Nucleic helix axis

Several complexes that involve intercalation of an acridine in a portion of a nucleic acid have been studied by X-ray crystallographic techniques. These include complexes of dinucleoside phosphates with ethidium bromide, 9-aminoacridine, acridine orange, proflavine and ellipticine (65-69). A representation of the geometry of an intercalated proflavine molecule is illustrated in Figure 6 (b) this is a view of the crystal structure of proflavine intercalated in a dinucleoside phosphate, cytidylyl- -S ) guano-sine (CpG) (70, TV). For comparison an example of the situation before such intercalation is also illustrated in Figure 6 (a) by three adjacent base pairs found in the crystal structure of a polynucleotide (72, 73). In this latter structure the vertical distance (parallel to the helix axis) between the bases is approximately... 

The hydrophobic effect stabilizes the three-dimensional structures of macromolecules. In the nucleic acid double helical structures, the hydrophobic bases are stacked along the helix axis and shielded from solvent by the hydrophilic sugar-phosphate backbone, which is heavily hydrated. A comparable scheme is found in many crystal structures of nucleosides and nucleotides, where the bases are stacked... 

Fig. 20.10. Base pairs found in homopolymer nucleic add self-complexes. The unsymmetrical uridine U-U and 2-thiouridine s2U-s2U base pairs lead to antiparaUel orientation of polynucleotide chains similar to the RNA double helix. In the symmetrical AH+ -AH+ and C-CH+ base pairs, the dyad axis coinddes with the helix axis and gives rise to parallel polynucleotide chains. For the same reason, the four polynucleotide chains in [poly(G)]4 are related by a fourfold rotation axis and are also parallel

FIGURE 12.44. Descriptors of base and base-pair (bp) orientations. Shown at the top (a) are idealized beise-pair arrangements viewed down the helix axis z). Perturbations are illustrated for (b) rotation of one base pair, (c) rotation of two base pairs adjacent in the nucleic-acid sequence, (d) translation for one base pair, and (e) translation for two base pairs adjacent in the nucleic-acid sequence. 

Displacement A conformational description of base pairs in nucleic acids. An axis of reference is taken as the line joining C6 of a pyrimidine and C8 of a purine. The displacement is the perpendicular deviation of this axis from the helix axis of the nucleic acid. 

Inclination (DNA) The angle between the plane containing a base pair in a nucleic acid structure and a plane perpendicular to the helix axis. 

Fig. 20. Protein-nucleic order-disorder patterns resembling primitive thermotropic action (top to bottom) Hypothetical B-DNA-prealbumin complex in skeletal presentation, viewed along and perpendicular to the B-DNA helix axis. Thermotropic n-alkoxybenzoic acid dimer.58... 

Recent reviews from this Laboratory provide an overview of the literature of MD simulations on DNA oligomers through 1993 (27) and theoretical and computational aspects of DNA hydration (28) and counterion atmosphere (29). References to the most recent literature can be found in (30). Experimental data for comparison with MD results are available for crystal structures in the Nucleic acids Data Bank (NDB) (31), and for NMR structure in a review by Ulyanov and James (52). The research described in this article is directed towards understanding the dynamical structure of the various right-handed helical forms of DNA, their deformations and interconversions. The canonical A and B structures of DNA are shown for reference in Figure 1. The A and B forms are distinguishable in three major ways the displacement of nucleotide base pairs from the helix axis, the inclination of base pairs with respect to the helix axis, and sugar puckers. Details on these and other structural features of DNA relevant to MD analysis is readily available (33). 

It is well established that helical conformations of nucleic acids are recognizable from a proportionality between the UV absorbance and CD spectrum [1]. For a helix the component of the absorption band polarized perpendicular to the helix axis gives rise to a unique CD curve. The X max at 258 nm and the crossover point through the 0 line of the CD spectrum at the same wave-length fulfill the theoretical prediction of the helical conformation of poly(ADP-ribose) [2,3]. Based on the following results, helical conformation of poly(ADP-ribose) was postulated. 

The second type of restricted difiiision is illustrated in Fig. 4b and has sometimes been dubbed the wobble-in-a-cone model because the orientation of the interaction vector (either DD vector or CSA tensor principal axis) is permitted free diffusion within the cone of half angle yo fhe cone is disposed toward a reference axis at a fixed angle fi. This model can be adapted for internal motions but is especially useful for characterizing segmental motions, in which case the reference axis can be the helix axis of the nucleic acid. Librational motions, such as predicted by molecular dynamics calculations on proteins (McCammon et al., 1977), are readily accommodated by the wobble-in-a-cone model (Howarth, 1979 Richarz et al, 1980), but the model has also accommodated other studies of dynamics, for example, the situation of halide ions bound to proteins (Bull etai, 1978). 

Figure 1 Molecular model of a 12-base pair duplex of canonical B-form DNA. The two 12-mer strands that intertwine to form the duplex are colored separately (black and gray). Nucleic acid base pairs are stacked perpendicular to the helical axis at 3.4-A intervals (center-to-center distance), and the duplex helix repeats its spiral structure every 10 base pairs. (Figure provided by Dr. Carolyn Kanagy using the Sybyl Version 6.3 molecular modeling program from Tripos, Inc. and standard B-form DNA substructures.)...

Reasoning from these data, Watson and Crick proposed a double helix as a model for the secondary structure of DNA. According to this model, two nucleic acid chains are held together by hydrogen bonds between base pairs on opposite strands. This double chain is wound into a helix with both chains sharing the same axis. The base pairs are on the inside of the helix, and the sugar-phosphate backbone is on the outside (Fig. 25.8). The pitch of the helix is such that 10 successive nucleotide pairs give rise to one complete turn in 34 A (the repeat distance). The exterior width of the spiral is about 20 A, and the internal distance between 1 positions of ribose units on opposite chains is about 11 A. 

When two nucleic acid strands have complementary nucleic acid sequence, they can undergo hybridization to form double-stranded duplex structures. DNA forms a double-stranded helix composed of two complementary helical polynucleotide chains, aligned antiparallel, which are coiled around a common axis. In helix form, the anionic backbone lies on the outside of the structure with the nucleobases in the core, perpendicular to the axis and separated by a distance of 3.4 A. This B-form helix (Figure 2a) has a right-handed coil that repeats itself every 34 A with a turn every... 

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