Agarose double helices

Amott S, Fulmer A, Scott WE et al (1974) The agarose double helix and its function in agarose gel structure. J Mol Biol 90 269-284... 

S. Arnott, A. Fulmer, WE. Scott, l.C. Dea, R. Moorhouse, D.A. Rees, The agarose double helix and its function in eigcuose gel structure. Journal of Molecular Biology, 90, 269-72, INll, 1974. 

FIGURE 7.31 The favored conformation of agarose in water is a double helix with a threefold screw axis. 

Fig. 26.—Stereo view of over one turn of the 3-fold double helix of agarose (25). The two chains are distinguished by open and filled bonds for clarity. The vertical line is the helix axis. Only van der Waals forces stabilize the double helix.

Small-angle X-ray scattering (SAXS), circular dichroism (CD), and UV spectroscopy at different temperatures were used to investigate the nature of calf-thymus DNA in aqueous solution, in the presence of [Me Sn] " (n = 1-3) species. The results demonstrate that the [MeSn(IV)] moiety does not influence the structure and conformation of the DNA double helix, and does not degrade DNA, as indicated by agarose gel electrophoresis. Inter alia, the radii of gyration, Rg, of the cross section of native calf-thymus DNA, determined by SAXS in aqueous solution in the presence of [Me Sn] " (n = 1-3) species are constant and independent of the nature and concentration of the [Me Sn] species. 

Agarose and its O-methyl, sulfate, 0-(2-hydroxyethyl), and 0-(car-boxyethylidene) derivatives give diffraction diagrams corresponding to a common molecular structure. A double helix having an axial periodicity of 9.5 A (950 pm) was proposed. Each chain in the double helix is a left-handed, threefold helix of pitch 19.0 A (1.90 nm), and it is translated axially, relative to its partner, by 9.5 A (950 pm). 

Figure 7. Mutually perpendicular views of the (a) agarose, (b) iota-carrageenan, and (c) kappa-carrageenan double-helix structures. The two chains are shown with open and full bonds, and the 06—02 hydrogen bonds by broken lines. (Reproduced with permission from ref. 28. Copyright 1989 Elsevier.)...

Figure 1. Proposed model for the interaction between the double helix of k-cot-rageenan or agarose with galactomannan...

Fig. 202. Model for agarose network formation crosslinks involve both double helix formation and substantial association of double helices to form microcrystalline junction zones. Refnoduced from AdvPolym Sci [Ref. 1] by the courtesy the authors and of SteinkopffPublishers Darmstadt, FRG...

FIGURE 10.11 Phosphopolysaccharide double helix. Double helical structure which may be present in agarose gels and phospho-analogues. 

This is illustrated below for the thermally induced order-disorder transition of agarose, as monitored by changes in intensity of the higher wavelength band. The pronounced hysteresis is ascribed (3l) to quaternary association (aggregation) stabilising the double helix at temperatures substantially above those at which it would form spontaneously in isolation. 

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