Conformational characteristics of the trinucleoside diphosphated(ApApA) from energy-minimization studies

A Monte Carlo method for generating structures of short single-stranded DNA sequences

A Monte Carlo method has been developed for generating the conformations of short single-stranded DNAs from arbitrary starting states. The chain conformers are constructed from energetically favorable arrangements of the constituent mononucleotides. Minimum energy states of individual dinucleotide monophosphate molecules are identified using a torsion angle minimizer. The glycosyl and acyclic backbone torsions of the dimers are allowed to vary, while the sugar rings are held fixed in one of the two preferred puckered forms. A total of 108 conformationally distinct states per dimer are considered in this first stage of minimization. The torsion angles within 5 kcal/mole of the global minimum in the resulting optimized states are then allowed to vary by +/- 10 degrees in an effort to estimate the breadth of the different local minima. The energies of a total of 2187 (3(7)) angle combinations are examined per local conformational minimum. Finally, the energies of all dinucleotide conformers are scaled so that the populations of differently puckered sugar rings in the theoretical sample match those found in nmr solution studies. This last step is necessitated by limitations in the theoretical methods to predict DNA sugar puckering accurately. The conformer populations of the individual acyclic torsion angles in the composite dimer ensembles are found to be in good agreement with the distributions of backbone conformations deduced from nmr coupling constants and the frequencies of glycosyl conformations in x-ray crystal structures, suggesting that the low energy states are reasonable. The low energy dimer forms (consisting of 150-325 conformational states per dimer step) are next used as variables in a Monte Carlo algorithm, which generates the conformations of single-stranded d(CXnG) chains, where X = A, T and n = 3, 4, 5. The oligonucleotides are built sequentially from the 5' end of the chain using random numbers to select the conformations of overlapping dimer units. The simulations are very fast, involving a total of 10(6) conformations per chain sequence. The potential errors in the buildup procedure are minimized by taking advantage of known rotational interdependences in the sugar-phosphate backbone. The distributions of oligonucleotide conformations are examined in terms of the magnitudes, positions, and orientations of the end-to-end vectors of the chains. The differences in overall flexibility and extension of the oligomers are discussed in terms of the conformations of the constituent dinucleotide steps, while the general methodology is discussed and compared with other nucleic acid model building techniques.

Base sequence effects in double helical DNA. I. Potential energy estimates of local base morphology

A series of potential energy calculations have been carried out to estimate base sequence dependent structural differences in B-DNA. Attention has been focused on the simplest dimeric fragments that can be used to build long chains, computing the energy as a function of the orientation and displacement of the 16 possible base pair combinations within the double helix. Calculations have been performed, for simplicity, on free base pairs rather than complete nucleotide units. Conformational preferences and relative flexibilities are reported for various combinations of the roll, tilt, twist, lateral displacement, and propeller twist of individual residues. The predictions are compared with relevant experimental measures of conformation and flexibility, where available. The energy surfaces are found to fit into two distinct categories, some dimer duplexes preferring to bend in a symmetric fashion and others in a skewed manner. The effects of common chemical substitutions (uracil for thymine, 5-methyl cytosine for cytosine, and hypoxanthine for guanine) on the preferred arrangements of neighboring residues are also examined, and the interactions of the sugar-phosphate backbone are included in selected cases. As a first approximation, long range interactions between more distant neighbors, which may affect the local chain configuration, are ignored. A rotational isomeric state scheme is developed to describe the average configurations of individual dimers and is used to develop a static picture of overall double helical structure. The ability of the energetic scheme to account for documented examples of intrinsic B-DNA curvature is presented, and some new predictions of sequence directed chain bending are offered.

Conformational studies of nucleic acids: IV. The conformational energetics of oligonucleotides: d(ApApApA) and ApApApA

Utilizing a new method for modeling furanose pseudorotation (D. A. Pearlman and S.-H. Kim, J. Biomol. Struct. Dyn. 3, 85 (1985)) and the empirical multiple correlations between nucleic acid torsion angles we derived in the previous report (D. A. Pearlman and S.-H. Kim, previous paper in this issue), we have made an energetic examination of the entire conformational spaces available to two nucleic acid oligonucleotides: d(ApApApA) and ApApApA. The energies are calculated using a semi-empirical potential function. From the resulting body of data, energy contour map pairs (one for the DNA molecule, one for the RNA structure) have been created for each of the 21 possible torsion angle pairs in a nucleotide repeating unit. Of the 21 pairs, 15 have not been reported previously. The contour plots are different from those made earlier in that for each point in a particular angle-angle plot, the remaining five variable torsion angles are rotated to the values which give a minimum energy at this point. The contour maps are overall quite consistent with the experimental distribution of oligonucleotide data. A number of these maps are of particular interest: delta (C5'-C4'-C3'-O3')-chi (O4'-C1'-N9-C4), where the energetic basis for an approximately linear delta-chi correlation can be seen: zeta (C3'-O3'-P-O5')-delta, in which the experimentally observed linear correlation between zeta and delta in DNA(220 degrees less than zeta less than 280 degrees) is clearly predicted; zeta-epsilon (C4'-C3'-O3'-P), which shows that epsilon increases with decreasing zeta less than 260 degrees; alpha (O3'-P-O5'-C5')-gamma (O5'-C5'-C4'-C3') where a clear linear correlation between these angles is also apparent, consistent with experiment; and several others. For the DNA molecule studied here, the sugar torsion delta is predicted to be the most flexible, while for the RNA molecule, the greatest amount of flexibility is expected to reside in alpha and gamma. Both the DNA and RNA molecules are predicted to be highly polymorphic. Complete energy minimization has been performed on each of the minima found in the energy searches and the results further support this prediction. Possible pathways for B-form to A-form DNA interconversion suggested by the results of this study are discussed. The results of these calculations support use of the new sugar modeling technique and torsion angle correlations in future conformational studies of nucleic acids.

Conformational characteristics of the dinucleoside triphosphate pCpGp from energy-minimization studies

The influence of the 3'- and 5'- terminal phosphates on the conformational characteristics of the dinucleoside monophosphate CpG is described in this paper. The computed potential energy of the system is minimized with respect to the relevant 10 dihedral angles permitting the two sugar rings to adopt the alternative puckering states, 2E and 3E. Of the 84 conformations considered, 22 become energetically accessible. The familiar A-, B-, Z- and Watson-Crick-type backbone states of DNA subunits become low-energy forms for this RNA unit pCpGp also. The Watson-Crick-type backbone is invariably preferred in all the four sugar pucker sequences, indicating its importance in the dynamics of sugar pucker fluctuations and in the DNA-RNA association. The interphosphate geometries and the possible hydrogen-bonded states are discussed in relation to the varied folded/extended polynucleotide structures.

Conformational characteristics of the trinucleoside diphosphate dApdApdA and its constituents from nuclear magnetic resonance and circular dichroism studies. Extrapolation to the stacked conformers

Proton NMR studies at 360 MHz were carried out on the trinucleoside diphosphate dApdApdA, the dinucleoside monophosphate dApdA and the methylphosphate esters of the monomers pdA, pdAp and dAp. The compounds were also investigated by means of circular dichroism at varying temperatures. Complete NMR spectral assignments are given. The thermodynamics of stacking derived from the circular dichroic spectra was used to extrapolate the observed coupling constants, measured at a range of temperatures, to values appropriate to the pure stacked states of the dimer and the trimer. The data were interpreted in terms of the N and S deoxyribose pseudorotational ranges [Altona, C. and Sundaralingam, M. (1972) J. Am. Chem. Soc. 94, 8205--8212] and it is shown that the right-handed single helix of the trimer occurs in two distinct forms: the major one corresponds to a B-DNA-like structure, S-S-S; the minor one (30%) has the sugar rings in a hitherto unsuspected S-S-N conformational sequence. The dimer behaves quite similarly, a mixture of 70% S-S and 30% S-N stacks being indicated. The detailed geometry of teh S-type sugar rings is not invariable but appears to undergo a slight shift when another base stacks on top of a given nucleotide unit. The backbone angles of the fully stacked B-DNA-like single helix in solution are (starting the notation at P) beta = 187 degrees, gamma = 50 degrees, delta = 138 degrees, epsilon = 186 degrees.

Thermal perturbation differential spectra of ribonucleic acids. III. Chain length effect

Thermal perturbation differential spectra of several adenylic acid oligomers, two single-strand polyribonucleotides, poly(A) and poly(C), and five trinucleoside diphosphates, U-A-A, U-A-G, U-G-A, C-U-C and C-U-A, were obtained and analysed. It is shown that these differential spectra cannot be entirely described by the nearest-neighbour approximation devised from the appropriate mononucleotides and dinucleoside monophosphates. In an attempt to determine the origin of this discrepancy, we have examined the possible optical changes arising from increased electronic interactions, changes in conformation, solvent accessibility or thermodynamic properties. This study indicates that dinucleoside monophosphates on one the hand and trinucleoside diphosphates on the other hand, are separate classes from the conformational point of view. The capacity to assume stacks, absent or negligible in higher oligomers or polymers, makes them poor models for the stacking interaction in longer nucleic acids. It is also shown that in trinucleoside diphosphates, interaction between the two terminal bases arising from bulging out of the middle base is very likely to occur. This type of interaction has to be taken into account in the description of the temperature perturbation differential spectra of trimers.

Conformations of dinucleoside phosphates in aqueous solution

The conformations of dinucleoside phosphates have been reexamined by semiempirical potential energy calculations. Conformations I, II, and III, proposed by Lee & Tinoco [Lee, C. H., & Tinoco, I., Jr. (1977) Biochemistry 16, 5403], are possible species after refinement of their structures by potential energy minimization. These three conformers can represent three types of dinucleoside phosphate species in solution. Dhingra et al. [Dhingra, M. M., Sarma, R. H., Giessner-Prettre, C., & Pullman, B. (1978) Biochemistry 17, 5815] had concluded that conformations of type II and III were unlikely or impossible. They favored conformations g-g- (equivalent to I), g+g+,g+t, and tg+; the last three conformations have little stacking and are calculated to be energetically less favorable by more than 5 kcal/mol. Common structures of the types I, II, and III are found for dinucleoside phosphates with different purine-pyrimidine sequences. The sequence dependence of the potential energy of these three conformers has been calculated. The experimental nuclear magnetic resonance data of dinucleoside phosphates are consistent with these three conformations.