An NMR study of dinucleoside monophosphates with an O4-ethylated thymine. d(e⁴TpT) and d(Tpe⁴T)

Abstract

. Can. J. Chem. 67, 109 (1989). Syntheses are described for d ( e q p~) (1) and d (~~e ? ) (2), the 04-ethylated analogues of d(TpT) (3), and mass spectrometric (FAB), 'H nuclear magnetic resonance (300 MHz), and circular dichroic data are provided for the three molecules. The [M -HI-ions as well as the aggregates [2M -HI-and, in the case of 1, [3M -HI-, are easily detected by FAB mass spectrometry operating in the negative ion mode. In contrast with the modified nucleoside, e 4 d~, the two methylene protons of the 04-ethyl groups of 1 and 2 are nonequivalent in the NMR spectra, and their chemical shift difference decreases with increasing temperature. This chemical shift difference can be related to intramolecular base stacking. The vicinal coupling constants of the sugar rings reveal an unusual shift at low temperature towards the 3'-endo conformation of the e v p unit of 1, but this shift is not noted for the pe? unit of 2.04-Alkylation of either unit of 3 effects a large reduction in the amplitude of the negative CD peak at 252 nm. The CD spectra of 1 and 2 are qualitatively similar to those of d(CpT) and d(TpC), respectively, and suggest that in some respects an 04-alkylated thymine base is "cytosine-like". The amplitudes of the positive CD peaks of 1 and 3 are reduced by 40% as the temperature is increased from 10 to 65"C, indicating the presence of some base stacking at low temperatures. However, the CD spectrum of 2 shows a much smaller reduction (<lo%).Key words: 0-alkylation, oligonucleotides, stereochemistry, NMR, mass spectrometry. inhabituel, a basse temperature, vers la conformation endo-3' de l'unitC e 4~p du composC 1; toutefois, on n'observe pas ce dCplacement pour l'unitC pe? du compose 2. La 04-alkylation de l'une ou l'autre des unites du composC 3 provoque une rkduction importante de l'amplitude du pic nCgatif observC a 252 nm, dans le spectre de DC. Les spectres de DC des composts 1 et 2 sont respectivement similaires, d'un point de vue qualitatif, a ceux des composCs d(CpT) et d(TpC) et ces rksultats suggkrent que, sous certains aspects, une thymine alkylCe en position 4 devient semblable une cytosine. Lorsqu'on augmente la temptrature de 10 a 65"C, les amplitudes des pics positifs de DC des composCs 1 et 2 sont rCduits de 40%; ces rCsultats indiquent que, i basse tempkrature, il se produit un empilement des bases. Toutefois, le spectre de DC du composC 2 montre que la rkduction est beaucoup plus faible (<lo%).Mots clPs : 0-alkylation, ~l i~o n u c l~o t i d e s , stCrCochimie, RMN, spectromCtrie de masse.[Traduit par la revue]

Synthesis and properties of DNA oligomers containing an O4-ethylated thymine. d(e4TpA), d(Ape4T), d(Ape4TpA), and d(Tpe4TpT)

“…5'-0-4,4'-Dimethoxytrityl-6-N-benzoyladenosine was obtained from Cruachem Inc. whereas the protected thymidines were synthesized and purified as described by Buchko et al (14). Chromatographic solvents were purchased from Fisher Scientific.…”

“…The extension initially requires the removal of the 5'-protecting group from 15. If TBDMS had been used for 5'-protection, then 5'-deprotection of 15 would have required tetra-n-butylammonium fluoride (TBAF), a reagent that also effects an undesirable removal of the 2-chlorophenyl group used for phosphate protection (14,16). On the other hand, the 5'-DMT group is conveniently removed by a reagent, ZnBr2, that leaves the protected phosphate intact.…”

“…Since this base is labile in acid and basic solution (9,13), these syntheses require considerable care, and for this reason our investigation was begun with molecules containing only r4Thy and the parent Thy base. Initially we described (14) the synthesis of e4TpT and Tpe4T, the 0 4 -ethylated analogues of TpT. This was followed (15) by the synthesis of the corresponding 04-isopropylated dimers, i4TpT and Tpi4T, and the trimer Tpi4TpT.…”

“…Resonance in Biological Systems, Madison, WI, August [14][15][16][17][18][19]1988. 2Author to whom correspondence may be addressed.…”

“…(4), ApT (5), and ApTpA (6), and with the oligomers discussed 3~i n c e we discuss only DNA oligomers, for convenience T~T will in Our earlier manuscripts (14,15). The data are discussed be used to represent d(TpT), and so on.…”