Examining the base stacking interaction in a dinucleotide context via reversible cyclobutane dimer analogue formation under UV irradiation

Abstract

Substituted tolyl groups are considered as close isosteres of the thymine (T) residue. They can be recognized by DNA polymerases as if they were thymine. Although these toluene derivatives are relatively inert toward radical additions, our recent finding suggests that the dinucleotide analogue TpTo (To = 2'-deoxy-1-(3-tolyl)-β-D-ribofuranose) supports an ortho photocycloaddition reaction upon UV irradiation, producing two cyclobutane pyrimidine dimer (CPD) analogues 2 and 3. Our report here further shows that formation of these CPD species is reversible under UVC irradiation, resembling the photochemical property of the CPD species formed between two Ts. Analyzing the stability of these CPD analogues suggests that one (2) is more stable than the other (3). The TpTo conformer responsible for 2 formation is also more stable than that responsible for 3 formation, as indicated by the Gibbs free energy change calculated from the constructed Bordwell thermodynamic cycle. These different stabilities are not due to the varying photochemical properties, as proved by quantum yields determined from the corresponding photoreactions. Instead, they are ascribed to the different stacking interaction between the T and the To rings both in the TpTo dinucleotide as well as in the formed CPD analogues. Factors contributing to the ring stacking interactions are also discussed. Our proof-of-concept approach suggests that a carefully designed Bordwell cycle coupled with reversible CPD formations under UV irradiation can be very useful in studying DNA base interactions.

Using Organic Synthesis and Chemical Analysis to Understand the Photochemistry of Spore Photoproduct and Other Pyrimidine Dimers

“…Moreover, just like regular CPDs, the CPD formation in TpTo and TpX photoreactions is reversible. 35 Between the two products generated from the TpTo photoreaction, the quantum yield of 1 is 1.7-fold higher than that of 2. Because the outcome of DNA photoreactions is largely determined by the nucleobase stacking conformation before UV excitation, 54,65 the conformer responsible for the formation of 2, in which the toluenyl methyl group may hydrophobically interact with the thymine ring, is 0.11 kJ mol −1 more stable at 77 K than the conformer responsible for the formation of 3.…”

“…33 Using an SP-containing oligonucleotide, we solved the first structure of the dinucleotide SP in duplex DNA, and found that SP induces only a minor disturbance of the DNA helical structure. 34 Additionally, using thymine isosteres, we recently extended our studies to the under-standing of the CPD 35,36 and 6-4PP photochemistry, 37 and have gained interesting mechanistic insights into the formation of these two dimers.…”

“…Because the outcome of DNA photoreactions is largely determined by the nucleobase stacking conformation before UV excitation, 54,65 the conformer responsible for the formation of 2, in which the toluenyl methyl group may hydrophobically interact with the thymine ring, is 0.11 kJ mol −1 more stable at 77 K than the conformer responsible for the formation of 3. 35 The CPD structures from the TpTo and TpX photoreactions indicate that although the substituted toluene closely mimics the size and shape of thymine, 62,63 its stronger hydrophobicity may change the DNA local structure by rotating about 60° away from the TpT conformation. More interestingly, toluene or substituted toluene possesses rather different electronic structures from that of thymine due to their higher symmetries, absence of the nπ* states, and lack of tautomeric structures, 3,66 making them rather photoinert.…”