, restriction fragments, and recombinant plasmids have revealed the following: A) A family of left-handed DNA conformations exists for (dC-dG)n.(dC-dG)n. The observation of a particular conformation is dependent on the salt, the salt concentration and dehydrating agent. B) In sodium acetate solutions, (dC-dG)n.(dC-dG)n forms left-handed, psi(+)-condensed structures as detected by Raman spectroscopy and circular dichroism. C) (dT-dG)n.(dC-dA)n undergoes a right-to-left-handed transition only when reacted with AAF and at high salt concentrations. D) Transitions observed for polymer DNAs also are observed for restriction fragments containing both (dC-dG).(dC-dG) and (dT-dG).(dC-dA) sequences, but the transitions in the fragments generally require higher salt concentrations than observed for the polymers. E) Studies with recombinant plasmids containing (dC-dG) sequences from 10 to 58 bp in length demonstrate that left-handed Z-DNA segments can exist contiguous to B-DNA segments. F) Negative supercoil density (sigma less than or equal to -0.072) is sufficient to convert the (dC-dG) regions in those plasmids into left-handed structures under physiological ionic conditions (200 mM NaCl). G) The favorable free energy contribution of methylation in stabilizing the Z form in fragments and plasmids is approximately offset by the unfavorable free energy contributions of the B/Z junctions. H) Sl and BAL 31 nucleases recognize aberrant structural features at the confluence of the B and Z regions. I) Detailed mapping of Sl nuclease cleavage on supercoiled plasmids shows that the nuclease sensitive regions extend over at least five to ten bp. J) Even though the (dT-dG)n.(dC-dA)n polymer requires base modification and high salt conditions to undergo the R----L transition, supercoiling (sigma less than or equal to -0.07) can supply enough energy to allow a plasmid containing the intervening sequence of a human fetal globin gene with (dT-dG).(dC-dA) sequences to undergo a R----L transition.     

Conformational lability of poly(dG-m5dC):poly(dG-m5dC).

The remarkable conformational lability of poly(dG-m5dC):poly(dG-m5dC) is demonstrated by the observation of an acid-mediated conformational hysteresis. An acid-mediated Z conformation that exists in solutions containing low sodium concentrations that would normally favor the B conformation is described in this report. This Z conformation is reached by an acid-base titration of a B-poly(dG-m5dC):poly(dG-m5dC) solution which is not far from the B-Z transition midpoint. The resulting Z conformation is thermally very stable, with direct melting into single strands at approximately 100 degrees C. In contrast, the B form DNA, initially in solutions of the same ionic strength but without exposure to acidic pH, exhibits a biphasic melting profile, with conversion into the Z form (with high cooperativity) prior to an eventual denaturation into single strands at around 100 degrees C. Cooling experiments reveal that such biphasic transitions are quite reversible. The transition midpoint for the thermally poised B to Z transformation depends strongly on the NaCl concentration and varies with sample batch. The acid-mediated Z form binds ethidium more weakly than its B counterpart, and the ethidium induced Z to B conversion occurs in a step-wise (non-allosteric) fashion without the requirement of a threshold concentration. The acid-mediated as well as the thermally poised Z conformations are reversed by the addition of EDTA, suggesting the involvement of trace amounts of multivalent metal ions.     

Delta V0 of the Na(+)-induced B-Z transition of poly[d(G-C)] is positive

The equilibrium between the right- and left-handed conformations of poly[d(G-C)] in aqueous NaCl shifts towards the right-handed (B) form with increasing pressure. The optical density at 290 and 260 nm was determined at 50 and 180 MPa for solutions in which approximately equal amounts of the two conformations were present at 0.1 MPa (atmospheric pressure). Interpretation of the observed changes in terms of a two-state unimolecular reaction mechanism results in an average molar reaction volume (delta V0) equal to 26 cm3 mol-1 at 22 degrees C; that is, the partial molar volume of B form poly[d(G-C)] is smaller than that of the left-handed (Z) form. Based upon the thermodynamics of ion-pair formation in polar solvents, it is proposed that the positive delta V0 reflects a favorable entropy change for the reaction toward the Z conformation. The larger entropy change of the Z form may derive from the release of water molecules from the hydration spheres of the cation and the poly[d(G-C)] due to the formation of ionic interactions with the Z conformer. The delta V0 of the transition is similar in sign and magnitude to the calculated molar volume change of the interaction of Na+ with H2PO4- in water.     

An FT-IR study of DNA and RNA conformational transitions at low temperatures

Fourier Transform Infrared (FT-IR) spectra of solid samples of DNA and RNA obtained from freeze-drying at solid CO2 and liquid nitrogen temperatures, have been recorded and correlation between the conformational transitions and spectral changes is proposed. It is concluded that an equilibrium exists between A, B and Z conformations at low temperatures for the DNA molecule, which is temperature dependent, whereas the RNA molecule exhibits only the A conformation. The results have been compared with the metal-adducts of DNA and RNA, where one of the conformations is predominant. Marker infrared bands for the B conformer have been found to be the strong band at 825 cm-1 (sugar conformer mode) and a band with medium intensity at 690 cm-1 (guanine breathing mode). The A conformation showed characteristic bands at 810 and 675 cm-1. The B to Z conformational transition was characterized by the strong absorption bands near 820-810 cm-1 and at 665-600 cm-1.     

Cation-specific vacuum ultraviolet circular dichroism behaviour of alginate solutions,gels and solid films

The vacuum ultraviolet circular dichroism of alginate solutions, gels and solid films is reported. Two previously observed bands at ～215 and ～203 nm are assigned to $\text{n → π}{}^1$ transitions of carboxy groups under different conditions of local environment. Three bands not previously observed are at ～185 nm, assigned to carboxy $\text{π → π}{}^1$ transitions, and at ～169 and ～149 nm, assigned to transitions of the polymer backbone. In the course of the sol (Na⁺)-gel (Ca²⁺), the sol (Na⁺-film (Na⁺) and the gel (Ca²⁺)-film (Ca²⁺) transitions, intensity changes are observed in both the low energy and high energy bands. The c.d. changes during the three transitions differ in magnitude, but are qualitatively the same, from which we conclude that the chain conformations in the gel and films are similar, and that the principal spectral changes have their origin in perturbation of chromophores by site-bound cations.     

Ultrapolymorphic DNA: B, A, Z, and Z* conformations of poly(dA-dC).poly(dG-dT)

The synthetic polynucleotide poly(dA-dC).poly(dG-dT) at low ionic strength is shown to undergo conformational changes in the presence of [tris(2-aminoethyl)amine]zinc(II) chloride (ZnN4). At 100 microM ZnN4, circular dichroism and 31P NMR spectra show the formation of Z DNA. With an increase of the concentration up to 600 microM, an A-like form is obtained, and at still higher concentration, the polynucleotide reverts to the original B form. Experiments on polynucleotide samples in which some sequence errors were observed showed that spermine was necessary as well as ZnN4 to induce the Z form. At higher concentrations of spermine and ZnN4, a second Z form (Z*) is observed. Raising the ionic strength inhibits the formation of the Z form, whereas the presence of ethylene glycol favors it.     

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.     

Left-handed Z-DNA Helices in Polymers,Restriction Fragments,and Recombinant Plasmids

Abstract

Studies on DNA polymers, restriction fragments, and recombinant plasmids have revealed the following: A) A family of left-handed DNA conformations exists for (dC-dG)_n·(dC-dG)_n. The observation of a particular conformation is dependent on the salt, the salt concentration and dehydrating agent. B) In sodium acetate solutions, (dC-dG)_n·(dC-dG)_n forms left-handed, ψ(+)-condensed structures as detected by Raman spectroscopy and circular dichroism. C) (dT-dG)_n·(dC-dA)_n undergoes a right-to-left-handed transition only when reacted with AAF and at high salt concentrations. D) Transitions observed for polymer DNAs also are observed for restriction fragments containing both (dC-dG)·(dC-dG) and (dT-dG)·(dC-dA) sequences, but the transitions in the fragments generally require higher salt concentrations than observed for the polymers. E) Studies with recombinant plasmids containing (dC-dG) sequences from 10 to 58 bp in length demonstrate that left-handed Z-DNA segments can exist contiguous to B-DNA segments. F) Negative supercoil density (σ≤ ?0.072) is sufficient to convert the (dC-dG) regions in those plasmids into left-handed structures under physiological ionic conditions (200 mM NaCl). G) The favorable free energy contribution of methyla- tion in stabilizing the Z form in fragments and plasmids is approximately offset by the unfavorable free energy contributions of the B/Z junctions. H) S₁ and BAL 31 nucleases recognize aberrant structural features at the confluence of the B and Z regions. I) Detailed mapping of S₁ nuclease cleavage on supercoiled plasmids shows that the nuclease sensitive regions extend over at least five to ten bp. J) Even though the (dT-dG)_n·(dC-dA)_n polymer requires base modification and high salt conditions to undergo the R?L transition, supercoiling (σ ?0.07) can supply enough energy to allow a plasmid containing the intervening sequence of a human fetal globin gene with (dT-dG)·(dC-dA) sequences to undergo a R?L transition.     

DNA polymorphism: spectroscopic and electro-optic characterizations of Z-DNA and other types of left-handed helical structures induced by Ni2+

CD and uv spectroscopy reveal that the synthetic polynucleotides poly(dG–dC) · poly(dG–dC) and poly(dG–m⁵dC) · poly(dG–m⁵dC) undergo a transition induced by small amounts of Ni⁺⁺ cation from a right-handed B-form to left-handed Z-type conformations. We describe the application of steady-state and transient electric birefringence to the characterization of the transition observed at very low ionic strength (10 mM Tris HCl, pH 7.4). Dialysis experiments show that the changes in spectroscopic and electro-optic properties upon addition of Ni⁺⁺ are completely reversible. The differences in shape of the inverted CD spectra suggest the existence of a family of left-handed conformations, depending on the polymer used and on the amounts of cation added. The stoichiometry required for inducing the Z-conformation of poly(dG–m⁵dC) is 1 cation/4 nucleotide phosphates. The transition is accompanied by a decrease in birefringence, an increase in length, and the more important contribution of a permanent or slowly induced dipole moment to the orientation mechanism. High concentrations of Ni⁺⁺ promote the Z → Z* transition. Upon increasing the Ni⁺⁺ concentration, poly(dG–dC) undergoes a biphasic transition, first to one intermediate conformation that is neither B- nor Z-like and then to a left-handed form that is probably different from Z*. These conversions are accompanied by regular decreases both in birefringence and in chain length, but no transient appears in the field-reversal experiments.     

Water-DNA interactions as studied by X-ray and neutron fibre diffraction

X-ray fibre-diffraction studies indicate a high degree of stereochemical specificity in interactions between water and the DNA double helix. Evidence for this comes from data that show that the molecular conformations assumed by DNA in fibres are highly reproducible and that the hydration-driven transitions between these conformations are fully reversible. These conformational transitions are induced by varying the relative humidity of the fibre environment and hence its water content. Further evidence for stereochemical specificity comes from the observed dependence of the conformation assumed on the ionic content of the fibre and the nucleotide sequence of the DNA. For some transitions, information on stereochemical pathways has come from real-time X-ray fibre diffraction using synchrotron radiation; information on the location of water with respect to the double helix for a number of DNA conformations has come from neutron fibre diffraction. This structural information from fibre-diffraction studies of DNA is complemented by information from X-ray single-crystal studies of oligonucleotides. If the biochemical processes involving DNA have evolved to exploit the structural features observed in DNA fibres and oligonucleotide single crystals, the challenges in developing alternatives to a water environment can be expected to be very severe.     

Co-culture with Tetragenococcus halophilus changed the response of Zygosaccharomyces rouxii to salt stress

Zygosaccharomyces rouxii and Tetragenococcus halophilus exhibit remarkable salt tolerance and play roles in high-salt fermented food production. This study investigated the effect of co-culture with T. halophilus on Z. rouxii based on analysis of the viability of Z. rouxii in high-salt environments, the plasma membrane integrity, Na⁺, K⁺-ATPase activity, amino acid content of Z. rouxii cell after salt stress and organic acids assay. The results showed both T. halophilus broth supernatant and intracellular component of T. halophilus increased the viability of Z. rouxii in the 12 % environment. Co-cultured Z. rouxii cells maintained better plasma membrane integrity and lowered Na⁺, K⁺-ATPase activity than single-cultured after salt stress. Co-cultured Z. rouxii cells exhibited higher contents of aspartic acid, threonine, serine, asparagine, glutamic acid, alanine, α-amino-n-butyric acid, methionine, homo-cystine, arginine and proline compared with single-cultured after salt stress. More contents of propionic acid, lactic acid and L-pyroglutamic acid and lower contents of L-malic acid and citric acid were detected in co-culture broth. This study shows preculture of T. halophilus and then co-culture with Z. rouxii enhanced the viability of Z. rouxii in high-salt environment. The results may contribute to further understand the interactions between Z. rouxii and T. halophilus in high-salt environments.     

1H nuclear magnetic resonance study of the dynamic properties of the B and Z-forms of poly[d(A-br5C).d(G-T)]

Poly[d(A-br5C).d(G-T)], a synthetic polynucleotide with a 50% A-T base composition, undergoes a reversible, highly co-operative transition between the right-handed B and left-handed Z conformations. The latter is stabilized at both elevated temperature and ionic strength. The B and Z-forms of poly[d(A-br5C).d(G-T)] coexist in 4.6 M-NaCl at 45 degrees C. Due to slow exchange, two sets of Tim and Gim resonances are observed and can be assigned to the B and Z conformations (the chemical shifts are, respectively, Tim = 13.4, 14.1 p.p.m. (parts/million); and Gim = 11.9, 12.4 p.p.m.). Measurements of the 1H spin-lattice (R1) and spin-spin (R2) relaxation rates of the exchangeable thymine (Tim) and guanine (Gim) imino protons have been used to probe the internal dynamics of the B and Z-forms of poly[d(A-br5C).d(G-T)] and the mechanism of the B-Z transition. The proton exchange behavior in the B and Z conformations is quite different. At elevated temperature, R1 for both Tim and Gim in the B conformation is dominated by exchange with the solvent, with Tim exchanging more rapidly than Gim. This demonstrates that exchange involves the opening of single base-pairs and that neighboring A-T and G-br5C base-pairs exchange independently of each other. B-form poly[d(A-br5C).d(G-T)] is unusual in that there is an acceleration of the Tim exchange rate with increasing NaCl concentration. Conversion to the Z-form by addition of 4.5 M-NaCl dramatically reduces both the Tim and Gim exchange rates (estimated to be less than 2 s-1 at 70 degrees C). Thus, the G-br5C base-pair and, in particular, the A-T base-pair are stabilized in the Z conformation. By measuring relaxation rates at 45 to 50 degrees C where the B and Z-forms are in equilibrium, we find that the B-Z interconversion rates are less than two per second. In the B conformation at 25 degrees C, the dipolar contributions to the imino proton relaxation rates are about one-third of those expected on the basis of a rigid rod model for 65 base-pair fragments, a difference we assign to large amplitude (30 degrees high frequency (less than 100 ns) out-of-plane motions of the bases. Conversion to the Z conformation has little effect on the dipolar contributions to relaxation, i.e. on the internal motions.(ABSTRACT TRUNCATED AT 400 WORDS)     

Relative Stabilities and Transitions of DNA Conformations in 1:1 Electrolytes: A Theoretical Study

Abstract

We use a recently developed formalism (1) to calculate the salt dependent part of the free energy determining DNA conformational stability in 1:1 electrolytes. The conformations studied are the A,B,C and alternating-B right-handed forms and the Z₁Z_II left-handed forms of DNA. In the case of the B-Z₁ transition of d(G-C) · d(G-C) helices in NaCl solution, the free energy contribution considered suffices to describe the transition in a quantitative manner. The theory also predicts the occurrence of salt-induced B-A transitions which have been recently observed with poly[d(n²A-T)| and poly[d(G-C)|. In other cases, additional terms in the free energy balance, particularly due to hydration effects, must be at least as important as salt effects in determining conformational stability and structural transitions in solution. If diffuse ionic cloud electrostatic effects alone would dominate in all cases, the relative helical stabilities at 0.2 M monovalent salt would decrease in the order C > B > A > Z_II > Z₁ > alternating-B. At high salt concentrations (2.0 M - 5.0 M), the order would be alternating-B > Z, > A > Z_II > B > C.     

Conformational characteristics of dApdA,dApdT, dTpdA,and dTpdT from energy minimization studies

The conformational characteristics of the deoxydinucleoside monophosphates with adenine and thymine bases in all possible sequences, namely, dApdA, dApdT, dTpdA, and dTpdT have been studied using an improved set of energy parameters to calculate the total potential energy and an improved set of energy parameters to calculate the total potential energy and an improved version of the minimization technique to minimize the total energy by allowing all seven dihedral angles of the molecular fragment to vary simultaneously. The results reveal that the most preferred conformation in all these units usually corresponds to one of the four helical conformations, namely, the A-DNA, B-DNA, C-DNA, and Watson-Crick DNA models. These helical conformations differ in energies by about 3 kcal/mol with respect to one another. The conformations which could promote a loop or bend in the backbone are, in general, less stable by about 3.5 kcal/mol with respect to the respective lowest-energy helical conformation. The results indicate that there is a definite influence of bases and their actual sequences on the preferred conformations of the deoxydinucleoside monophosphates. The lowest-energy structure, although corresponding to one of the four helical conformations, differ with the type of the deoxydinucleoside monophosphate. Good or reasonable base stacking is noted in dApdA and dTpdA with both C(3′)-endo and C(2′)-endo sugars and in dApdT and dTpdT with only C(3′)-endo sugar. The inversion of the base sequence in deoxydinucleoside monophosphates alters the order of preference of low-energy conformations as well as the base-stacking property of the unit. The paths linking the starting and final states in the (ω′, ω) plane show interesting features with regard to the energy spread, thus providing insight into the path of conformational movement ofthe molecule under slight perturbation. The stabilities of the A and B forms, including the internal energies of the C(3′)-endo ans C(2′)-endo sugar systems, indicate that for dTpdT the B → A transition is less probable. For dApdA, dApdT, and dTpdA this transition is probable in the same order of preference. We propose that the T-A sequence in the polynucleotide chain might serve as the site accessible for B ? A transitions. The theoretical predictions are in good agreement with the experimental observations.     

A comparison of the hairpin stability of the palindromic d(CGCG(A/T)4CGCG) oligonucleotides.

The palindromic deoxyribonucleotides 5'-CGCGA-TATCGCG-3' and 5'-CGCGTTAACGCG-3' have been characterized by 1H NMR spectroscopy. The NMR data identified both B-DNA duplex conformations and hairpin conformations, the latter with loop regions consisting of the four central nucleotides. The resonances of the various conformations were assigned by use of two-dimensional NMR methods. The relative stability of the various conformations was investigated as a function of temperature, ionic strength and nucleotide concentration. The duplexes were found to be stabilized at high ionic strength and at low temperature, while the hairpins were stabilized at low ionic strength and at medium temperature. The thermodynamics of the duplex-hairpin and the hairpin-random coil transitions were examined, and compared to the other two oligonucleotide in the palindromic d(CGCG(A/T)4CGCG) oligonucleotide family. The relative stabilities of the duplex conformations with respect to the random coil conformations are similar for the d(CGCGAATTCGCG), d(CGCGATATCGCG) and d(CGCGTATACGCG) oligonucleotides. The duplex conformation of d(CGCGTTAACGCG) is less stable. The hairpin of d(CGCGTTAACGCG) seems also to be less stable relative to the random coil conformation than in the case of the other oligonucleotides at an equal oligonucleotide concentration. A cruciform intermediate between the duplex and hairpin conformations is suggested to explain some discrepancies observed in this work in case of the d(CGCGTTAACGCG) oligonucleotide. This is similar to what has been reported for the d(CGCGTATACGCG) oligonucleotide.