A model is presented for double-stranded polynucleotides which involves side-by-side meshing of the two strands rather than double helical intertwining. The sugarphosphate backbone has a twisted strip-like character, yet base-pairing of the Watson-Crick type is still possible. Structural features of the basic model are described and coordinates are presented for a representative example. The structure has, on the whole, reasonable stereochemical contacts, and can be shown to produce a fiber diffraction pattern with x-rays not unlike that of the B form of DNA.The Watson-Crick model (1) has been outstandingly successful in providing a framework for understanding a wide range of observations of duplex structures. Initial concern about its intertwined nature (2) has now diminished. Nonetheless, as this feature remains something of a puzzle, we recently attempted to construct a base-paired model where the strands do not intertwine. We have found that such a model, having a sideby-side association of single strands, can be built without gross stereochemical difficulty. While this structure may not be generally applicable to duplexes it does have sufficiently attractive features for us to consider it appropriate to present the model at this time for appraisal as an additional or alternative conformation to the double helix. We outline broad structural details of the initial model together with a preliminary analysis of it in relation to various physical properties of duplexes. One key feature of the side-by-side (SBS) model is that it can be mathematically shown to be capable of producing the characteristic x-ray diffraction pattern of the B form of DNA. Structural basis of the model Using the Watson-Crick mode of base pairing and antiparallel strands we have constructed a model that does not involve gross intertwining of the phosphate backbones. This was achieved by constructing approximately half of the repeat unit in a basically Watson-Crick manner for a right-handed double helix with acceptable structural parameters (3), and then continuing the model in the form of a left-handed double helix. The model retains the essential features of base stacking and repeat distance of the Watson-Crick model that are required by x-ray data. However, by alternating the helical sense every half-repeat distance a net winding of the phosphate strands is minimized and the structure becomes a side-by-side intermeshing of strands rather than an intertwining of them. Various views of the side-by-side (SBS) structure are shown in Figs. 1-4. One view (Figs. 2b and 3a) resembles that of the Watson-Crick model. Other views (Figs. 1-4) however reveal marked differences. The SBS structure has a twisted strip-like character that contrasts with the rod-like appearance of a double helix. The structure approximates to that of a strip of corrugated sheet cut on the diagonal with the cut edges representing the phosphate strands. In constructing the model, two kinds of bending of the backbone (p and q) were employed. The p bend involves a ch...
Evidence for the structure of double-stranded DNA and related duplexes is considered in relation to the existing double helix model and a possible alternative to it. It is shown by mathematical analysis that an alternative side-by-side (SBS) model is capable of producing the gross features of the X-ray diffraction pattern of moist DNA fibres. This is complemented by model-independent calculations based on X-ray data for paracrystalline B-DNA that suggest the duplex molecule may not have tne circular (axial projection) symmetry expected for a regular double helix structure. In addition, the application of the SBS model to other areas of DNA structure and function are considered. Long-standing problems assocIated with the highly intertwined feature of the helix model, esrecially the problem of unwinding, do not arise for the SBS model. In particular, electron micrograph evidence for the formation of "bubble" regions during the melting of DNA raises serious questions about earlier attempts to rationalise kinetic data for strand separation. INTRODUCTIONThe Watson-Crick double helix model for DNA and related structures appears to be very well established from a wide range of physical studies. As far as we know the basic right-handed helical character of the model has never been seriously challenged, although doubts have been expressed about the reliability of the model as deduced from X-ray studies (Donohue 1969(Donohue , 1970.
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