Abstract
Palindromic DNA sequences have the potential to form branched structures called cruciforms, in which the interstrand base pairs within the symmetric region are replaced with intrastrand base pairs. Cruciforms can sometimes form in vivo (1), and circumstantial evidence suggests that they may serve functional roles in such processes as transcription (1) or DNA replication (2). In addition, the four-way branch at the base of the cruciform is structurally equivalent to the Holliday junction, an intermediate in homologous DNA recombination (3,4). Thus, an understanding of the thermodynamics and kinetics of cruciform formation may illuminate a number of processes in nucleic acid metabolism.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
van Holde, K. and Zlatanova, J. (1994) Unusual DNA structures, chromatin and transcription. Bioessays 16, 59–68.
Pearson, C. E., Ruiz, M. T., Price, G. B., and Zannis-Hadjopoulos, M. (1994) Cruciform DNA binding protein in HeLa cell extracts. Biochemistry 33, 14,185–14,196.
Holliday, R. (1964) A mechanism for gene conversion in fungi. Genet. Res. 5, 282–304.
Lilley, D. M. and Kemper, B. (1984) Cruciform-resolvase interactions in super-coiled DNA. Cell 36, 413–422.
Hsieh, T.-S. and Wang, J. C. (1975) Thermodynamic properties of superhelical DNAs. Biochem. 14, 527–535.
Courey, A. J. and Wang, J. C. (1983) Cruciform formation in a negatively super-coiled DNA may be kinetically forbidden under physiological conditions. Cell 33, 817–829.
Gellert, M., O’Dea, M. H., and Mizuuchi, K. (1983) Slow cruciform transitions in palindromic DNA. Proc. Natl. Acad. Sci. USA 80, 5545–5549.
Lilley, D. M. and Hallam, L. R. (1984) Thermodynamics of the ColE1 cruciform. Comparisons between probing and topological experiments using single topoisomers. J. Mol. Biol. 180, 179–200.
Haniford, D. B. and Pulleyblank, D. E. (1985) Transition of a cloned d(AT)n-d(AT)n tract to a cruciform in vivo. Nucleic Acids Res. 13, 4343–4363.
Murchie, A. I. and Lilley, D. M. (1992) Supercoiled DNA and cruciform structures. Methods Enzymol. 211, 158–180.
Courey, A. J. and Wang, J. C. (1988) Influence of DNA sequence and supercoiling on the process of cruciform formation. J. Mol. Biol. 202, 35–43.
Peck, L. J. and Wang, J. C. (1983) Energetics of B-to-Z transition in DNA. Proc. Natl. Acad. Sci. USA 80, 6206–6210.
Depew, D. E. and Wang, J. C. (1975) Conformational fluctuations of DNA helix. Proc. Natl. Acad. Sci. USA 72, 4275–4279.
Keller, W. (1975) Determination of the number of superhelical turns in a simian virus 40 DNA by gel electrophoresis. Proc. Natl. Acad. Sci. USA 72, 4876–4880.
Leach, D. R. (1994) Long DNA palindromes, cruciform structures, genetic instability and secondary structure repair. Bioessays 16, 893–900.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1999 Humana Press Inc.
About this protocol
Cite this protocol
Courey, A.J. (1999). Analysis of Altered DNA Structures. In: Bjornsti, MA., Osheroff, N. (eds) DNA Topoisomerase Protocols. Methods in Molecular Biology, vol 94. Humana, Totowa, NJ. https://doi.org/10.1385/1-59259-259-7:29
Download citation
DOI: https://doi.org/10.1385/1-59259-259-7:29
Published:
Publisher Name: Humana, Totowa, NJ
Print ISBN: 978-0-89603-444-0
Online ISBN: 978-1-59259-259-3
eBook Packages: Springer Protocols