Abstract
The asymmetric carbon atoms present in the sugars of nucleotides and in all the amino acids (with the exception of glycine) results in nucleic acids and proteins displaying optical activity. Further contributions to the optical activity of the polymers result from their ability to form well-defined secondary structures, in particular helices, which themselves possess asymmetry. As a consequence, circular dichroism (CD) has found widespread use in secondary structure prediction of proteins (1). Similar studies, though less widespread, have sought to correlate structural parameters of DNA with their CD spectrum (2), with some success particularly in assigning quaternary structures to nucleic acids (e.g., in the case of DNA triplexes and G-quartet mediated structures) (3,4). It follows that the disruption of secondary structure by, for example, denaturation or ligand binding can be usefully followed by circular dichroism.
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References
Johnson, W. C., Jr. (1990) Protein secondary structure and circular dichroism: a practical guide. PROTEINS: Struct. Funct. Genet. 7, 205–214.
Johnson, B. B., Dakl, K. S., Tinoco, I., Jr., Ivanov, V. I., and Zhurkin, V. B. (1981) Correlations between deoxyribonucleic acid structural parameters and cal-culated circular dichroism spectra. Biochemistry 20, 73–78.
Gray, D. M., Hung, S. H., and Johnson, K. H. (1995) Absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes. Methods Enzymol. 246, 19–34.
Hardin, C. C., Henderson, E., Watson, T., and Prosser, J. K. (1991) Monovalent cation induced structural transitions in telomeric DNAs: G-DNA folding intermediates. Biochemistry 30, 4460–4472.
Carpenter, M. L. and Kneale, G. G. (1991) Circular dichroism and fluorescence analysis of the interaction of Pf1 gene 5 protein with poly(dT). J. Mol. Biol. 27, 681–689.
Kansy, J. W., Cluck, B. A., and Gray, D. M. (1986) The binding of fd gene 5 protein to polydeoxyribonucleotides: evidence from CD measurements for two binding modes. J. Biomol. Struct. Dynam. 3, 1079–1110.
Culard, F. and Maurizot, J. C. (1981) Lac repressor-lac operator interaction. Circular dichroism study. Nucleic Acids Res. 9, 5175–5184.
Wartell, R. M. and Adhya, S. (1988) DNA conformational change in Gal repres-sor-operator complex: involvement of central G-C base pair(s) of dyad symmetry. Nucleic Acids Res. 16, 11,531–11,541.
Torigoe, C., Kidokoro, S., Takimoto, M., Kyoyoku, Y., and Wada, A. (1991) Spectroscopic studies on lambda cro protein-DNA interactions. J. Mol. Biol. 219, 733–746.
Connor, F., Cary, D., Read, C., Preston, N. S., Driscoll, P. C., Denny, P., et al. (1994) DNA binding and bending properties of the post-meiotically expressed Sry-related protein Sox-5. Nucleic Acids Res. 22, 3339–3346.
Taylor, I. A., Davis, K. G., Watts, D., and Kneale, G. G. (1994) DNA binding induces a major structural transition in a type I methyltransferase. EMBO J. 13, 5772–5778.
Powell, M. D. and Gray, D. M. (1995) Role of Tyr-22 in the binding of Pf3 ssDNA binding proteins to nucleic acids. Biochemistry 34, 5635–5643.
Mark, B. L. and Gray, D. M. (1997) Tyrosine mutant helps define overlapping CD bands from fd gene 5 protein-nucleic acid complexes. Biopolymers 42, 337–348.
General Reading
Bayley, P. M. (1973) The analysis of circular dichroism of biomolecules. Prog. Biophys. 27, 1–76.
Bush, C. A. (1974) Ultraviolet spectroscopy, circular dichroism and optical rotatory dispersion, in Basic Principles in Nucleic Acid Chemistry, vol. 2 (Ts’O, P.O.P., ed.), Academic, New York, pp. 91–169.
Drake, A. F. (1994) Circular dichroism. Methods Mol. Biol. 22, 219–44.
Gratzer, W. B. (1971) Optical rotatory dispersion and circular dichroism of nucleic acids, in Procedures in Nucleic Acid Research, vol. 2 (Cantoni G. L. and Davies D. R., eds.), Harper and Row, New York, pp. 3–30.
Woody, R. W. (1995) Circular dichroism. Methods Enzymol. 246, 34–71.
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© 2001 Humana Press Inc., Totowa, NJ
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Carpenter, M.L., Oliver, A.W., Geoff Kneale, G. (2001). Circular Dichroism for the Analysis of Protein-DNA Interactions. In: Moss, T. (eds) DNA-Protein Interactions. Methods in Molecular Biology, vol 148. Humana Press. https://doi.org/10.1385/1-59259-208-2:503
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DOI: https://doi.org/10.1385/1-59259-208-2:503
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