Characterization of DNA Structures by Circular Dichroism

G. Reid Bishop1, Jonathan B. Chaires2

1 Mississippi College, Clinton, Mississippi, 2 University of Mississippi Medical Center, Jackson, Mississippi
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 7.11
DOI:  10.1002/0471142700.nc0711s11
Online Posting Date:  February, 2003
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Circular dichroism (CD) of nucleic acids is commonly used to provide a signature for a given secondary structure. CD is particularly powerful for monitoring structural changes resulting from changes in environmental conditions such as temperature, ionic strength, and pH. A number of commercially available instruments are available for the measurement of CD spectra. Since the details of instrumental operation differ for each machine, this unit provides a descriptive guide, rather than a strict protocol. It describes considerations that the experimentalist will face when attempting to examine nucleic acid structures by CD spectropolarimetry. Specific details are also given for cell filling and cleaning, and for instrumental calibration. Finally, several examples of CD spectra are given to provide useful reference points for a variety of nucleic acid structures, ranging from singleā€stranded to triplex and quadruplex forms.

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Table of Contents

  • Guidelines for Carrying Out a CD Exxperiment
  • Sample CD Spectra
  • Figures
  • Tables
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Literature Cited

Literature Cited
   Crabbe, P. 1965. Optical Rotatory Dispersion and Circular Dichroism in Organic Chemistry. Holden‐Day, San Francisco,Calif.
   Drake, A.F. 2001. Circular dichroism. In Protein‐ Ligand Interactions: Structure and Spectroscopy (S.E. Harding and B.Z. Chowdhry, eds.) pp. 123‐167. Oxford University Press, Oxford, U.K.
   Gray, D.M., Hung, S.W., and Johnson, K.H. 1995. Absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes. Methods Enzymol. 246:19‐71.
   Greenfield, N.J. 1996. Methods to estimate the conformation of proteins and polypeptides from circular dichroism data. Anal. Biochem. 235:1‐10.
   Ivanov, V.I., Minchenkova, E., Schyolkina, A.K., and Poletayev, A.I. 1973. Different conformations of double‐stranded nucleic acid in solution as revealed by circular dichroism. Biopolymers 12:89‐110.
   Johnson, W.C. Jr. 1985. Circular dichroism and its empirical application to biopolymers. Meth. Biochem. Anal. 31:61‐163.
   Johnson, W.C. Jr. 1990. Spectroscopic and kinetic data: Physical data I. Section 3.1: Electronic circular dichroism (CD) spectroscopy of nucleic acids. In Landolt‐Bornstein Numerical Data and Functional Relationships in Science and Technology Vol. VII/1/c (W. Saenger, ed.) pp. 1‐24. Springer‐Verlag, Heidelberg, Germany.
   Johnson, W.C. Jr. 2000a. CD of nucleic acids. In Circular Dichroism: Principles and Applications 2nd ed. (N. Berova, K. Nakanishi, and R.W. Woody, eds.) pp. 703‐718. Wiley‐VCH, New York.
   Johnson, W.C. Jr. 2000b. Determination of the conformation of nucleic acids by electronic CD. In Circular Dichroism and The Conformational Analysis of Biomolecules (G.D. Fasman, ed.) pp. 433‐468. Plenum Press, New York.
   Lowry, T.M. 1964. Optical Rotatory Power. Dover Publications, New York.
   Maurizot, J.C. 2000. Circular dichroism of nucleic acids: Nonclassical conformations and modified oligonucleotides. In Circular Dichroism: Principles and Applications, 2nd ed. (N. Berova, K. Nakanishi, and R.W. Woody, eds.) pp. 719‐739. Wiley‐VCH, New York.
   Porumb, H., Monnot, M., and Fermandjian, S. 2002. Circular dichroism signatures of features simultaneously present in structured guanine‐rich oligonucleotides: A combined spectroscopic and electrophoretic approach. Electrophoresis 23:1013‐1020.
   Steely, H.T. Jr., Gray, D.M., and Ratliff, R.L. 1986. CD of homopolymer DNA‐RNA hybrid duplexes and triplexes containing A‐T or A‐U base pairs. Nucl. Acids Res. 14:10071‐10090.
   Sun, X.G., Cao, E.H., He, Y.J., and Qin, J.F. 1999. Spectroscopic comparison of different DNA structures formed by oligonucleotides. J. Biomolec. Struct. Dynam. 16:863‐872.
   Tinoco, I. Jr., and Cantor, C. 1970. Application of optical rotatory dispersion and circular dichroism to the study of biopolymers. Meth. Biochem. Anal. 18:81‐203.
   Venyaminov, S.Y. and Yang, J.T. 2000. Determination of protein secondary structure. In Circular Dichroism and the Conformational Analysis of Biomolecules (G.D. Fasman, ed.) pp. 69‐107. Plenum Press, New York.
   Woody, R. 1995. Circular Dichroism. Methods Enzymol. 246:19‐71.
Key References
   Johnson, 1985. See above.
  A detailed practical guide for measuring CD spectra.
   Johnson, 1990. See above.
  A valuable compilation of nucleic acid CD spectra.
   Rodger, A. and Norden, B. 1997. Circular Dichroism and Linear Dichroism. Oxford University Press, Oxford, U.K.
  A brief lucid introduction to the theory of circular dichroism, with many examples of nucleic acid spectra.
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