Energetics of left and right handed models of DNA

It has been shown by model building studies that various right handed and left handed models are compatible with X-ray data of B-DNA and C-DNA. These models are also found to be in good agreement with infrared dichroism data. Detailed potential energy calculations have now been carried out for these models, viz., right and left handed B-DNA and right and left handed C-DNA. It is found that base sugar stacking and interactions involving the phosphate groups are the dominant forces for stabilizing a particular structure. For some sequences, viz., A-A, T-A and C-A, left handed stacking is quite favourable in both B and C structures. But intranucleotide interactions make the left B-DNA unfavourable while the left C-DNA structure is more stable, for all the sequences, than the right C-DNA structure, proposed from fibre data. For the hexanucleoside pentaphosphate fragments the same trend is observed, with the right handed B-DNA being the most stable of the four models studied. However, the left C-DNA structure is only marginally higher in energy, particularly if the shielding effect of the counter ions, on the phosphate group is taken into consideration.     

Conformations of C-DNA in Agreement with Fiber X-ray and Infrared Dichroísm

Abstract

Different left handed double helices are proposed as models for DNA fibers in the C form. These conformations have geometrical parameters which agree well with fiber X-ray data and the orientations of their phosphate groups are in good agreement with infrared dichroísm results. A complete set of atomic coordinates and dihedral angles are given together with curves of calculated diffracted intensities. The present results are compared with experimental values and with the other C-DNA models.     

Conformational transitions of the phosphodiester backbone in native DNA: two-dimensional magic-angle-spinning 31P-NMR of DNA fibers.

Solid-state 31P-NMR is used to investigate the orientation of the phosphodiester backbone in NaDNA-, LiDNA-, MgDNA-, and NaDNA-netropsin fibers. The results for A- and B-DNA agree with previous interpretations. We verify that the binding of netropsin to NaDNA stabilizes the B form, and find that in NaDNA, most of the phosphate groups adopt a conformation typical of the A form, although there are minor components with phosphate orientations close to the B form. For LiDNA and MgDNA samples, on the other hand, we find phosphate conformations that are in variance with previous models. These samples display x-ray diffraction patterns that correspond to C-DNA. However, we find two distinct phosphate orientations in these samples, one resembling that in B-DNA, and one displaying a twist of the PO4 groups about the O3-P-O4 bisectors. The latter conformation is not in accordance with previous models of C-DNA structure.     

Conformations of C-DNA in agreement with fiber X-ray and infrared dichroism

Different left handed double helices are proposed as models for DNA fibers in the C form. These conformations have geometrical parameters which agree well with fiber X-ray data and the orientations of their phosphate groups are in good agreement with infrared dichroism results. A complete set of atomic coordinates and dihedral angles are given together with curves of calculated diffracted intensities. The present results are compared with experimental values and with the other C-DNA models.     

DNA polymorphism and local variation in base-pair orientation: a theoretical rationale.

Basepair stacking calculations have been carried out to understand the conformational polymorphism of DNA and its sequence dependence. The recently developed self-consistent parameter set, which is specially suitable for describing irregular DNA structures, has been used to describe the geometry of a basepair doublet. While for basepairs without any propeller, the favourable stacking patterns do not appear to have very strong features, much more noticeable sequence dependent stacking patterns emerge once a propeller is applied to the basepairs. The absolute minima for most sequences occurs for a doublet geometry close to the B-DNA fibre models. Hence in the B-DNA region, no strong sequence dependent features are found, but the range of doublet geometries observed in the crystal structures generally lie within the low energy contours, obtained from stacking energy calculations. The doublet geometry corresponding to the A-DNA fibre model is not energetically favourable for the purine-pyrimidine sequences, which prefer small roll angle values when the slide has a large negative value as in A-DNA. However positive roll with large negative slide is allowed for GG, GA, AG and the pyrimidine-purine steps. This is consistent with the observed geometries of various steps in A-DNA crystals. Thus the general features of the basepair doublets predicted from these theoretical studies agree very well with the results from crystal structure analysis. However, since most sequences show an overall preference for B-type doublet geometry, the B----A transition for random sequence DNA cannot be explained on the basis of basepair stacking interactions.     

The electrostatic contribution to DNA base-stacking interactions.

Base-stacking and phosphate-phosphate interactions in B-DNA are studied using the finite difference Poisson-Boltzmann equation. Interaction energies and dielectric constants are calculated and compared to the predictions of simple dielectric models. No extant simple dielectric model adequately describes phosphate-phosphate interactions. Electrostatic effects contribute negligibly to the sequence and conformational dependence of base-stacking interactions. Electrostatic base-stacking interactions can be adequately modeled using the Hingerty screening function. The repulsive and dispersive Lennard-Jones interactions dominate the dependence of the stacking interactions on roll, tilt, twist, and propellor. The Lennard-Jones stacking energy in ideal B-DNA is found to be essentially independent of sequence.     

Crystal and molecular structure of the ammonium salt of the dinucleoside monophosphate d(CpG)

The crystal and molecular structure of the ammonium salt of deoxycytidylyl-(3'-5')-deoxyguanosine has been determined from 0.85 A resolution single crystal X-ray diffraction data. The crystals obtained by acetone diffusion technique at -20 degrees C, are orthorhombic, P212121, a = 12.880(2), b = 17444(2) and c = 27.642(2) A. The structure was solved by high resolution Patterson and Fourier methods and refined to R = 0.136. There are two d(CpG) molecules in the asymmetric unit forming a mini left handed Z-DNA helix. This is in contrast to the earlier reported forms of d(CpG) where the molecules form self base paired duplexes. There are two ammonium ions in the asymmetric unit. The major groove NH+4 ion interacts with N7 of guanines through water bridges besides making H-bonded interactions directly with the phosphate oxygen atoms. A second NH+4 ion is found in the minor groove interacting directly with the phosphate oxygen atoms. Symmetry related molecules pack in such a way that the cytosine base stacks on cytosine and guanine base on guanine. Our structure demonstrates that alternating d(CpG) sequences have the ability to adopt the left handed Z-DNA structure even at the dimer level i.e., in a sequence which is only two base pairs long.     

A left-handed helix molecular model of C-DNA in agreement with fiber X-ray and infrared

A left handed double helix is proposed as a model for C-DNA. This conformation presents geometrical parameters which are in agreement with X-ray data as well as with infrared measurements. Dihedral angles and atomic coordinates are given together with a stereo view. Curves of the calculated diffracted intensities are compared with experimental data.     

Local conformational variations observed in B-DNA crystals do not improve base stacking: computational analysis of base stacking in a d(CATGGGCCCATG)(2) B<-->A intermediate crystal structure

The crystal structure of d(CATGGGCCCATG)₂ shows unique stacking patterns of a stable B↔A-DNA intermediate. We evaluated intrinsic base stacking energies in this crystal structure using an ab initio quantum mechanical method. We found that all crystal base pair steps have stacking energies close to their values in the standard and crystal B-DNA geometries. Thus, naturally occurring stacking geometries were essentially isoenergetic while individual base pair steps differed substantially in the balance of intra-strand and inter-strand stacking terms. Also, relative dispersion, electrostatic and polarization contributions to the stability of different base pair steps were very sensitive to base composition and sequence context. A large stacking flexibility is most apparent for the CpA step, while the GpG step is characterized by weak intra-strand stacking. Hydration effects were estimated using the Langevin dipoles solvation model. These calculations showed that an aqueous environment efficiently compensates for electrostatic stacking contributions. Finally, we have carried out explicit solvent molecular dynamics simulation of the d(CATGGGCCCATG)₂ duplex in water. Here the DNA conformation did not retain the initial crystal geometry, but moved from the B↔A intermediate towards the B-DNA structure. The base stacking energy improved in the course of this simulation. Our findings indicate that intrinsic base stacking interactions are not sufficient to stabilize the local conformational variations in crystals.     

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.     

Structural characterisation of a uracil containing hairpin DNA by NMR and molecular dynamics.

Three-dimensional (3D) structure of a hairpin DNA d-CTAGAGGATCCTTTUGGATCCT (22mer; abbreviated as U4-hairpin), which has a uracil nucleotide unit at the fourth position from the 5' end of the tetra-loop has been solved by NMR spectroscopy. The(1)H resonances of this hairpin have been assigned almost completely. NMR restrained molecular dynamics and energy minimisation procedures have been used to describe the 3D structure of the U4 hairpin. This study establishes that the stem of the hairpin adopts a right handed B-DNA conformation while the T(12)and U(15)nucleotide stack upon 3' and 5' ends of the stem, respectively. Further, T(14)stacks upon both T(12)and U(15)while T(13)partially stacks upon T(14). Very weak stacking interaction is observed between T(13)and T(12). All the individual nucleotide bases adopt ' anti ' conformation with respect to their sugar moiety. The turning phosphate in the loop is located between T(13)and T(14). The stereochemistry of U(15)mimics the situation where uracil would stack in a B-DNA conformation. This could be the reason as to why the U4-hairpin is found to be the best substrate for its interaction with uracil DNA glycosylase (UDG) compared to the other substrates in which the uracil is at the first, second and third positions of the tetra-loop from its 5' end, as reported previously.     

The stereochemistry of a four-way DNA junction: a theoretical study.

The stereochemical conformation of the four-way helical junction in DNA (the Holliday junction; the postulated central intermediate of genetic recombination) has been analysed, using molecular mechanical computer modelling. A version of the AMBER program package was employed, that had been modified to include the influence of counterions and a global optimisation procedure. Starting from an extended planar structure, the conformation was varied in order to minimise the energy, and we discuss three structures obtained by this procedure. One structure is closely related to a square-planar cross, in which there is no stacking interaction between the four double helical stems. This structure is probably closely similar to that observed experimentally in the absence of cations. The remaining two structures are based on related, yet distinct, conformations, in which there is pairwise coaxial stacking of neighbouring stems. In these structures, the four DNA stems adopt the form of two quasi-continuous helices, in which base stacking is very similar to that found in standard B-DNA geometry. The two stacked helices so formed are not aligned parallel to each other, but subtend an angle of approximately 60 degrees. The strands that exchange between one stacked helix and the other are disposed about the smaller angle of the cross (i.e. 60 degrees rather than 120 degrees), generating an approximately antiparallel alignment of DNA sequences. This structure is precisely the stacked X-structure proposed on the basis of experimental data. The calculations indicate distortions from standard B-DNA conformation that are required to adopt the stacked X-structure; a widening of the minor groove at the junction, and reorientation of the central phosphate groups of the exchanging strands. An important feature of the stacked X-structure is that it presents two structurally distinct sides. These may be recognised differently by enzymes, providing a rationalisation for the points of cleavage by Holliday resolvases.     

Designing of peptides with left handed helical structure by incorporating the unusual amino acids

The conformational behaviour of delta Ala has been investigated by quantum mechanical method PCILO in the model dipeptide Ac-delta Ala-NHMe and in the model tripeptides Ac-X-delta Ala-NHMe with X = Gly, Ala, Val, Leu, Abu and Phe and is found to be quite different. The computational results suggest that in the model tripeptides the most stable conformation corresponds to phi 1 = -30 degrees, psi 1 = 120 degrees and phi 2 = psi 2 = 30 degrees in which the > C = 0 of the acetyl group is involved in hydrogen bond formation with N-H of the amide group. Similar results were obtained for the conformational behaviour of D-Ala in Ac-D-Ala-NHMe and Ac-Ala-D-Ala-NHMe. The conformational behaviour of the amino acids delta Ala, D-Ala, Val and Aib in model tripeptides have been utilized in the designing of left handed helical peptides. It is shown that the peptide HCO-(Ala-D-Ala)3-NHMe can adopt both left and right handed helix whereas in the peptide Ac-(Ala-delta Ala)3-NHMe the lowest energy conformer is beta-bend ribbon structure. Left handed helical structure with phi = 30 degrees, psi = 60 degrees for D-Ala residues and phi = psi = 30 degrees for delta Ala is found to be more stable by 4 kcal mole-1 than the corresponding right handed helical structure for the peptide Ac-(D-Ala-delta Ala)3-NHMe. In both the peptides Ac-(Val-delta Ala)3-NHMe and Ac-(D-Val-delta Ala)3-NHMe the most stable conformer is the left handed helix. Comparisons of results for Ac-(Ala-delta Ala)3-NHMe and Ac(Val-delta Ala)3-NHMe and Ac-(D-Ala-delta Ala)3-NHMe and Ac-(D-Val-delta Ala)3-NHMe also reveal that the Val residues facilitate the population of 3(10) left handed helix over the other conformers. It is also shown that the conformational behaviour of Aib residue depends on the chirality of neighbouring amino acids, i.e. Ac-(Aib-Ala)3-NHMe adopts right handed helical structure whereas Ac-(Aib-D-Ala)3-NHMe is found to be in left handed helical structure.     

Circular dichroism of flow-oriented nucleic acids. II. Comparison between observed and calculated spectra.

The ultraviolet circular dichroism (CD) of oriented DNA and RNA molecules is calculated by an extension of Johnson and Tinoco's theory [(1969) Biopolymers 7 , 727–749] for unoriented molecules. The calculations are carried out for molecular models of A-DNA, B-DNA, planar B-DNA, C-DNA, and RNA-11-α. The calculated curves are compared to measured spectra [(1975) J. Mol. Biol. 92 , 449–466] Chung and Holzwarth, for oriented solutions of DNA in buffer, DNA in 6 M LiCl or in ethylene glycol, and double-stranded viral RNA. The calculation, which considers only base–base interactions, predicts that the CD of B-DNA, measured with light propagating parallel to the helix axis, should be large and semiconservative, whereas the CD for light propagating perpendicular to the helix axis should be nonconservative. These predictions agree qualitatively with the experimental observations for DNA in buffer; agreement improves if one assumes the bases to be exactly perpendicular to the helix axis. For the other geometries, agreement is less satisfactory, but qualitative agreement with experiment is obtained and the signs of the specific CD spectra are in accord with observations.     

A Kinked Model for the Solution Structure of DNA Tridecamers with Inserted Adenosines: Energy Minimization and Molecular Dynamics

Abstract

Structural modelling techniques using energy minimization and molecular dynamics have been employed to generate kinked models for the solution structure of two DNA tridecamer sequences containing inserted adenosines: d(CGCAGAATTCGCG)₂ and d(CGCAGAGCTCGCG)₂. These models are consistent with NMR studies of these sequences in solution. The overall shapes of the two models are similar, consisting of three B-DNA sections: two outer segments on the same side of the central portion, with the additional adenosines acting as wedges to kink the structure. An alternative scheme for the hydrogen bond pairing at the kink site is suggested as a way for the additional adenosines to be stabilized in the duplex.     

DNA Models for A,B, C and D Conformations Related to Fiber X-ray,Infrared and NMR Measurements

Abstract

A conformational analysis of the A, B, C and D DNA forms was made in order to establish molecular models presenting a good agreement with experimental data obtained from fiber X-ray, infrared linear dichroism and ³¹P NMR. The proposed models have been refined and do present good stereochemistry and optimized H-bond distances between bases associated with the Watson-Crick pairing. The DNA conformations proposed are a left handed double helix for the C form and right handed helices for A, B and D. Relations to conformational transitions between these forms are discussed.     

Characterization of the base stacking interactions in DNA by means of Lennard-Jones empirical potentials

Three empirical potentials of the Lennard-Jones type taken from literature were used to calculate van der Waals contributions to the base-pair couples stacking energies in B-DNA and A-DNA type double helical conformations. The information obtained can be summarized as follows: (1) Purine-pyrimidine and purine-purine (pyrimidine-pyrimidine in the complementary strand) sequences preferred right-handed helical arrangement, whereas pyrimidine-purine sequences favoured left-handed (C-G) or unwound (T-A) stacking geometry; in the latter case this only held for B- but not A-DNA (the C-G sequence was not studied in A-DNA owing to difficulties (see below) with the G amino group in B-DNA); (2) Positive propeller twist of base-pairs was stable in both B- and A-DNA; the thymine methyl group promoted the propeller and this effect was strongest in the A-T step; (3) Tilt of base pairs occurred around zero in B-DNA and between 15-20 degrees C in A-DNA, in agreement with the experimental observations; (4) Vertical separation of base pairs was optimal within 0.33-0.34 nm for B-DNA and around 0.29 nm for A-DNA using the 9-6 potential. The 12-6 potential gave similar results with B-DNA as the 9-6 potential if, however, base pairs were separated by 0.35-0.36 nm; (5) The calculated effect of the guanine amino group was substantially stronger than expected on the basis of data derived from X-ray diffraction studies of oligonucleotide single crystals; (6) In comparison with the 9-6 potential, the 12-6 potential provided more strict energy minima. In summary, the empirical potentials reproduce, at least semiquantitatively, many but not all DNA properties; this should be taken into account whenever the potentials are used for prediction purposes.     

Energetics of intercalation specificity. I. Backbone unwinding.

An empirical partitioned-potential function with optimized parameters was employed to investigate the basis of intercalation specificity recently observed by experimental techniques. The nature of this specificity is discussed in terms of component interactions for all non-truncated complementary dinucleoside triphosphate mini- (or miniature) helices. Our calculations agree with available evidence indicating the preference of Pyr(3′-5′)Pur sequences over Pur(3′-5′)Pyr sequences to change from the B-DNA to the intercalated conformation. Base–base (stacking) and base–phosphate interactions control the specificity. The extent of net electrostatic charge on the phosphate groups play an important but limited role in establishing the observed specificity. These results should apply for the class of aromatic agents involved in nonspecific intercalation with nucleic acids but not necessarily for aromatic agents involved in specific reactions with a particular nucleotide base.