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Phosphodiester/Phosphorothioate/Methylphosphonate Oligonucleotide Triplexes-An Assesment for Stability

L. M. Tsay, Shanshan Lin, L.-S. Kan

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Abstract

The results of UV mixing titration and melting temperature experiments indicate that oligomers with a basic sequence of 5'-d-T-(C-T-)2C-(T-)4C-(T-C-)2T ([CC]) form a hairpin type triplex with a ribo-oligomer, 5'-r-A-(G-A-)2G ([AG-6)) in 1 M NaCI, pH 4.5. The stability of formed hairpin triplex increases as the increase of the number of cytidine base replaced by 5-methylcytidine in [CC]. This system is also used to test the stability of triplex formation using [CC] with methyl phosphonate and phosphorothioate linkage toward both ribo-[AG-6] and deoxyribo-[AG-6] targets. The relative order of stability of hairpin type triplex formation is that [CC] with phosphodiester ＞ phosphorothioate ≈ methyl phosphonate at the aforementioned experimental conditions.

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What this paper is about

The results of UV mixing titration and melting temperature experiments indicate that oligomers with a basic sequence of 5'-d-T-(C-T-)2C-(T-)4C-(T-C-)2T ([CC]) form a hairpin type triplex with a ribo-oligomer, 5'-r-A-(G-A-)2G ([AG-6)) in 1 M NaCI, pH 4.5. The stability of formed hairpin triplex increases as the increase of the number of cytidine base replaced by 5-methylcytidine in [CC]. This system is also used to test the stability of triplex formation using [CC] with methyl phosphonate and phosphorothioate linkage toward both ribo-[AG-6] and deoxyribo-[AG-6] targets. The relative order of stability of hairpin type triplex formation is that [CC] with phosphodiester ＞ phosphorothioate ≈ methyl phosphonate at the aforementioned experimental conditions.

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Available abstract

The results of UV mixing titration and melting temperature experiments indicate that oligomers with a basic sequence of 5'-d-T-(C-T-)2C-(T-)4C-(T-C-)2T ([CC]) form a hairpin type triplex with a ribo-oligomer, 5'-r-A-(G-A-)2G ([AG-6)) in 1 M NaCI, pH 4.5. The stability of formed hairpin triplex increases as the increase of the number of cytidine base replaced by 5-methylcytidine in [CC]. This system is also used to test the stability of triplex formation using [CC] with methyl phosphonate and phosphorothioate linkage toward both ribo-[AG-6] and deoxyribo-[AG-6] targets. The relative order of stability of hairpin type triplex formation is that [CC] with phosphodiester ＞ phosphorothioate ≈ methyl phosphonate at the aforementioned experimental conditions.

Key concepts: Phosphodiester bond, Phosphonate, Oligonucleotide, Chemistry, Deoxyribonucleotide, Cytidine, Titration, Oligomer

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