Reactions of 5-methylcytosine cation radicals in DNA and model systems: Thermal deprotonation from the 5-methyl group vs. excited state deprotonation from sugar

Abstract

Purpose: To study the formation and subsequent reactions of the 5-methyl-2′-deoxycytidine cation radical (5-Me-2′-dC•⁺) in nucleosides and DNA-oligomers and compare to one-electron oxidized thymidine.

Materials and methods: Employing electron spin resonance (ESR), cation radical formation and its reactions were investigated in 5-Me-2′-dC, thymidine (Thd) and their derivatives, in fully double-stranded (ds) d[GC*GC*GC*GC*]₂ and in the 5-Me-C/A mismatched, d[GGAC*AAGC:CCTAATCG], where C* = 5-Me-C.

Results: We report 5-Me-2′-dC•⁺ production by one-electron oxidation of 5-Me-2′-dC by Cl₂•− via annealing in the dark at 155 K. Progressive annealing of 5-Me-2′-dC•⁺ at 155 K produces the allylic radical (C-CH₂•). However, photoexcitation of 5-Me-2′-dC•⁺ by 405 nm laser or by photoflood lamp leads to only C3′• formation. Photoexcitation of N3-deprotonated thyminyl radical in Thd and its 5′-nucleotides leads to C3′• formation but not in 3′-TMP which resulted in the allylic radical (U-CH₂•) and C5′• production. For excited 5-Me-2′,3′-ddC•⁺, absence of the 3′-OH group does not prevent C3′• formation. For d[GC*GC*GC*GC*]₂ and d[GGAC*AAGC:CCTAATCG], intra-base paired proton transferred form of G cation radical (G(N1-H)•: C(+ H⁺)) is found with no observable 5-Me-2′-dC•⁺ formation. Photoexcitation of (G(N1-H)•:C(+ H⁺)) in d[GC*GC*GC*GC*]₂ produced only C1′• and not the expected photoproducts from 5-Me-2′-dC•⁺. However, photoexcitation of (G(N1-H)•:C(+ H⁺)) in d[GGAC*AAGC:CCTAATCG] led to C5′• and C1′• formation.

Conclusions: C-CH₂• formation from 5-Me-2′-dC•⁺ occurs via ground state deprotonation from C5-methyl group on the base. In the excited 5-Me-2′-dC•⁺ and 5-Me-2′,3′-ddC•⁺, spin and charge localization at C3′ followed by deprotonation leads to C3′• formation. Thus, deprotonation from C3′ in the excited cation radical is kinetically controlled and sugar C-H bond energies are not the only controlling factors in these deprotonations.

Keywords::

• 5-Methylcytosine
• DNA-oligomers
• thymidine
• ESR
• TD-DFT calculations
• HFCC values
• cation radical
• one-electron oxidation