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The cyclobutane dimers of 5-methylcytosine and their deamination products

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Abstract

The photochemical reactions of 5-methylcytosine (m5C), a minor component of mammalian DNA, have been studied at a concentration of 2 mM in frozen 10 mM aqueous NaCl solution at dry ice temperature (194.5 K). For these studies, low-pressure lamps emitting mainly UVB radiation were used. We have isolated and characterized three cyclobutane dimers, namely the cis-anti (c,a) the cis-syn (c,s) and the trans-syn (t,s) forms. While the c,a and the t,s cyclobutane dimers are relatively stable towards deamination upon standing in solution at 277 K, the c,s isomer is gradually converted into the corresponding c,s m5C-thymine (Thy) mixed dimer; this latter reaction occurs considerably faster at 310 K. The t,s cyclobutane dimer is converted into the corresponding m5C-Thy mixed dimer upon incubation at 373 K, while the c,a dimer is converted into a mixture of m5C and c,a mixed dimer when incubated at 310 K. Irradiation of equimolar mixtures of Thy (1 mM) and m5C (1 mM) under similar conditions yields each of the three m5C cyclobutane dimers, as well as significant amounts of c,a, c,s and t,s m5C-Thy mixed cyclobutane dimers. These m5C-Thy dimers undergo decompositions similar in nature to the processes undergone by m5C cyclobutane dimers. Pseudo-first order rate constants for deamination of the c,s m5C homodimer and c,s m5C-Thy heterodimer at various temperatures and at pH 7.7 have been measured and the enthalpies and entropies of activation have been evaluated for the deamination processes for these two compounds. The two dimers have half-lives of about 14 and 22 h, respectively, at 310 K; however, at 273 K, the corresponding half-lives can be evaluated as being around 30 and 36 days, respectively.

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Abbreviations

CBD:

cyclobutane dimer

c,a:

cis-anti

c,s:

cis-syn

DAD:

diode array detector

DMSO:

dimethylsulfoxide

Gua:

guanine

MALDI:

matrix assisted laser desorption ionization

m5C:

5-methylcytosine

MeOH:

methanol

a:

trans-anti

Thy:

thymine

TMS:

tetramethylsilane

t,s:

trans-anti

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Authors and Affiliations

  1. Department of Pharmaceutical Chemistry School of Pharmacn, University of California, San Francisco, CA, 94143-0446, USA

    Martin D. Shetlar, Vladimir J. Basus, Arnold M. Falick & Anwer Mujeeb

  2. Mass Spectrometry Laboratory, Howard Hughes Medical Institute, University of California, Berkeley, California, 94720-3202, USA

    Arnold M. Falick

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  1. Martin D. Shetlar
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  2. Vladimir J. Basus
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Correspondence to Martin D. Shetlar.

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Shetlar, M.D., Basus, V.J., Falick, A.M. et al. The cyclobutane dimers of 5-methylcytosine and their deamination products. Photochem Photobiol Sci 3, 968–979 (2004). https://doi.org/10.1039/b404271a

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