Relative stabilities and transitions of DNA conformations in 1:1 electrolytes: a theoretical study

Electrostatic interaction between helical macromolecules in dense aggregates: an impetus for DNA poly- and meso-morphism

DNA exhibits a surprising multiplicity of structures when it is packed into dense aggregates. It undergoes various polymorphous transitions (e.g., from the B to A form) and mesomorphous transformations (from hexagonal to orthorhombic or monoclinic packing, changes in the mutual alignment of nearest neighbors, etc). In this report we show that such phenomena may have their origin in the specific helical symmetry of the charge distribution on DNA surface. Electrostatic interaction between neighboring DNA molecules exhibits strong dependence on the patterns of molecular surface groups and adsorbed counter-ions. As a result, it is affected by such structural parameters as the helical pitch, groove width, the number of base pairs per helical turn, etc. We derive expressions which relate the energy of electrostatic interaction with these parameters and with the packing variables characterizing the axial and azimuthal alignment between neighboring macromolecules. We show, in particular, that the structural changes upon the B-to-A transition reduce the electrostatic energy by approximately kcal/mol per base pair, at a random adsorption of counter ions. Ion binding into the narrow groove weakens or inverts this effect, stabilizing B-DNA, as it is presumably the case in Li+-DNA assemblies. The packing symmetry and molecular alignment in DNA aggregates are shown to be affected by the patterns of ion binding.

Stabilization of the B conformation in unoriented films of calf thymus DNA by NaCl: a Raman and IR study

Unoriented films of calf thymus NaDNA with either 3.0 or 5.0 NaCl per base pair were prepared by dehydrating unstressed gels. These films were studied by Raman and ir spectroscopy. The 5.0 samples showed very strong vibrational modes characteristic of the B conformation at relative humidities (RH) as low as 30%, indicating that those samples were entirely in the B conformation. The 3.0 samples showed weaker features: some of the DNA in these samples were in the B conformation at 80% RH while the DNA is essentially in a disordered phase at 30% RH.

Conformational transitions of alternating purine-pyrimidine DNAs in perchlorate ethanol solutions

Conformational transitions of poly(dA-dC).poly(dG-dT), poly(dA-dT).poly(dA-dT), and other alternating purine-pyrimidine DNAs were studied in aqueous ethanol solutions containing molar concentrations of sodium perchlorate, which is a novel solvent stabilizing non-B duplexes of DNA. Using CD and UV absorption spectroscopies, we show that this solvent unstacks bases and unwinds the B-forms of the DNAs to transform them into the A-form or Z-form. In the absence of divalent cations poly(dA-dC).poly(dG-dT) can adopt both of these conformations. Its transition into the Z-form is induced at higher salt and lower ethanol concentrations, and at higher temperatures than the transition into the A-form. Submillimolar concentrations of NiCl2 induce a highly cooperative and slow A-Z transition or Z-Z' transition, which is fast and displays low cooperativity. Poly(dA-dT).poly(dA-dT) easily isomerizes into the A-form in perchlorate-ethanol solutions, whereas high perchlorate concentrations denature the polynucleotide, which then cannot adopt the Z-form. At low temperatures, however, NiCl2 also cooperatively induces the Z'-form in poly(dA-dT).poly(dA-dT). Poly(dI-dC).poly(dI-dC) is known to adopt an unusual B-form in low-salt aqueous solution, which is transformed into a standard B-form by the combination of perchlorate and ethanol. NiCl2 then transforms poly(dI-dC).poly(dI-dC) into the Z'-form, which is also adopted by poly(dI-br5dC).poly(dI-br5dC).

The interaction of metal ions with synthetic DNA: induction of conformational and structural transitions

The propensity of a large number of metal ions to induce cooperative conformational or structural transitions in double-stranded poly d(G-C) was assessed by UV and CD spectrometry. This ability was seen to be an intrinsic property of most metal ions. The observed (metal ion)/(polydeoxynucleotide) mole ratio calculated per G-C base pair and corresponding to the midpoints of the principal transition ranged from 0.3 (Ag(II) to 100 (Al(III)). A strong correlation was seen [y = -1.01(log x) + 3.26, r = 0.95, n = 20] between the (metal ion)/(poly d(G-C)) mole ratio required for the transition midpoint (x) and a covalent index to complex stability (y) of the metal ions. This relationship was independent of the types of transitions observed (monophasic or biphasic) or of specific conformations (e.g., B, Z, psi). The y index measures the ability of metal ions to bind to nitrogen and/or sulphur donor atoms in ligands compared to oxygen centers; equilibrium analysis indicates that the mole-ratio x decreases with increasing affinity of metal ions for poly d(G-C). Thus the observed relationship suggests that base-nitrogen binding facilitates the induced transitions. In general, metal ions designated as Class B or nitrogen/sulphur seeking (Ag(I), Hg(II), and Ru(III)) induced monophasic transitions, whereas Class A or oxygen seeking ions (La(III), Ce(III), Tb(III), Dy(III)) induced biphasic transitions. Transitions generated by ions of more ambivalent ligand preference (Borderline ions) were either monophasic (Mn(II), Fe(III), Cu(II), Cd(II), In(III), and Pb(II)) or biphasic (Cr(III), Co(II), Ni(II) and Zn(II)). Poorly defined transition-curve profiles were observed for Pt(II), Pd(II), and Al(III). Specific conformational assignments were made for some of the observed transitions. For a limited number of metal ions (Ni(II), Cu(II), Cd(II), Ag(I), Hg(II)), interaction with calf thymus DNA was similarly examined. In these instances, the susceptibility to DNase I digestion of both the DNA and polydeoxynucleotide complexes was assessed.

Composite cylinder models of DNA: application to the electrostatics of the B-Z transition

We develop and test a Poisson-Boltzmann model of the electrostatics of the B-Z transition of DNA. Starting from the detailed geometries of the two forms, we compute at each radius the fractions of DNA matter, of volume forbidden (for nonpoint-like ions), and of volume accessible to the center of ions. These radial distributions are incorporated in a composite cylinder model; availability to ions (porosity) and the dielectric constant at each radial distance are then obtained. The phosphate charge is distributed with cylindrical symmetry on two layers at the appropriate radial distances. The porous sheath, between the axis and the charge distribution, provides much more room for ions in B-DNA than in Z-DNA. By using previously developed methods, the Poisson-Boltzmann problem of such cylinders is easily solved. The computational load is small, so that results can be obtained for a large set of salt concentrations and for a number of ionic radii. The variation of the electrostatic free energy difference with salt concentration compares favorably with the experimental value (it is half as large). There is also qualitative agreement with experiments on supercoiled DNA, including a maximum of the free energy difference at submolar salt concentrations. The results for this cylinder with porous sheath are in line with those of the earlier simple planar model and of a plain cylinder with sheath, which is also presented here. They are thus insensitive to details of the model. They support the proposition that the main electrostatic feature of the B-Z transition is the better immersion of the B-DNA phosphates into the solution. They also give confidence in the validity of the Poisson-Boltzmann approach, despite the large salt concentrations involved. Prior studies using an approach based on the potential of mean force are discussed.

The effects of cobalt-hexammine and cobalt-pentammine cations on the solution structure of calf-thymus DNA. DNA condensation and structural features studied by FTIR difference spectroscopy

The interaction of calf-thymus DNA with cobalt-hexammine and cobalt-pentammine cations was investigated, in aqueous solution at pH 6-7 with cation/DNA(phosphate) molar ratios r = 1/80, 1/40, 1/20, 1/10, 1/4, 1/2 and 1, using Fourier Transform infrared (FTIR) difference spectroscopy. Correlations between spectral changes, DNA condensation and helical stabilization due to the cation interaction as well as conformational features are established. At a very low cation concentration (r = 1/80), the binding of cobalt-hexammine cation with DNA is through the H-bond formation between cation NH3 groups and the PO2 groups of the backbone, resulting in duplex stability. As the cation concentration increases, hydrogen bonding expands towards guanine N-7 and O-6 atoms. At r > 1/20, DNA condensation occurs with major reduction in the intensity of several DNA in-plane vibrations and that of the phosphate group. The cobalt-pentammine cation binding is via the PO2 groups (directly) at very low metal cation concentration (r = 1/80) and the guanine N-7 and the O-6 groups (indirectly) at higher ratios. At r > 1/10, DNA condensation begins with some degree of direct cation-base binding. No major conformational changes from the B-family structure were observed before and after DNA collapse, in the presence of cobalt-ammine cations.

On the metastability of left-handed DNA motifs

Alternating purine-pyrimidine DNA sequences such as poly [d(C-G)] or poly[d(m5C-G)] undergo a cooperative, salt-induced structural transition from a right-handed B conformation, which prevails at relatively low ionic strength, into a left-handed Z form, generally believed to be stabilized by high salt concentrations. We report here that upon a monotonous increase of the ionic strength, the well-established B to Z transition is followed by a second, hitherto unobserved conformational change leading from Z-DNA back into a right-handed B-like form. This observation indicates that, in contrast with the current convention, the Z motif represents an unstable configuration relative to the B form at both low and high salt concentrations and that the occurrence of a left-handed DNA structure, presently depicted as a step function of the ionic strength, should rather be treated in terms of a pulse. The reported transition underscores the inherent metastability of the Z configuration, and indicates, consequently, that this motif is ideally suited to act as a structural regulatory element, as such an element should be endowed with a large susceptibility to cellular parameters.

The effects of monovalent cations Li+, Na+, K+, NH4+, Rb+ and Cs+ on the solid and solution structures of the nucleic acid components. Metal ion binding and sugar conformation

The interactions of the monovalent ions Li+, Na+, K+, NH4+, Rb+ and Cs+ with adenosine-5'-monophosphoric acid (H2-AMP), guanosine-5'-monophosphoric acid (H2-GMP) and deoxyguanosine-5'-monophosphoric acid (H2-dGMP) were investigated in aqueous solution at physiological pH. The crystalline salts M2-nucleotide.nH2O, where M = Li+, Na+, K+ NH4+, Rb+ and Cs+, nucleotide = AMP, GMP and dGMP anions and n = 2-4 were isolated and characterized by Fourier Transform infrared (FTIR) and 1H-NMR spectroscopy. Spectroscopic evidence showed that these ions are in the form of M(H2O)n+ with no direct metal-nucleotide interaction, in aqueous solution. In the solid state, Li+ ions bind to the base N-7 site and the phosphate group (inner-sphere), while the NH4+ cations are in the vicinity of the N-7 position and the phosphate group, through hydrogen bonding systems. The Na-nucleotides and K-nucleotides are structurally similar. The Na+ ions bind to the phosphate group of the AMP through metal hydration shell (outer-sphere), whereas in the Na2-GMP, the hydrated metal ions bind to the base N-7 or the ribose hydroxyl groups (inner-sphere). The Na2-dGMP contains hydrated metal-carbonyl and metal-phosphate bindings (inner-sphere). The Rb+ and Cs+ ions are directly bonded to the phosphate groups and indirectly to the base moieties (via H2O). The ribose moiety shows C2'-endo/anti conformation for the free AMP acid and its alkali metal ion salts. In the free GMP acid, the ribose ring exhibits C3'-endo/anti conformer, while a C2'-endo/anti sugar pucker was found in the Na2-GMP and K2-GMP salts and a C3'-endo/anti conformation for the Li+, NH4+, Rb+ and Cs+ salts. The deoxyribose has C3'-endo/anti conformation in the free dGMP acid and O4'-endo/anti in the Na2-dGMP, K2-dGMP and a C3'-endo/anti for the Li+, NH4+, Rb+ and Cs+ salts. An equilibrium mixture of the C2'-endo/anti and C3'-endo/anti sugar puckers was found for these metal-nucleotide salts in aqueous solution.

Modeling DNA structures

For a molecule of biological importance, one expects a strong correlation between the three-dimensional structure and its biological function(s). Molecular simulations allow the prediction of physical properties of macromolecules. Many of these properties are closely related to the molecular structure. Model-building studies may thus supplement structurally low-resolution experimental data with detailed three-dimensional hypothetical atomic models. Such studies may give a consistent integral view of a wealth of experimental data. In most cases, such models will predict the outcome of certain experiments. Their actual results will often either confirm the model, be used for further refinement, or demand a major revision. Empirical force-fields provide a large amount of physicochemical knowledge concerning structural and other physical properties about various classes of molecules. They give reasonable bond distances and angles and prevent short van der Waals contacts. Difficulties arise for the prediction of large-scale structural elements. These are not only determined by short-range interactions, but also result from long-range electrostatic, hydration, and hydrophobic forces. In the case of the ionically driven DNA B-Z transition, the point of transition as a function of ionic strength and size can be correctly predicted (33). More must be done for a better understanding of the hydration forces (6). What type of questions will be reliably answered by a force-field? Relatively safe answers concern the local geometry of the molecules. If a conformation leads to strong distortions of bond distances or angles or to close van der Waals contacts, it can safely be rejected. Optimizing such unfavorable structures energetically may lead to structures showing how to avoid such distortions. More difficult are energetic questions: Which of two conformers is more stable, or what is the free energy of the substrate in the active site (63)? One cannot always be sure that the force-field provides the correct answers. Therefore, one should concentrate on questions that can be checked experimentally. The application of such concepts to model curved DNA (19, 60) and the DNA four-way junction (61) provides promising results. To explore the knowledge contained in the force-fields, several methods have been proposed. Taking advantage of structural symmetries may improve critically the convergence, while refining the target molecule or its building blocks. A numerically stable derivative for the torsion potential has been proposed. The optimization method of conjugated gradients (see Section II,B) is a powerful tool to find the way downhill toward a local minimum. To surmount barriers and escape local minima requires nonlocal optimization procedures.(ABSTRACT TRUNCATED AT 400 WORDS)

Comparison of different approaches for calculation of polyelectrolyte free energy

We consider the problem of the mean field (Poisson-Boltzmann) calculation of the electrostatic free energy for a strongly charged polyelectrolyte such as DNA in a salt solution. We compare two approaches to calculate the free energy: (i) direct one starting from the statistical-mechanical expression for the electrostatic free energy and (ii) the polyion charge variation method. In the infinite dilution limit (in respect to polyion) and in excess salt (IDLES) the two approaches are fully equivalent. This is shown by straight forward algebra. We have performed specific calculations of the free energy difference for the case of B-Z transition in DNA as a function of ionic strength. As expected, the two approaches led to identical results. The ionic strength dependence of the B-to-Z free energy proves to be concaved up and as a result Z-DNA is stabilized at low ionic concentration as well as at high salt, in full agreement with our previous results (M.D.Frank-Kamenetskii et al., J. Biomol. Struct. Dyn. 3, 35-42 (1985]. Our data quantitatively agree with the results of Soumpasis (D.M.Soumpasis, J. Biomol. Struct. Dyn. 6, 563-574 (1988]. However, his claim about the absence of the effect of stabilization of Z-DNA at low salt proves to be groundless, and the criticism of our earlier approach seems to be irrelevant.

Computation of ionic distributions around charged biomolecular structures: results for right-handed and left-handed DNA

We introduce an efficient computational methodology employing the potentials of mean force approach for estimating the detailed three-dimensional ionic distributions around arbitrarily complex charged biomolecular structures for all monovalent salt concentrations of practical interest (e.g., 0.1-5.0 M NaCl). Such distributions are required for specifying thermodynamic and structure-specific features of ion-mediated interactions of charged proteins, DNA and RNA, membranes, and macromolecular assemblies. As a first application, we present results for distributions around the B and ZI conformers of the DNA oligomer d(C-G)18.d(C-G)18. The ionic microenvironment depends strongly on the DNA conformation, sequence, and bulk salt concentrations.

A Raman study of low frequency intrahelical modes in A-, B-, and C-DNA

We have obtained low frequency (less than 200 cm-1) Raman spectra of calf-thymus DNA and poly(rI).poly(rC) as a function of water content and counterion species and of d(GGTATACC)2 and d(CGCGAATTCGCG)2 crystals. We have found that the Raman scattering from water in the first and second hydration shells does not contribute directly to the Raman spectra of DNA. We have determined the number of strong Raman active modes by comparing spectra for different sample orientations and polarizations and by obtaining fits to the spectra. We have found at least five Raman active modes in the spectra of A- and B-DNA. The frequencies of the modes above 40 cm-1 do not vary with counterion species, and there are only relatively small changes upon hydration. These modes are, therefore, almost completely internal. The mode near 34 cm-1 in A-DNA is mostly internal, whereas the mode near 25 cm-1 is dominated by interhelical interactions. The observed intensity changes upon dehydration were found to be due to the decrease in interhelical distance. Polymer length appears to play a role in the lowest frequency modes.

Energetics of the hairpin to mismatched duplex transition of d(GCCGCAGC) on NaCl solution

We report Potential of Mean Force studies to describe the relative thermodynamic stabilities of d(GCCGCAGC) in a mismatched duplex and a hairpin monomer conformation in NaCl solution. The PMF calculations are combined with previous molecular mechanics and normal mode analysis in order to estimate the role of different components of the free energy in determining the relative stability of the duplex and hairpin structures. The high entropy associated with the loop region and the lack of minor groove phosphate-phosphate interactions in the hairpin compete against the gain in enthalpic contribution to the free energy due to base pairing in the mismatched duplex. The combined free energy calculations show that the hairpin is the most stable conformation at low salt and that a hairpin to duplex transition takes place at approximately 0.47 M NaCl. In addition, we studied the hairpin to partially stacked single helical conformation equilibrium at low salt. We found a small variation in transition temperature in salt concentration, delta Tm/delta log10(cs) approximately 2-3 degrees K/decade, in contrast to the duplex to hairpin or duplex to partially stacked single helix transition where the transition temperature exhibited marked dependence on salt concentration. This is in qualitative agreement with experimental data. Based on the Potential of Mean Force free energy calculation, the order of relative stability of the three-conformations studied varies with salt concentration. We observed the following orders of stability: stacked single helix greater than hairpin greater than duplex for cs less than 0.77 M NaCl; single helix greater than duplex greater than hairpin for 0.77 less than Cs less than 2.1 M; and duplex greater than hairpin greater than single strand for cs greater than 2.1 M. From the calculated PMF free energy curves in the NaCl concentration range, 0.012 less than cs less than 5.0 M, we can assign upper and lower bounds for the non-ionic differences in free energy between the duplex, hairpin, and stacked single helical states (at standard conditions: cs = 1.0 M, T = 25 degrees C, and 1 M oligomer concentration). We found that for delta G duplex single helix = G duplex - 2 x G single helix less than -7.38 Kcal/mol, the single helix is the least stable state. For the duplex-to-hairpin free energy difference in the range, -1.87 less than delta G duplex-hairpin less than 0.03 Kcal/mol, there will always be a salt-induced hairpin-to-duplex transition for 0.01 less than cs less than 1.6 M NaCl. If delta G duplex-hairpin less than -1.87, the duplex is always more stable than the hairpin; and for delta G duplex-hairpin greater than Kcal/mol, the hairpin state is always more stable than the duplex, for all salt concentrations.

The calculated free energy effects of 5-methyl cytosine on the B to Z transition in DNA

We have examined the free energy effects of 5-methylation of cytosine on the B in equilibrium Z conformational equilibrium in DNA. Free energy differences were calculated using the free energy perturbation approach, which uses an easily derived equation from classical statistical mechanics to relate the free energy difference between two states to the ensemble average of the potential energy difference between the states. Calculations were carried both in explicit solvent and (for comparison) in vacuo. The free energy values obtained for the explicit solvent systems are total free energies, with contributions from all parts of the system (solvent + solute), and so are relevant to the B in equilibrium Z transitions observed under real (physiological) conditions. We calculate that in solution, methylation makes the B in equilibrium Z transition more favorable by about -0.4 kcal/mole base pair (bp) in free energy. This value compares well with approximate experimentally derived values of about -0.3 kcal/mole-bp. We also discuss a method for determining the free energy difference between conformational states poorly maintained by a potential energy model. Finally, the effects of methylation on the melting temperature of DNA are examined.

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.

Cation radius effects on the helix-coil transition of DNA. Cryptates and other large cations

Most polyelectrolyte theories of the effect of ions on the thermal melting of DNA assume that the predominant influence of the cations comes through their charge. Ion size and structure are treated, for analytic convenience, as negligible variables. We have examined the validity of this assumption by measuring the melting temperature of calf thymus DNA as a function of salt concentration with four univalent cations of different hydrated radii. These are K+ (3.3 A), (n-Pr)4N+ (4.5 A), (EtOH)4N+ (4.5 A), and C222-K+ (5 A). C222-K+ is a complex of cryptand C222 with K+. With K+ as the sole cation, Tm varies linearly with the log of ionic strength over the range 0.001-0.1 M. With all the K+ sequestered by an equimolar amount of C222, Tm is depressed by 10-20 degrees C and the slope of Tm vs. ionic strength is lower. At low ionic strength, an even greater reduction in Tm is achieved with (n-Pr)4N+; but the similar-sized (EtOH)4N+ gives a curve more similar to K+. Theoretical modeling, taking into account cation size through the Poisson-Boltzmann equation for cylindrical polyelectrolytes, predicts that larger cations should be less effective in stabilizing the double helix; but the calculated effect is less than observed experimentally. These results show that valence, cation size, and specific solvation effects are all important in determining the stability of the double-helical form of DNA.

Counterion effects on the physical properties and the A to B transition of calf-thymus DNA films

We report measurements of the water content and swelling of wet-spun films of Na-, K-, Rb-, and Cs-DNA as a function of relative humidity (rh). The water contents (number of water molecules per base pair of DNA) of these films are found to be quite similar, indicating that the identity of the counterion species is unimportant for the water content. Since the A to B transition for these DNAs occurs at different rhs, the corresponding water contents of the A to B transition are found to be quite different. These films swell as a function of rh in a very similar manner, implying that the changes in the intermolecular bonds in the different DNAs are similar. Dramatic changes are observed in the dimensions of the films above 84% rh for all types of DNA. Combining the water content and swelling measurements yields the dependence of the volume per base pair on water content. The volume per base pair is observed to be a nonlinear function of water content, indicating nonideal mixing of the water with the DNA.

A numerical counterion condensation analysis of the B-Z transition of DNA

We examine the salt dependence of the B-Z transition in DNA by means of the counterion condensation theory adapted to structurally realistic coordinates of the phosphate groups. The ionic contribution to the free energy difference delta G is computed for both the ZI and ZII conformations over broad ranges of NaCl and MgCl2 concentrations and polymer lengths. For the solvent we employ both a constant-dielectric model (dielectric constant set to 78.3) and a dielectric saturation model (distance-dependent dielectric constant). Where comparison can be made, the results for the constant-dielectric model are similar to those obtained by other workers for the same model but with different computational methods. The existence of a low-salt transition, and its location when it does occur, depends strongly on the DNA length and on the dielectric model. The behavior of ZI and ZII are qualitatively similar throughout the entire salt range for the constant-dielectric model, but qualitatively different if dielectric saturation is simulated, as we think is necessary for a realistic description. The ionic delta G, in the presence of dielectric saturation, bears comparison with the high-salt trend of the measured total delta G if "Z-DNA" is predominantly ZI, but not if it is predominantly ZII.

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.

A duplex of the oligonucleotides d(GGGGGTTTTT) and d(AAAAACCCCC) forms an A to B conformational junction in concentrated salt solutions

The coexistence of both A form and B form tracts and formation of an A-B junction in the oligomer d(GGGGGTTTTT).d(AAAAACCCCC) in saturated sodium chloride solution have been detected by Raman spectroscopy. The entire duplex adopts the familiar B-form conformation in aqueous solution at low salt concentrations (0.1M NaCl). In 6M NaCl the adoption of an A form is observed within the G,C tract while a B-form is maintained in the A.T tract. The experimental results indicate that two different helical forms can co-exist in a rather short oligonucleotide and that formation of an A-B junction can occur over a fairly small span of bases. This is in agreement with recent rules governing the relation between base sequence and secondary structure of DNA published from this laboratory. The conformational preferences of each of the individual oligomers d(AAAAACCCCC) and d(GGGGGTTTTT) have also been investigated. The oligomer d(AAAAACCCCC) is single stranded but some evidence for base stacking is observed at 2 degrees C. In contrast, a double stranded B-form structure characterized by wobble G-T base pairing is observed for d(GGGGGTTTTT) in 0.1M and 6M NaCl.

Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution

We compute the full harmonic vibrational spectrum and eigenmodes of a DNA oligomer, d(C-G)3, in optimized B and Z conformations in various ionic environments (0.01-5.0 M NaCl). The statistical interactions of DNA with the diffuse ionic cloud surrounding it in solution are approximately represented within the potential of mean force framework. The lowest eigenfrequency of the B conformation is found to drastically decrease with increased NaCl concentration. This suggests that a soft mode mechanism may be a precursor for the B-to-Z conversion. The free energy balance governing the B-Z isomerization of d(C-G)3 is dominated by the solvent-averaged effective phosphate-phosphate interactions due to substantial cancelations between the much larger intramolecular energy contributions.

A rigorous basepair oriented description of DNA structures

We propose new, rigorous definitions for (i) basepair fixed coordinate systems and (ii) the twist, tilt, and roll angles (called tau, t, rho) describing the relative orientation of adjacent basepairs and bases in a pair, in arbitrary DNA structures obtained from x-ray diffraction, 2D NMR, or energy calculations. In contrast to the corresponding angular parameters (tg, theta T, theta R) and coordinate systems introduced by Dickerson and co-workers and currently in use, our angular parameters and coordinate systems, together with a set of three displacement parameters, dx, dy, dz, provide a mathematically correct and general description of DNA conformations at the basepairs and/or base level. For instance, our description is applicable when the DNA structure considered is inherently curved, irregular, and/or does not possess dyad (or pseudodyad) axes. We develop a computationally convenient algorithm for rigorous DNA conformational analysis and apply it to some of the known crystal structures. We establish the connection to the currently used parameters and test the consistency and efficiency of our methodology by reconstructing the Dickerson B dodecamer using only the sequence and the set of parameters obtained from the atomic coordinates. The six parameter (tau, t, rho, dx, dy, dz) basepair level reconstruction is good but not perfect. Perfect reconstruction is obtained when one also considers each base in a basepair (consideration of propeller twist alone is not sufficient). The variation of the rigorous parameters proposed along the sequence is much larger, but their average values agree with fiber and solution data much better than in the case of the currently used set. The results of our analysis do not support Trifonov's AA.TT wedge model for DNA curvature but provide some evidence in favor of the Crothers junction-bend model. We point out some of the limitations of basepair level approaches when applied to DNA structure prediction and quantitative understanding of sequence-dependent variations in structure.

Salt dependence of DNA structural stabilities in solution. Theoretical predictions versus experiments

The predictions of currently available theories for treating DNA-diffuse ionic cloud free energy contributions to conformational stability have been tested against experimental data for salt induced B-Z and B-A transitions. The theories considered are (i) Manning's counterion condensation approach (CC), (ii) the idealized Poisson-Boltzmann approximation (PB), and (iii) the potentials of mean force (PMF) approach proposed by Soumpasis. As far as we can judge from comparison with the set of experimental data currently available, it is found that only the latter theory yields satisfactory quantitative results for the dependence of the B-Z and B-A relative stabilities on monovalent salt concentration. The correct application of the PB and CC theories does not yield very low salt Z-B transitions, in contradiction to earlier assertions. At low salt concentrations the PB theory is qualitatively correct in predicting that the B form is electrostatically more favorable than both the A and Z forms, whereas the CC theory is qualitatively wrong predicting that Z-DNA is more stable than both B and A DNA.

Computers in molecular biology: current applications and emerging trends

The rate of generation of molecular sequence data is forcing the use of computers as a central tool in molecular biology. Current use of computers is limited largely to data management and sequence comparisons, but rapid growth in the volume of data is generating pressure for the development of high-speed analytical methods for deciphering the codes connecting nucleotide sequence with protein structure and function.

Formation of a left-handed RNA double helix: energetics of the A-Z transition of poly[r(G-C)] in concentrated NaClO4 solutions

Ultraviolet spectroscopic and nuclear magnetic resonance (NMR) studies have shown that poly[r(G-C)] in a solution of 4 M NaClO4 undergoes a transition to a left-handed Z-RNA helix upon raising the temperature to 60 degrees C [Hall, K., Cruz, P., Tinoco, I., Jr., Jovin, T. M., & van de Sande, J. H. (1984) Nature (London) 311, 584-586]. In the present report, the transition temperature of this particular order/order transition is shown to increase with decreasing NaClO4 concentration to about 110 degrees C, above which only the helix-to-random coil transition is detectable. The reversibility and cooperativity of the helix/helix conversion has facilitated the quantitative evaluation of the transition enthalpy by means of differential scanning microcalorimetry. In 5 M NaClO4, the transition temperature is 43 degrees C, the conversion enthalpy 4.2 kJ (1.0 kcal) per mole of base pair, and the corresponding entropy change 13 J (3.1 cal) deg-1. The van't Hoff enthalpy for the same process, determined from the temperature dependence of the optical transition, is 0.26 MJ (62 kcal) per mole of cooperative unit. The ratio of the two enthalpy values yields an apparent cooperative length for the A-Z transition of poly[r(G-C)] of approximately 60 base pairs, indicative of a concerted all-or-none process.

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.

The B-Z conformational transition and aggregation of poly[d(G-C)] induced by moderate concentrations of Mg(CIO4)2

Mg(ClO4)2 induces the cooperative B-to-Z transition of poly[d(G-C)]; the salt concentration at the midpoint is 0.26 M. A comparison with previous data for NaCl, MgCl2 and NaClO4 (F.M. Pohl and T.M. Jovin, J. Mol. Biol. 67 (1972) 375) indicates that Mg(ClO4)2 is more effective than would be anticipated from the simple additive effects of the Mg2+ and ClO4- ions (the ionic strengths of the respective transition points are: NaCl, 2.4; MgCl2, 2.1; NaClO4, 1.8 and Mg(ClO4)2, 0.78). These results suggest the importance of specific interactions involving ClO4-, particularly in the presence of Mg2+. The B-Z transition of poly[d(G-C)] can be monitored spectroscopically via the large hyperchromic shift at 295 nm and the inversion in the CD spectrum. The reaction is fully reversible and can be fitted by a monoexponential function with half times varying between 8 and 150 min. The observed relaxation times are strongly dependent on the concentration of Mg(ClO4)2 with a distinct maximum at the transition point, in accordance with a concerted mechanism involving only the B and Z states. As the polymer assumes the Z conformation it progressively aggregates into a gel-like precipitate, which, however, redissolves rapidly upon lowering the salt concentration. The natural DNA from Micrococcus lysodeikticus which has a high GC content of 72% is also precipitated by Mg(ClO4)2 but we do not have direct spectroscopic evidence for the involvement of the Z conformation in this phenomenon. Neither calf thymus DNA (41% GC) nor poly[d(A-T)] (0% GC) aggregates under the same conditions.