Abstract
The DNA double helix is highly malleable and, when constrained, either as a small circle or by the action of a protein, can be readily distorted from its energetically favored conformation. Such distortions may be relatively moderate, as exemplified by smooth bending (which maintains base stacking), or more extreme when this stacking can be disrupted. Deformations of this latter type include kinks, where the direction of the double helical axis is changed abruptly at a single-base step, and localized strand separation, which may be a direct consequence of protein-induced unwinding or of high negative superhelicity in free DNA. Both kinks and localized unwinding can arise transiently during the enzymatic manipulation of DNA by recombinases and by protein complexes involved in the establishment of unwound regions during the initiation of transcription or of DNA replication.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Lilley, D. M. J. and Palecek, C. (1984) The supercoil-stabilised cruciform of colE1 is hyper-reactive to osmium tetroxide. EMBO J. 3, 1187–1195.
Sasse-Dwight, S. and Gralla, J. D. (1989) KMnO4 as a probe for lac promoter DNA melting and mechanism in vivo. J. Biol. Chem. 264, 8074–8081.
Sigman, D. S., Spassky, A., Rimsky, S., and Buc, H. (1985) Conformational analysis of lac promoters using the nuclease activity of 1,10-phenanthroline-copper ion. Biopolymers 24, 183–197.
Hogan, M. E., Rooney, T. F., and Austin, R. H. (1987) Evidence for kinks in DNA folding in the nucleosome. Nature 328, 554–557.
Le Doan, T., Perrouault, L., Hélène, C., Chassignol, M., and Thuong, N. T. (1986) Targeted cleavage of polynucleotides by complementary oligonucleotides covalently linked to iron-porphyrins. Biochemistry 25, 6736–6739.
Tullius, T. D., Dombroski, B. A., Churchill, M. E. A., and Kam, L. (1987) Hydroxylradical footprinting: a high resolution method for mapping protein-DNA contacts. Methods Enzymol. 155, 537–558.
Ansari, A. Z., Chael, M. L., and O’Halloran, T. V. (1992) Allosteric underwinding of DNA is a critical step in positive control of transcription by Hg-MerR. Nature 355, 87–89.
Schultz, S. C., Shields, S. C., and Steitz, T. A. (1991) Crystal structure of a CAPDNA complex: the DNA is bent by 90°. Science 253, 1001–1007.
Buckle, M., Buc, H., and Travers, A. A. (1992) DNA deformation in nucleoprotein complexes between RNA polymerase, cAMP receptor protein and the lac UV5 promoter probed by singlet oxygen. EMBO J. 11, 2619–2625.
Rougée, M. and Bensasson, R. V. (1986) Détermination des constantes de vitesse de désactivation de l’oxygène singulet (1D7) en presénce de biomolécules. Comp. Rend. Acad. Sci. Paris 302, 1223–1226.
Travers, A. A., Lamond, A. I., Mace, H. A. F., and Berman, M. L. (1983) RNA polymerase interactions with the upstream region of the E. coli tyrT promoters. Cell 35, 265–273.
Maxam, A. M. and Gilbert, W. (1980) Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 155, 560–568.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2001 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
Buckle, M., Travers, A.A. (2001). Diffusible Singlet Oxygen as a Probe of DNA Deformation. In: Moss, T. (eds) DNA-Protein Interactions. Methods in Molecular Biology, vol 148. Humana Press. https://doi.org/10.1385/1-59259-208-2:151
Download citation
DOI: https://doi.org/10.1385/1-59259-208-2:151
Publisher Name: Humana Press
Print ISBN: 978-0-89603-625-3
Online ISBN: 978-1-59259-208-1
eBook Packages: Springer Protocols