Abstract
The technique of linear dichroism (LD) is a simple absorbance technique that uses two polarised light beams. Since only oriented molecules show different absorbances for different polarisations, LD detects only oriented molecules.
In aqueous solutions, flow orientation is an attractive orientation methodology as it selects long molecules or molecular assemblies. LD thus is selective for molecules that are particularly challenging to study by more standard biophysical techniques. In this article, a brief review of the application of LD to DNA, DNA–drug systems, DNA–protein enzymatic complexes, fibrous proteins and membrane peptides and proteins is given.
Keywords: linear dichroism, DNA, proteins
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References
- 1.Rajendra J., Baxendale M., Dit Rap L.G., and Rodger A. (2004) Flow linear dichroism to probe binding of aromatic molecules and DNA to single walled carbon nanotubes. J. Am. Chem. Soc., 126, 11182–11188. [DOI] [PubMed] [Google Scholar]
- 2.Rajendra J., and Rodger A. (2005) The binding of single stranded DNA and PNA to single walled carbon nanotubes probed by flow linear dichroism. Chem. Eur. J., 11, 4841–4848. [DOI] [PubMed] [Google Scholar]
- 3.Marrington R., Dafforn T.R., Halsall D.J., and Rodger A. (2004) Micro volume Couette flow sample orientation for absorbance and fluorescence linear dichroism. Biophys. J., 87, 2002–2012. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Couette M. (1890) Ann. Chim. Phys., 6, 433–510. [Google Scholar]
- 5.Mallock A. (1988) Proc. R. Soc. Lond., 1888, 45, 126. [Google Scholar]
- 6.Mallock A. (1896) Phil. Trans. R. Soc. Lond., Ser, A, 1896, 187, 41. [Google Scholar]
- 7.Donnelly R.J. Phys. Today, 1991, November, 32–39. [Google Scholar]
- 8.Taylor G.I. (1923) Proc. R. Soc. Lond. Ser. A, 223, 289–343. [Google Scholar]
- 9.Taylor G.I. (1936) Proc. R. Soc. Lond. Ser. A, 157, 546–564. [Google Scholar]
- 10.Taylor G.I. (1936) Proc. R. Soc. Lond. Ser. A, 157, 565–578. [Google Scholar]
- 11.Rodger A. (1993) Meth. Enzymol., 226, 232–258. [DOI] [PubMed] [Google Scholar]
- 12.Rodger A., Rajendra J., Marrington R., Ardhammar M., Nordén B., Hirst J.D., Gilbert A.T.B., Dafforn T.R., Halsall D.J., Woolhead C.A., Robinson C., Pinheiro T.J., Kazlauskaite J., Seymour M., Perez N., and Harmon M.J. (2002) Phys. Chem. Chem. Phys., 4, 4051–4057. [Google Scholar]
- 13.Albinsson B., and Nordén B. (1992) J. Phys. Chem., 96, 6204–6212. [Google Scholar]
- 14.Holmen A., Broo A., Albinsson B., and Nordén B. (1997) J. Am. Chem. Soc., 119, 12240–12250. [Google Scholar]
- 15.Dafforn T.R., Rajendra J., Halsall D.J., Serpell L.C., and Rodger A. (2004) Biophys. J., 86, 404–410. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16.Nordén B., Kubista M., and Kuruscev T. (1992) Q. Rev. Biophys., 25, 51–170. [DOI] [PubMed] [Google Scholar]
- 17.Nordén B. (1978) Appl. Spectrosc. Rev., 14, 157–248. [Google Scholar]
- 18.Meistermann I., Moreno V., Prieto M.J., Molderheim E., Sletten E., Khalid S., Rodger P.M., Peberdy J., Isaac C.J., Rodger A., and Hannon M.J. (2002) Intramolecular DNA coiling mediated by metallo-supramolecular cylinders: differential binding of P and M helical enantiomers. Proc. Natl Acad. Sci. USA, 99, 5069–5074. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 19.McDonnell U., Hicks M.R., Hannon M.J., and Rodger A. (2008) DNA binding and bending by dinuclear complexes comprising ruthenium polypyridyl centres linked by a bis(pyridylimine) ligand. J. Lnorg. Biochem., 102, 2052–2059. [DOI] [PubMed] [Google Scholar]
- 20.Pingoud A., Fuxreiter M., Pingoud V., and Wende W. (2005) Type II restriction endonucleases: structure and mechanism. Cell. Mol. Life Sci., 62, 685–707. [DOI] [PubMed] [Google Scholar]
- 21.Sambrook J., Fritsch E.F., and Maniatis T. (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, New York. [Google Scholar]
- 22.Kettling U., Koltermann A., Schwüle P., and Eigen M. (1998) Real-time enzyme kinetics monitored by dual-color fluorescence cross-correlation spectroscopy. Proc. Natl. Acad. Sci. USA, 95, 1416–20. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 23.Waters T.R., and Connolly B.A. (1992) Continuous spectrophotometric assay for restriction endonucleases using synthetic oligodeoxynucleotides and based on the hyperchromic effect. Analyt. Biochem., 204, 204–209. [DOI] [PubMed] [Google Scholar]
- 24.Marrington R., Small E., Rodger A., Dafforn T.R., and Addinall S.G. (2004) FtsZ fibre bundling is triggered by a calcium-induced conformational change in bound GTP. J. Biol. Chem., 47, 48821–48829. [DOI] [PubMed] [Google Scholar]
- 25.Small E., Marrington R., Rodger A., Scott D.J., Sloan K., Roper D., Dafforn T.R., and Addinall S.G. (2007) FtsZ polymer-bundling by the Escherichia coli ZapA orthologue, YgfE involves a conformational change in bound GTP. J. Mol. Biol., 369, 211–221. [DOI] [PubMed] [Google Scholar]
- 26.Marrington R., Seymour M., and Rodger A. (2006) A new method for fibrous protein analysis illustrated by application to tubulin microtubule polymerisation and depolymerisation. Chirality, 18, 680–690. [DOI] [PubMed] [Google Scholar]
- 27.van Amerongen H., and van Grondelle R. (1989) Orientation of the bases of single-stranded DNA and polynucleotides in complexes formed with the gene 32 protein of bacteriophage T4. A linear dichroism study. J. Mol. Biol., 209, 433–445. [DOI] [PubMed] [Google Scholar]
- 28.Ardhammar M., Mikati N., and Nordén B. (1998) Chromophore Orientation in Liposome Membranes Probed with Flow Linear Dichroism. J. Am. Chem. Soc., 120, 9957–9958. [Google Scholar]
- 29.Rodger A., Rajendra J., Marrington R., Ardhammar M., Nordén B., Hirst J.D., Gilbert A.T.B., Dafforn T.R., Halsall D.J., Woolhead C.A., Robinson C., Pinheiro T.J., Kazlauskaite J., Seymour M., Perez N., and Hannon M.J. (2002) Flow oriented linear dichroism to probe protein orientation in membrane environments. Phys. Chem. Chem. Phys., 4, 4051–4057. [Google Scholar]
- 30.Oesterhelt D., and Stoeckenius W. (1971) Rhodospin-like protein from the purple membrane of Halobacterium halobium. Nature New Biol., 233, 149–152. [DOI] [PubMed] [Google Scholar]
- 31.Henderson R., Baldwin J.M., Ceska T.A., Zemlin F., Beckmann E., and Downing K.H. (1990) Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J. Mol. Biol., 213, 899–929. [DOI] [PubMed] [Google Scholar]