A possible conformation for double-stranded polynucleotides.

Abstract

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...

On the structure of DNA

“…We show mathematically that the SBS structure is capable of producing the characteristic X-ray pattern from moist fibres of DNA (see also Rodley, Scobie, Bates, and Lewitt 1976). This indicates the two models may not be readily distinguished by X-ray diffraction alone, and points to the possibility that the exact nature of DNA may be too elusive for it to be possible to make an either-or choice between basic models.…”

“…Although we have not yet been able to explore all the possibilities or shortcomings of this model, we feel it does have sufficiently attractive features for it to be presented for public scrutiny. The details of the SBS structure have already been published (Rodley, Scobie, Bates, and Lewitt 1976). Here we outline reasons for believing that the SBS structure could be a viable alternative to the Watson-Crick model.…”

“…We first of all outline details of the SBS model, reported more fully elsewhere (Rodley, Scobie, Bates, and Lewitt 1976). Questions about the interpretation of X-ray data in terms of a double-helix model, and a discussion (supported in Appendix B) of the mathematical calculation of the expected X-ray fibre diffraction pattern for SBS molecules, are presented in the succeeding section.…”

Extending the Repertoire of Structures in DNA Nanotechnology

“…The contention of (Crick et al, 1979) that topology eliminated all side-byside structures is flawed and did not consider the structure set out in Fig. 1, nor did it fully explore the implications of the Rodley model (Rodley et al, 1976;Bates et al, 1980;Rodley et al, 1984;Rodley, 1995).…”

On the possibility of discriminating between two models of the conformation of DNA

“…There are two alternative models of the structure of DNA, known as the double-helix (DH) (Watson and Crick, 1953) and the side-by-side (SBS) (Rodley et al, 1976) models. Which is the closest to physical reality?…”