A Parallel Right-Handed Duplex of the Hexamer d(TpTpTpTpTpT) with Phosphate Triester Linkeges

Article abstract of DOI:10.1021/ja00247a015

We show in this work that stable parallel thymine-thymine (T-T) base pairs can be formed in aqueous solution.Initially, this observation was made with 3',5'-di-O-acetylthymidine in water which showed an imino resonance at 13.45 ppm in the 1H NMR spectrum.Using the nucleoside diphosphate d(pTp), the formation of T-T base pairs could only be induced via methylation of the phosphate groups.This leads to the suggestion that intramolecular electrostatic phosphate-phosphate repulsion preludes T-T base pairing for unmodified d(pTp).It is shown that T-T pairing is also manifest on the dinucleotide level, provided that the phosphate groups are methylated.Using the dinucleoside phosphate 1 which was separated in its diastereomeric forms, it was shown that the miniduplex melts at T_m ca. 30 deg C.Furthermore, it was shown that the duplex of 1 is parallel.From the detailed conformational analysis of the individual diastereomers it follows that the duplex has a right-handed helical sense, since the backbone bonds C_4'-C_5' and C_5'-O_5' are preferentially γ⁺ and β^t, and the furanoses reside primarily in the south conformation.With the hexamer d(TpTpTpTpTpTp), it was shown that T-T pairing also occurs on the hexanucleotide level, after methylation of the phosphate groups.The resulting duplex has a T_m value of approximately 65 deg C as was established with UV hyperchromicity and with variable-temperature 500-MHz 1H NMR.It could be clearly established that the duplex is parallel.Molecular modelling studies on the duplex of phosphate-methylated d(TpTpTpTpTpT) yielded a remarkably slim, parallel structure with about eight residues per turn.The possible relevance of these alternative DNA-like duplexes is briefly mentioned.