Abstract
UV irradiation induces intramolecular crosslinks in ribosomal RNA in the ribosome. These crosslinks occur between nucleotides distant in primary sequence and they are specific, limited in number and have crosslinking efficiencies sufficient to allow their use in monitoring conformational changes. In this work, the frequency of crosslinking for eight 16S rRNA crosslinks was determined as a function of wavelength of irradiation. For six of the crosslinks, the action spectra correspond to the absorption spectra of at least one of the participating nucleotides. For a crosslink between nucleotides C967 and C1400 the maximum frequency of crosslinking occurs at wavelengths blue-shifted from the absorbance maximum of cytidine and for a crosslink between C1402 and C1501 the maximum frequency of crosslinking is red-shifted. Photoreversal of the crosslinks was also studied by deproteinizing crosslinked RNA under mild conditions and then re-irradiating it with specific wavelengths under conditions in which the crosslinks were reversed but not formed. The different crosslinks exhibit significantly different extents of photoreversal versus wavelength profiles. The differences in the crosslinking action spectra can be accounted for in the absorbance spectra of the nucleotides that are involved in the crosslink as well as by the photoreversal action spectra.
Similar content being viewed by others
References
J. Cadet and P. Vigny, The photochemistry of nucleic acids, in Bioorganic Photochemistry, Vol 1, ed. H. Morrison, John Wiley & Sons, New York, 1990, 1–272.
R. Beukers and W. Berends, Isolation and identification of the irradiation product of thymine, Biochim. Biophys. Acta, 1960, 41, 550–551.
S. Y. Wang, Reversible behaviour of the ultra-violet irradiated deoxyribonucleic acid and its apuinic acid, Nature, 1970, 188, 844–846.
G. Fisher and H. Johns, Pyrimidine Photodimers, in Photochemistry and Photobiology of Nucleic Acids, ed. S. Y. Wang, Academic Press, New York, 1976, 225–294.
S. Y. Wang, Pyrimidine bimolecular photoproducts in Photochemistry and Photobiology of Nucleic Acids, ed. S. Y. Wang, vol. 1, Academic Press, New York, 1976, 296–356.
A. J. Varghese and C. S. Rupert, Ultraviolet irradiation of cytosine nucleosides in frozen solution produces cyclobutane-type dimeric products, Photochem. Photobiol., 1971, 13, 365–368.
A. J. Varghese, Acetone-sensitized dimerization of cytosine derivatives, Photochem. Photobiol., 1972, 15, 113–118.
D. E. Lemaire and B. P. Ruzsicska, Quantum yields and secondary photoreactions of the photoproducts of dTpdT, dTpdC and dTpdU, Photochem. Photobiol., 1993, 57, 755–769.
D. J. Fenick, H. S. Carr and D. E. Falvey, Synthesis and photochemical cleavage of cis-syn pyrimidine cyclobutane dimer analogs, J. Org. Chem., 1995, 60, 624–631.
K. C. Smith, Physical and chemical changes induced in nucleic acids by ultraviolet light, Radiat. Res. Suppl., 1966, 6, 54–79.
P. E. Gallagher and N. Duker, Formation of purine photoproducts in a defined human DNA sequence, Photochem. Photobiol., 1989, 49, 599–605.
D. Pörschke, Analysis of a specific photoreaction in oligo- and polydeoxyadenylic acids, J. Am. Chem. Soc., 1973, 95, 8440–8446.
S. Kumar, P. Joshi, N. Sharma, S. Bose, R. J. H. Davies, N. Takeda and J. McCloskey, Adenine photodimerization in deoxyadenylate sequences: elucidation of the mechanism through structural studies of a major d(ApA) photoproduct, Nucleic Acids Res., 1991, 19, 2841–2847.
J. Atmadja and R. Brimacombe, Investigation of the tertiary folding of Escherichia coli 16S RNA by in situ intra-RNA cross-linking within 30S ribosomal subunits, Nucleic Acids Res., 1985, 13, 6919–6937.
C. Wilms, J. W. Noah, D. Zhong and P. Wollenzien, Exact determination of UV-induced crosslinks in 16S ribosomal RNA in 30S ribosomal subunits, RNA, 1997, 3, 602–612.
J. W. Noah, T. Shapkina and P. Wollenzien, UV-induced crosslinks in the 16S rRNA of Escherichia coli, Bacillus subtilis and Thermus aquaticus and their implication for ribosome structure and photochemistry, Nucleic Acids Res., 2000, 28, 3785–3792.
A. Branch, B. Benefeld and H. Robertson, Ultraviolet light-induced crosslinking reveals a unique region of local tertiary structure in potato spindle tuber viriod and HeLa 5S RNA, Proc. Natl. Acad. Sci. USA, 1985, 82, 6590–6594.
C. Guerrier-Takada, N. Lumelsky and S. Altman, Specific interations in RNA enzyme-substrate complexes, Science, 1989, 246, 1578–1584.
W. Downs and T. Cech, An ultraviolet-inducible adenosine-adenosine cross-link reflects the catalytic structure of the tetrahymena ribozyme, Biochemistry, 1990, 29, 5605–5613.
S. Butcher and J. Burke, A photo-cross-linkable tertiary structure motif found in functionally distinct RNA molecules is essential for catalytic function of the hairpin ribozyme, Biochemistry, 1994, 33, 992–999.
J.-S. Sun, S. Valadkhan and J. Manley, A UV-crosslinkable interaction in human U6 snRNA, RNA, 1998, 4, 489–497.
S. Valadkhan and J. Manley, A tertiary interaction detected in a human U20U6 snRNA complex assembled in vitro resembles a genetically proven interaction in yeast, RNA, 2000, 6, 206–219.
L. I. Lebedeva, R. M. Ostrovskaia and V. G. Tsimmerman, Possible role of protein in the development of UV-induced isochromatid breaks, Genetika (Moscow), 1978, 14, 256–266.
T. Matsunaga, K. Heida and O. Nikaido, Wavelength dependent formation of thymine dimers and (6–4) photoproducts in DNA by monochromatic ultraviolet light ranging from 150 to 365 nm, Photochem. Photobiol., 1991, 54, 403–410.
R. H. Rothman and R. B. Setlow, An action spectrum for cell killing and pyrimidine dimer formation in Chinese hamster V-79 cells, Photochem. Photobiol., 1979, 29, 57–61.
J. Doniger, E. D. Jacobson, K. Krell and J. A. DiPaolo, Ultraviolet light action spectra for neoplastic transformation and lethality of Syrian hamster embryo cells correlate with spectrum for pyrimidine dimer formation in cellular DNA, Proc. Natl. Acad. Sci. USA, 1981, 78, 2378–2382.
C. Zweib, A. Ross, J. Rinke, M. Meinke and R. Brimacombe, Evidence for RNA-RNA cross-link formation in Escherichia coli ribosomes, Nucleic Acids Res., 1978, 5, 2705–2719.
C. Zweib and R. Brimacombe, Localization of a series of intra-RNA cross-links in 16S RNA, induced by ultraviolet irradiation of Escherichia coli 30S ribosomal subunits, Nucleic Acids Res, 1980, 8, 2397–2411.
T. Doring, B. Greur and R. Brimacombe, The topography of the 3′-terminal region of Escherichia coli 16S ribosomal RNA: an intra-RNA cross-linking study, Nucleic Acids Res., 1992, 20, 1593–1597.
V. I. Makhno, N. N. Peshin, Yu. P. Semenkov and S. V. Kirillov, Modified method of producing “tight” 70S ribosomes from Escherichia coli, highly active in individual stages of the elongation cycle, Mol. Biol., 1988, 22, 528–537.
T. E. England and O. C. Uhlenbeck, 3′-Terminal labeling of RNA with T4 RNA ligase, Nature, 1978, 275, 560–561.
T. Shapkina, M. A. Dolan, P. Babin and P. Wollenzien, Structural effects of initiation factor IF3 on the 16S rRNA structure in complexes with mRNA and tRNAfMet, J. Mol. Biol., 2000, 299, 615–628.
B. P. Ruzsicska and D. E. Lemaire, DNA Photochemistry, in CRC Handbook of Organic Photochemistry and Photobiology; eds. W. M. Horspool and P. S. Song, CRC Press, Boca Raton FL, 1995, 1289–1317.
M. Daniels, Excited states of the nucleic acids: bases, mononucleosides, and mononucleotides. in Photochemistry and Photobiology of Nucleic Acids, ed. S. Y. Wang, Academic Press, New York, 1, 1976, 23–109.
J. J. Fox, D. Van Praag, I. Wempen, I. L. Doerr, L. Cheong, J. E. Knoll, M. L. Eidennoff, A. Bendich and G. B. Brown, Thiation of nucleosides. II. Synthesis of 5-methyl-2′-deoxycytidine and related pyrimidine nucleosides, J. Am. Chem. Soc., 1959, 81, 178–187.
D. E. Lemaire and B. P. Ruzsicska, Kinetic analysis of the deamination reactions of cyclobutane dimers of thymidylyl-3′,5′-2′deoxycytidine and 2′-deoxycytidylyl-3′,5′-thymidine, Biochemistry, 1993, 32, 2525–2533.
J. J. Cannone, S. Subramanian, M. N. Schnare, J. R. Collett, L. M. D’Souza, Y. Du, B. Feng, N. Lin, L. V. Madabusi, K. M. Muller, N. Pande, Z. Shang and R. R. Gutell, The comparative RNA Web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron and other RNAs, BioMed Central Bioinformatics, 2002, 3, 2.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Zhirnov, O.V., Wollenzien, P. Action spectra for UV-light induced RNA–RNA crosslinking in 16S ribosomal RNA in the ribosome. Photochem Photobiol Sci 2, 688–693 (2003). https://doi.org/10.1039/b208677h
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1039/b208677h