A. R. Srinivasan

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.

Flexing and folding double helical DNA.

DNA base sequence, once thought to be interesting only as a carrier of the genetic blueprint, is now recognized as playing a structural role in modulating the biological activity of genes. Primary sequences of nucleic acid bases describe real three-dimensional structures with properties reflecting those structures. Moreover, the structures are base sequence dependent with individual residues adopting characteristic spatial forms. As a consequence, the double helix can fold into tertiary arrangements, although the deformation is much more gradual and spread over a larger molecular scale than in proteins. As part of an effort to understand how local structural irregularities are translated at the macromolecular level in DNA and recognized by proteins, a series of calculations probing the structure and properties of the double helix have been performed. By combining several computational techniques, complementary information as well as a series of built-in checks and balances for assessing the significance of the findings are obtained. The known sequence dependent bending, twisting, and translation of simple dimeric fragments have been incorporated into computer models of long open DNAs of varying length and chemical composition as well as in closed double helical circles and loops. The extent to which the double helix can be forced to bend and twist is monitored with newly parameterized base sequence dependent elastic energy potentials based on the observed configurations of adjacent base pairs in the B-DNA crystallographic literature.

Properties of the nucleic-acid bases in free and Watson-Crick hydrogen-bonded states: computational insights into the sequence-dependent features of double-helical DNA

The nucleic-acid bases carry structural and energetic signatures that contribute to the unique features of genetic sequences. Here, we review the connection between the chemical structure of the constituent nucleotides and the polymeric properties of DNA. The sequence-dependent accumulation of charge on the major- and minor-groove edges of the Watson–Crick base pairs, obtained from ab initio calculations, presents unique motifs for direct sequence recognition. The optimization of base interactions generates a propellering of base-pair planes of the same handedness as that found in high-resolution double-helical structures. The optimized base pairs also deform along conformational pathways, i.e., normal modes, of the same type induced by the binding of proteins. Empirical energy computations that incorporate the properties of the base pairs account satisfactorily for general features of the next level of double-helical structure, but miss key sequence-dependent differences in dimeric structure and deformability. The latter discrepancies appear to reflect factors other than intrinsic base-pair structure.

Structure, Dynamics, and Branch Migration of a DNA Holliday Junction: A Single-Molecule Fluorescence and Modeling Study

The Holliday junction (HJ) is a central intermediate of various genetic processes, including homologous and site-specific DNA recombination and DNA replication. Elucidating the structure and dynamics of HJs provides the basis for understanding the molecular mechanisms of these genetic processes. Our previous single-molecule fluorescence studies led to a model according to which branch migration is a stepwise process consisting of consecutive migration and folding steps. These data led us to the conclusion that one hop can be more than 1 basepair (bp); moreover, we hypothesized that continuous runs over the entire sequence homology (5 bp) can occur. Direct measurements of the dependence of the fluorescence resonance energy transfer (FRET) value on the donor-acceptor (D-A) distance are required to justify this model and are the major goal of this article. To accomplish this goal, we performed single-molecule FRET experiments with a set of six immobile HJ molecules with varying numbers of bps between fluorescent dyes placed on opposite arms. The designs were made in such a way that the distances between the donor and acceptor were equal to the distances between the dyes formed upon 1-bp migration hops of a HJ having 10-bp homology. Using these designs, we confirmed our previous hypothesis that the migration of the junction can be measured with bp accuracy. Moreover, the FRET values determined for each acceptor-donor separation corresponded very well to the values for the steps on the FRET time trajectories, suggesting that each step corresponds to the migration of the branch at a defined depth. We used the dependence of the FRET value on the D-A distance to measure directly the size for each step on the FRET time trajectories. These data showed that one hop is not necessarily 1 bp. The junction is able to migrate over several bps, detected as one hop and confirming our model. The D-A distances extracted from the FRET properties of the immobile junctions formed the basis for modeling the HJ structures. The composite data fit a partially opened, side-by-side model with adjacent double-helical arms slightly kinked at the four-way junction and the junction as a whole adopting a global X-shaped form that mimics the coaxially stacked-X structure implicated in previous solution studies.

DNA associations: Packing calculations in A-, B-, and Z-DNA structures

Abstract A detailed theoretical study has been carried out to examine the modes of DNADNA interactions on the basis of hard-sphere contact criteria. Two helices of identical structure and length are oriented side-by-side and their relative positions are controlled by translations along and rotations about specific axes. Short atomic contacts between pairs of atoms in the structures are assessed and contact-free configurations are compiled. The computed contact-free arrangements of A, B, and Z double helices are found to be remarkably similar to the packing motifs observed in DNA crystals and stretched fibers. Equally interesting in the study are the broad ranges of sterically acceptable arrangements that preserve the overall packing morphology of neighboring duplexes: Among the most notable morphological features in the helical complexes are extended “super” major and minor grooves which might facilitate the wrapping and packaging of DNA chains in supramolecular assemblies. The hard-sphere computations, however, are insufficient for quantitative interpretation of the packing of DNA helices in the solid state. The results are, nevertheless, a useful starting point for energy based studies as well as relevant to the analysis of long-range interactions in DNA supercoils and cruciforms.

The translation of DNA primary base sequence into three-dimensional structure

A procedure is outlined to obtain a reliable computer-generated representation of the DNA duplex from its primary sequence of base pairs. The calculations are based on the potential energies of interaction of adjacent side groups. The methods are, however, completely general and can be adapted to any set of base sequence dependent conformational rules. Static representations of the DNA are compared with the distributions of conformations obtained from Monte Carlo simulation studies. Direct matrix generator calculations of the average (equilibrium) extension and orientation of various sequences and numerical estimates of the flexibility of the chains as a whole are also reported. The methods are applied to three short fragments of kinetoplast DNA from Crithidia fasciculata which exhibit dramatically different behavior on non-denaturing polyacrylamide gels.

Spatial density distributions for illustrating the base sequence dependent features of double helical DNA: computer graphic visualization of Monte Carlo chain simulations

Abstract The sequence-directed flexibility of double helical DNA is examined with color-coded representations of the spatial probability density distributions of the chain ends. The distributions are derived from Monte Carlo simulations that incorporate local sequence-dependent bending of neighboring Watson-Crick base pairs. The density functions are compared with typical rigid representations of the double helix and with sample Monte Carlo trajectories. Applications are presented for three short fragments of kinetoplast DNA from Crithidia fasciculata, which exhibit dramatically different behavior on nondenaturing polyacrylamide gels. The distributions (based on 10 6 configurations per chain) are useful descriptors of overall chain flexibility, illustrating the effects of chain length and base sequence on macromolecular configuration and revealing characteristic differences between curved and rodlike DNA.

An interactive FORTRAN program for three-dimensional molecular visualization

Abstract An interactive FORTRAN program executable in the VAX/VMS computer environment has been developed for three-dimensional molecular visualization on the Evans & Sutherland Picture System 390. The essential features of this program are described and the FORTRAN source code is available upon request.

Base Sequence Effects in Curved and Rodlike DNA

A number of intriguing structural studies have prompted efforts to understand how the sequence of heterocyclic bases governs the conformation and properties of double helical DNA. The side groups introduce subtle irregularities in the local geometries of crystalline oligomers (Conner et al.; Dickerson & Drew 1981a; Fratini et al.; Kneale et al.; McCall et al. 1985, 1986; Shakked et al.; Viswamitra et al.; Wang et al. 1982a, 1982b) and affect the observed twisting of adjacent residues in solution (Kabsch et al.; Peck & Wang; Rhodes & Klug; Strauss et al.). The chain sequence also influences the overall dimensions of the DNA, the alternating poly d(GC) duplex being more extended (Thomas & Bloomfield) and the alternating poly d(AT) duplex more compact (Chen et al.) than random sequence B-DNA (Borochov et al.; Hagerman 1981; Kam et al.; Kovacic & van Holde; Rizzo & Schellman). Moreover, certain sequences curve naturally in solution, moving more slowly than expected on nondenaturing Polyacrylamide gels (Anderson; Bossi & Smith; Challberg & Englund; Diekmann 1985, 1986; Diekmann & Wang; Hagerman 1985, 1986; Kitchin et al.; Koepsel & Khan; Koo et al.; Ryder et al.; Simpson; Snyder et al.; Wu & Crothers; Zahn & Blattner 1985a, 1985b), exhibiting unusual rotational relaxation properties (Hagermann 1984; Levene et al.; Marini et al.), and adopting arc-like shapes under the electron microscope (Griffith et al.; Ray et al.). Finally, the chemical composition of the bases determines the extent to which intercalated fluorescent dyes wobble between adjacent residues, those within the poly dA · poly dT duplex fluctuating to a much greater extent than those within the poly dG · poly dC complex (Hogan et al.)