Total optical activity of agarose: relation to observable transitions in the vacuum ultraviolet

Anhydro sugar and linkage contributions to circular dichroism of agarose and carrageenan, with conformational implications

The geometry-dependent linkage contributions to the circular dichroism (CD) of agarose and carrageenan were determined by subtracting the monomeric CD from the CD of the polymers. For this purpose, the CD of methyl 3,6-anhydro-alpha-D-galactopyranoside, and of other anhydro sugars, was measured. Application of empirical quadrant rules indicates the observed CD to be that expected for the helical conformations of agarose and carrageenan as derived from diffraction data and modeling calculations. The difference in CD sign in the two polymers arises from a translocation of the beta-D-galactose O-2 atom from one quadrant to the neighboring quadrant of the C-5-O-5-C-1 ether chromophore of the preceding anhydro sugar residue, demonstrating the unusually high spatial resolution of conformational analysis that can be achieved with CD under favorable circumstances.

A conformational study of agarose by vacuum UV CD

Agarose films were prepared using a variety of casting conditions, heat treatments, and solvation treatments. Films represented the high temperature sol, the room temperature gel, and a high temperature state with cross-links intact. The vacuum uv CD of the film samples varies considerably, but the similarities between the film CD and the previously reported solution CD show that dehydration per se does not affect the CD. Combining the CD results for the dried sol with the x-ray results of Foord and Atkins leads to a description of the high temperature sol in terms of locally extended chain conformations. The CD of the gel and its peculiarly high uv absorption are satisfactorily, albeit not uniquely, interpreted in terms of the double-helix model of the gel, in agreement with previous conformational studies based on chiroptical properties.

Electric birefringence imaging of DNA in agarose electrophoresis gels: noise limits and prolonged electric field effects

Electric birefringence imaging (EBI) maps stresses in agarose electrophoresis gels. Both DNA and gel alignment can be monitored using this technique. Previously, we have reported birefringence images associated with resolved small (< 48 kbp) and partially resolved large 48 kb-(2 Mbp) DNA fragments oriented with relatively short electric field pulses. In this paper, differences between images acquired using short and long (DC) voltage pulses are presented. It is shown that stress signals distribute over long distances when exposed to prolonged electric fields. Resolution also affects band shapes. Refinements in instrumental design and evaluation of limiting noise sources of the technique are also described.

A semiempirical theory of the optical activity of saccharides

A semiempirical theory of optical activity of saccharides is developed that (a) goes beyond previous empirical treatments, (b) yields calculated NaD rotations which correlate well with experimental data, and (c) accounts for a characteristic c.d. band observed for polysaccharides in the vacuum u.v. spectrum.