Loop formation in polynucleotide chains. II. Flexibility of the anticodon loop of tRNAPhe

Conformations of t-RNA: base pairing and stacking

The Phe t-RNA structure can be fit with one point per nucleotide to lattice models, and a fit for the 76 points to a face-centered cubic lattice is achieved with an RMS of 1.76 A. There are 32 chain folds possible upon these points. Because it is impossible to calculate directly all combinations of potential base pairs for these cases, an alternative is to determine low energy secondary structures and subsequently the tertiary pairs. For each lattice fold, the low energy secondary structures are generated from a list of proximal bases. From the lists of remaining possible tertiary pairs, all combinations are generated, and these include 2,365,440 allowed conformers. Among the possible types of non-native conformational variations observed is slip pairing, accompanied by a bulge, at the end of a stem. Small changes in secondary structure can result in different tertiary pairs. Other calculations, not constrained to the t-RNA shape, are presented that involve the packing of rigid stems on a flexible internal loop. For a simple cubic lattice there are 36,484,128 lattice folds for the sixteen bases enclosing the internal loop. By attaching rigid stems and accounting for their excluded volume these are reduced to only 258,979 possible configurations. The most common stacking arrangements involve the usual two pairs of stacked stems indicated in the crystal structure. The present enumerations suggest that a completely thorough exploration of three dimensional RNA structures is feasible only with prior specification of restrictions on conformational freedom, such as those given by secondary structures.

Theoretical predictions of DNA hairpin loop conformations: correlations with thermodynamic and spectroscopic data

A computational procedure for generating conformations of DNA hairpin loop structures from a broad range of low-energy starting states is described. The starting point of the modeling is the distribution of oligonucleotide chain conformations obtained from Monte Carlo simulations of feasible dinucleotide steps. Structures which meet the spatial criteria for hairpin loop formation are selected from the distributions and subsequently minimized using all-atom molecular mechanics. Both d(CTnG) and d(CAnG) oligomers, where n = 3, 4, or 5, are modeled. These sequences are chosen because of the large number of published NMR and thermodynamic studies on DNA hairpins containing thymine or adenine residues. The minimized three-dimensional hairpin loop structures are compared with one another as well as analyzed in terms of available experimental data. The computational approach provides the first detailed analysis of DNA hairpin loop structure in terms of a multistate conformational model. Investigation of the minimized conformations reveals several interesting structural features. First, hairpin loops of the same sequence adopt several distinctly different conformations, as opposed to minor variants of the same equilibrium structure, that could potentially interconvert in solution. Second, in contrast to double-helical nucleic acids, the hairpin loop models exhibit hydrophobic and hydrophilic surfaces. The different disposition of hydrophobic groups in loops versus duplexes could modulate both protein-nucleic acid interactions and nucleic acid self-associations. Third, perpendicular aromatic interactions of loop residues are observed in many of the computed hairpins. This sort of interaction might be important in the stabilization of non-hydrogen-bonded nucleic acid secondary and tertiary structures. The predicted structural features in the models help, in addition, to account for the unusual thermodynamic properties of DNA hairpin loops. Comparison of the theoretically-generated NOEs in different structures further reveals that very different molecular structures and interactions can, in principle, produce the same NOEs. The multistate description suggested by this observation differs from the conventional interpretation of DNA solution structure in terms of the fluctuations about a single preferred chain conformation. There is not necessarily only one set of closely related structures consistent with the observed data.

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.

Computer simulation of DNA supercoiling

Major goals of this research are to comprehend and visualize the detailed three-dimensional arrangements of supercoiled DNA. Attention has been focused in the initial stages on mathematical procedures to generate the spatial coordinates of the B-DNA double helix constrained to specific spatial pathways and on simple energy models of chain conformation. The new treatment of superhelical DNA in terms of parametric curves is an important first step in being able to generate and examine tertiary structure systematically. The location of every residue is implicitly determined by the equation of the closed curve, with the number of computational variables sharply reduced compared to the number required for explicit specification of all chain units. Furthermore, the constraints of ring closure in cyclic chains and/or the end-to-end limitations on constrained open chains are automatically satisfied by the formulations (cubic B-splines and finite Fourier series) chosen in this work. The predicted conformations of elastic DNA do not appear to be tied to either the form of chain representation or the computer simulation method. Significantly, two very different minimization and modeling approaches come to the same structural conclusions. The most stable configurations of the closed circular elastic DNA model are found to be interwound superhelices that are critically dependent on the specified linking number difference. The total elastic energy is proportional to the imposed linking number difference, and beyond the critical linking number difference separating the circular and figure-eight forms, the writhing number of the DNA superhelices is directly proportional to delta Lk. The measured proportionality constant between Wr and delta Lk, however, is somewhat greater than that deduced from experimental observations of plectonemically interwound DNA chains and an assumed structural model. Furthermore, at large delta Lk, the interwound structures appear to curve. The treatment of the DNA double helix as an ideal elastic rod is clearly incorrect. The chain cannot bend with the same ease in all directions. The degree of bending observed in atomic level models is also tied to the angular twist so that the presumed partitioning of bending and twisting components is in error. Furthermore, the local chain bending and twisting are base sequence dependent, with certain residues able to flex more symmetrically than others. The polyelectrolyte character of the DNA is additionally expected to govern the overall folding of the chain and to influence the local secondary structure. The next step in this work is to compare the properties of such "real" DNA with conventional elastic models.(ABSTRACT TRUNCATED AT 400 WORDS)