Looking at long molecules in solution: what happens when they are subjected to Couette flow?

Abstract

Knowing the structure of a molecule is one of the keys to deducing its function in a biological system. However, many biomacromolecules are not amenable to structural characterisation by the powerful techniques often used namely NMR and X-ray diffraction because they are too large, or too flexible or simply refuse to crystallize. Long molecules such as DNA and fibrous proteins are two such classes of molecule. In this article the extent to which flow linear dichroism (LD) can be used to characterise the structure and function of such molecules is reviewed. Consideration is given to the issues of fluid dynamics and light scattering by such large molecules. A range of applications of LD are reviewed including (i) fibrous proteins with particular attention being given to actin; (ii) a far from comprehensive discussion of the use of LD for DNA and DNA-ligand systems; (iii) LD for the kinetics of restriction digestion of circular supercoiled DNA; and (iv) carbon nanotubes to illustrate that LD can be used on any long molecules with accessible absorption transitions.

Ruthenium polypyridyl complexes and their modes of interaction with DNA: Is there a correlation between these interactions and the antitumor activity of the compounds?

“…In this study we used a Couette cell, in which one cylinder rotates inside another, with the sample in the gap between the cylinders [66]. Since the base pairs are oriented perpendicular to the DNA helix axis, a negative LD signal is expected for B-DNA (Fig.…”

Tacrine derivatives as dual topoisomerase I and II catalytic inhibitors

“…4A). An increase in the amplitude of the negative 260 nm LD band of DNA is usually associated with DNA stiffening [47][48][49], which suggests that the effect of tacrine derivative 1 on this DNA LD signal is consistent with intercalation of the tacrine ligands. In addition, compound 1 also caused a significant shift (cca.…”

“…4A) show that this tacrine derivative bind to DNA in specific, non-random orientations. Moreover, the negative sign of the LD signal which arose in the region of 310-370 nm suggests that the angle of the long axis of tacrine derivative 1 to the axis of the DNA double helix is greater than 54°, the angle which is characteristic for an intercalator [48]. The DNA LD bands (220-300 nm) confirm that the DNA in the presence of tacrine derivative 1 remains in the B-DNA conformation; however, some structural changes in DNA are suggested by the increase in the amplitude of the DNA negative LD band at 260 nm upon the addition of tacrine derivative 1 (Fig.…”

The Synergistic Action of Melittin and Phospholipase A2 with Lipid Membranes: Development of Linear Dichroism for Membrane-Insertion Kinetics

“…LD spectra were collected using a Jasco J-815 spectropolarimeter adapted for LD measurements in a microvolume Couette flow cell manufactured by Crystal Precision Optics, Rugby, UK and now available via Kromatek Ltd., (Great Dunmow, UK). 7,[10][11][12][22][23][24][25][26] Far UV CD and LD spectra (190-320 nm) were collected using a data pitch of 0.2 nm, continuous scanning mode, scanning speed of 100 nm/min, response of 1 s, band width of 1 or 2 nm. The Couette cell rotation speed was ~3000 rpm (setting: 3.0 V).…”