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

Abstract

Repetitive nucleic acid sequences, which occur in abundance throughout the mammalian genome, are of enormous research interest due to their potential to adopt fascinating and unusual molecular structures such as the i-motif. In remarkable contrast to the DNA double helix, i-motif conformations are stabilized by protonated cytosine base pairs, (Cyt)H + (Cyt), that are centrally located in the core of the i-motif and intercalated vertically in an antiparallel fashion. An in-depth understanding of how modifications influence the stability of i-motif conformations is a prerequisite to understanding their biological functions and the development of effective means of tuning their stability for specific medical and technological applications. Here, the influence of the 2′-and 3′-hydroxy substituents of the sugar moieties and 5-methylation of the cytosine nucleobases on the base-pairing interactions of protonated cytidine nucleoside analogue base pairs, (xCyd)H + (xCyd), are examined by complementary threshold collision-induced dissociation techniques and computational methods. The xCyd nucleosides examined include the canonical DNA and RNA cytidine nucleosides, 2′-deoxycytidine (dCyd) and cytidine (Cyd), as well as several modified cytidine nucleoside analogues, 2′,3′-dideoxycytidine (ddCyd), 5-methyl-2′-deoxycytidine (m 5 dCyd), and 5-methylcytidine (m 5 Cyd). Comparisons among these model base pairs indicate that the 2′-and 3′-hydroxy substituents of the sugar moieties have very little influence on the strength of the base-pairing interactions, whereas 5-methylation of the cytosine nucleobases is found to enhance the strength of the base-pairing interactions. The increase in stability resulting from 5-methylation is only modest but is more than twice as large for the DNA than RNA protonated cytidine base pair. Overall, present results suggest that canonical DNA i-motif conformations should be more stable than analogous RNA i-motif conformations and that 5-methylation of cytosine residues, a significant epigenetic marker, provides greater stabilization to DNA than RNA i-motif conformations.

Influence of 5-Halogenation on the Base-Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of Synthetici-Motif Structures for DNA Nanotechnology Applications

“…Modeling of reaction is based on a loose PSL TS . The PSL TS model has been shown to provide the most accurate correction for kinetic shifts observed for CID reactions of noncovalently bound complexes. − ,,,− The molecular parameters (vibrational frequencies and rotational constants) that describe the energized ( x Cyd)­H + ( x Cyd) base pair and corresponding PSL TSs used for the threshold analyses are listed in Tables S1 and S2. The threshold energies, E 0 (PSL), along with the modeling parameters obtained from these analyses and observed kinetics shifts are summarized in Table .…”

“… a Present results except as noted, uncertainties are listed in parentheses. b Theoretical BPEs are computed based on structures optimized at the B3LYP/6-311+G­(d,p) level of theory including ZPE and BSSE corrections. c Calculated at the B3LYP/6-311+G­(2d,2p) level of theory. d Calculated at the B3LYP/def2-TVZPPD level of theory. e Calculated at the B3P86/6-311+G­(2d,2p) level of theory. f Calculated at the M062 X /6-311+G­(2d,2p) level of theory. g Values taken from ref . h Values taken from ref . i Average experimental uncertainty (AEU) of the BPEs determined in the present study. Mean absolute deviation (MAD) between the measured and calculated BPEs determined in the present study. …”

“…However, the BPEs of the 5-halogenated protonated cytosine-cytosine base pairs also significantly exceed the BPEs of the (Gua) · (Cyt) and (Cyt) · (Cyt) base pairs, indicating that i -motif conformations should be stable to 5-halogenation. The model systems investigated were extended to nucleosides with the examination of protonated nucleoside base pairs of the canonical DNA and RNA cytidine nucleosides, 2′-deoxycytidine (dCyd) and cytidine (Cyd) as well as several modified nucleosides including 2′,3′-dideoxy­cytidine (ddCyd), 5-methyl-2′-deoxycytidine (m 5 dCyd), and 5-methylcytidine (m 5 Cyd). , Comparisons among these systems and the protonated nucleobase pairs previously examined thus enable the influence of both 5-methylation and the sugar moiety on the BPE to be elucidated. The measured BPEs of the protonated cytidine nucleoside analogue base pairs indicate that the 2′- and 3′‑hydroxy substituents have very little impact on the base-pairing interactions, whereas 5-methylation was found to enhance the BPE of dCyd and Cyd.…”

Impact of Covalent Modifications on the Hydrogen Bond Strengths in Diaminotriazine Supramolecules

“…[28] They have also developed design principles to rationally modulate the HBs in DDAA-AADD (D = donor, A = acceptor, DÀ H•••A) and DAA-ADD dimers. [29] Recently, Rodgers et al, [30] have also shown that 5-methylation on protonated cytidine dimers increases its hydrogen bonding energy. Besides, Szatylowicz et al [31] have analyzed the effects of substituents like NO 2 , Cl, F, H, CH 3 , and NH 2 in three remote positions of adenine and its three cyclic tetramers.…”

“…They have also developed design principles to rationally modulate the HBs in DDAA‐AADD (D=donor, A=acceptor, D−H⋅⋅⋅A) and DAA‐ADD dimers [29] . Recently, Rodgers et al., [30] have also shown that 5‐methylation on protonated cytidine dimers increases its hydrogen bonding energy. Besides, Szatylowicz et al [31] .…”