Base-Pairing Energies of Proton-Bound Dimers and Proton Affinities of 1-Methyl-5-Halocytosines: Implications for the Effects of Halogenation on the Stability of the DNAi-Motif

Abstract

Abstract. (CCG) n •(CGG) n trinucleotide repeats have been found to be associated with fragile X syndrome, the most widespread inherited cause of mental retardation in humans. The (CCG) n •(CGG) n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of noncanonical proton-bound dimers of cytosine (C + •C). Halogenated cytosine residues are one form of DNA damage that may be important in altering the structure and stability of DNA or DNA-protein interactions and, hence, regulate gene expression. Previously, we investigated the effects of 5-halogenation and 1-methylation of cytosine on the base-pairing energies (BPEs) using threshold collision-induced dissociation (TCID) techniques. In the present study, we extend our work to include proton-bound homo-and heterodimers of cytosine, 1-methyl-5-fluorocytosine, and 1-methyl-5-bromocytosine. All modifications examined here are found to produce a decrease in the BPEs. However, the BPEs of all of the proton-bound dimers examined significantly exceed those of Watson-Crick G•C, neutral C•C base pairs, and various methylated variants such that DNA i-motif conformations should still be preserved in the presence of these modifications. The proton affinities (PAs) of the halogenated cytosines are also obtained from the experimental data by competitive analysis of the primary dissociation pathways that occur in parallel for the proton-bound heterodimers. 5-Halogenation leads to a decrease in the N3 PA of cytosine, whereas 1-methylation leads to an increase in the N3 PA. Thus, the 1-methyl-5-halocytosines exhibit PAs that are intermediate.

Influence of 5-Methylation and the 2′- and 3′-Hydroxy Substituents on the Base Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities ofi-Motif Structures

“…Two sequential dissociation pathways, both of which involve glycosidic bond cleavage occur in competition. In all cases, the excess proton is preferentially retained by the departing base, reaction , whereas retention of the excess proton by the sugar moiety is much less favorable (by more than an order of magnitude), reaction . The fragmentation patterns observed for the ( x Cyd)­H + ( x Cyd) base pairs parallel those observed in previous studies of protonated base pairs of cytosine nucleobase and cytidine nucleoside analogues as well as that of iosloated protonated cytidine nucleoside analogues using TCID − , and IRMPD − techniques.…”

“…The much stronger base-pairing interactions in the (Cyt)­H + (Cyt) base pair were thus interpreted as important contributors to the stability of genomic i -motif conformations. This initial study as well as a series of parallel follow-on investigations introduced increasing complexity to the (Cyt)H + (Cyt) base pair model for the i -motif by examining the effects of a series of modifications at the 1- and 5-positions of the nucleobase. − Consistent with previous findings that 5-methylation stabilizes noncanonical i -motif conformations, the BPE of the (m 5 Cyt)­H + (m 5 Cyt) base pair was measured as 177.4 ± 5.3 kJ/mol, an increase of 7.5 ± 7.0 kJ/mol in the strength of base pairing. A somewhat smaller increase in the BPE to 173.4 kJ/mol was predicted by theory.…”

“…These discrepancies are a proper reflection of the poorer ability of the B3P86 and M06-2X functionals for accurately describing the noncovalent interactions that contribute to the stability of these base pairs. Although there is no gold standard in the choice of computational method for evaluating the structures and energetics of noncovalently bound complexes, B3LYP/6-311+G­(2d,2p) and B3LYP/def2-TVZPPD have been shown to be reliable in describing similar hydrogen-bonding interactions in parallel protonated nucleobase pairs previously investigated. − …”

Cationic Noncovalent Interactions: Energetics and Periodic Trends

“…TCID studies of the protonated base pairs of cytosine and its variants have been reported, − with values listed in Table . It can be seen that the effects are subtle, with all base pairing energies (BPEs) within a range of 20 kJ/mol.…”

A Combined Experimental and Computational Study of Halogen and Hydrogen Bonding in Molecular Salts of 5-Bromocytosine

“…In the i -motif, based on the association of cytosine molecules protonated under neutral or slightly acidic conditions to form neutral cytosine—hemi-protonated cytosine base pairs (C:CH + ), two parallel-stranded duplexes are held together in an antiparallel orientation by intercalated C:CH + pairs [ 22 , 23 , 24 , 25 ]. Noteworthy, by decreasing the proton affinity of the N3 atom, 5-halogenation of 1-methylcytosine does not destroy the i -motif in DNA, but may alter the number of trinucleotide repeats required to induce the structural conversion from Watson and Crick ( WC ) base-pairing to the i -motif association [ 26 ].…”