Abstract
It has long been known that the uranyl(VI) ion (UO2 2+) forms strong complexes with various inorganic and organic anions, including phosphates, and that the photochemically excited state of this ion is a very strong oxidant (1). For instance, uranyl-mediated photooxidation of alcohols has been studied in detail (2,3). It is also widely recognized that uranyl chemistry and photophysics/photochemistry are very complex. Thus monomeric UO2 2+is only present at low pH (pH approx 2), whereas polynuclear species and various “hydroxides,” which often precipitate, form at a higher pH (4).
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Burrows, H. D. and Kemp, T. J. (1974) The photochemistry of the uranyl ion. Chem. Soc. Rev. 3, 138–165.
Azenha, M. E. D. G., Burrows, H. D., Furmosinho, S. J., and Miguel, M. G. M. (1989) Photophysics of the excited uranylionin aqueous solutions. Part 6. Quenching effects of aliphatic alcohols. J. Chem. Soc. Faraday Trans. 85, 2625–2634.
Cunningham, J. and Srijaranai, S. (1990) Sensitized photo-oxidations of dissolved alcohols in homogeneous and heterogenous systems. 1. Homogeneous photosentization by uranyl ions. J. Photochem. Photobiol. A. Chem. 55, 219–232.
Greenwood, N. N. and Earnshaw, A. (1986) In Chemistry of the Elements. Oxford, Pergamon, p. 1478.
Nielsen, P. E., Jeppesen, C., and Buchardt, O. (1988) Uranyl salts as photochemical agents for cleavage of DNA and probing of protein-DNA contacts. FEBSLett. 235, 122–124.
Jeppesen, C. and Nielsen, P. (1989) Uranyl mediated photofootprinting reveals strong E. coli RNA polymerase-DNA backbone contacts in the+10 region of the deoP1 promoter open complex. Nucleic Acids Res. 17, 4947–4956.
Nielsen, P. E., Møllegaard, N. E., and Jeppesen, C. (1990) Uranyl photoprobing of conformational changes in DNA induced by drug binding. Anti-Cancer Drug Design 5, 105–110.
Nielsen, P. E., Møllegaard, N. E., and Jeppesen, C. (1990) DNA conformational analysis in solution by uranyl mediated photocleavage. Nucleic Acids Res. 18, 3847–3851.
Bailly, C., Møllegaard, N. E., Nielsen, P. E., and Waring, M. J. (1995) The influence of the 2-amino group of guanine on DNA conformation. Uranyl and DNase I probing of inosine/diaminopurine substituted DNA. EMBO J. 9, 2121–2131.
Sönnichsen, S. H. and Nielsen, P. E (1996) Enhanced uranyl photocleavage across the minor groove of all (A/T)4 sequences indicates a similar narrow minor groove conformation. J. Mol. Recogn. 9, 219–227.
Møllegaard, N. E., Murchie, A. I. H. Lilley, D. M. J., and Nielsen, P. E. (1994) Uranyl photoprobing of a four-way DNA junction. Evidence for specific metal ion binding. EMBO J. 13, 1508–1513.
Bassi, G. S. Møllegaard, N. E., Murchie, A. I., von Kitzing, E., and Lilley, D. M. (1995) Ionic interactions and the global conformations of the hammerhead ribozyme. Nature Struct. Biol. 2, 45–55.
Nielsen, P. E. and Møllegaard, N. E. (1996) Sequence/structure selective thermal and photochemical cleavage of yeast-tRNAPhe by UO2 2+ J. Mol. Recogn. 9, 228–232.
Møllegaard, N. E. and Nielsen, P. E. (2000) Applications of uranyl cleavage mapping of RNA structure. Meth. Enzymol. 318, 43–47.
Wittberger, D., Berens, C., Hamman, C., Westhof, E., and Schroeder, R. (2000) Evaluation of uranyl photocleavage as a probe to monitor ion binding and flexibility in RNAs. J. Mol. Biol. 300, 339–352.
Nielsen, P. E. and Jeppesen, C. (1990) Photochemical probing of DNA complexes. Trends Photochem. Photobiol. 1, 39–47.
Møllegaard, N. E., Rasmussen, P. B., Valentin-Hansen, P., and Nielsen, P. E. (1993) Characterization of promoter recognition complexes are formed by CRP and CytR for repression and by CRP and RNA polymerase for avtivation of transcription on the E. coli deoCp2 promoter. J. Biol. Chem. 268, 17,471–17,477.
Nielsen, P. E. (1992) Uranyl photofootprinting of triple helical DNA. Nucleic Acids Res. 20, 2735–2739.
Nielsen, P. E., Cons, B. M. G., Fox, K. R., and Sommer, V. B. (1990) Uranyl photofootprinting. DNA structural changes upon binding of mithramycin, in Molecular Basis of Specificity in Nucleic Acid Drug Interactions, vol. 23 (Pullman, B. and Jortner, J., eds.), Kluwer Academic, Dordrecht, pp. 423–432.
Møllegaard, N. E. and Nielsen, P. E. (1997) Uranyl photoprobing of DNA structures and drug-DNA complexes, in Drug-DNA Interaction Protocols (Fox, K. R., ed.), Humana, Totowa, NJ, pp. 43–50.
Nielsen, P. E., Hiort, C., Buchardt, O., Dahl, O., Sönnichsen, S. H., and Nordèn, B. (1992) DNA Binding and Photocleavage by Uranyl(VI) (UO2 2+) Salts. J. Amer. Chem. Soc. 114, 4967–4975.
Schultz, S. C., Shields, G. C., and Steitz, T. A. (1991) Crystal structure of a CAP-DNA complex: the DNA is bent by 90°. Science 253, 1001–1007.
Tullius, T. D. and Dombroski, B. A. (1986) Hydroxyl radical “footprinting”: high-resolution information about DNA protein contacts and application to lambda repressor and Cro protein. Proc. Natl. Acad. Sci. USA 83, 5469–5473.
Burkhoff, A. M. and Tullius, T. D. (1987) The unusual conformation adopted by the adenine tracts in kinetoplast DNA. Cell 48, 935–943.
Siebenlist, U., Simpson, R. B., and Gilbert, W. (1980) E. coli RNA polymerase interacts homologously with two different promoters. Cell 20, 269–281.
O’Halloran, T. V., Frantz, B., Shin, M. K., Ralston, D. M., and Wright, J. G. (1989) The MerR heavy metal receptor mediates positive activation in a topologically novel transcription complex. Cell 56, 119–129.
Vrana, K. E., Churchill, M. E. A., Tullius, T. D., and Brown, D. D. (1988) Mapping functional regions of transcription factor TFIIIA. Mol. Cell. Biol. 8, 1684–1696.
Berens, C. Streicher, B., Schroeder, R., and Hillen, W. (1998) Visualizing metal-ion-binding sites in group I introns by iron(II)-mediated Fenton reactions. Chem. Biol. 5, 163–175.
Zaychikov, E., Martin, E., Denissova, L., Kozlov, M., Markovtsov, V., Kashlev, M., et al. (1996) Mapping of catalytic residues in the RNA polymerase active center. Science 273, 107–109.
Maniatis, T. Fritsch, E. F., and Sambrook, J. (1982) Molecular Cloning. A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
Amann, E., Brosins, J., and Ptasne, M. (1983) Vectors bearing a hybrid trp-lac promoter useful for regulated expression of cloned genes in Escherichia coli. Gene 25, 167–178.
Jeppesen, C. and Nielsen, P. E. (1989) Photofootprinting of drug-binding sites on DNA using diazo-and azido-9-aminoacridine derivatives. Eur. J. Biochem. 182, 437–444.
Dabrowiak, J. C., Kissinger, K., and Goodisman, J. (1989) Quantitative foot-printing analysis of drug-DNA interactions: Fe(III)methidium-propyl-EDTA as a probe. Electrophoresis 10, 404–412.
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
Nielsen, P.E. (2001). Uranyl Photofootprinting. In: Moss, T. (eds) DNA-Protein Interactions. Methods in Molecular Biology, vol 148. Humana Press. https://doi.org/10.1385/1-59259-208-2:111
Download citation
DOI: https://doi.org/10.1385/1-59259-208-2:111
Publisher Name: Humana Press
Print ISBN: 978-0-89603-625-3
Online ISBN: 978-1-59259-208-1
eBook Packages: Springer Protocols