A comparative study of the thermal stability of oligodeoxyribonucleotides containing 5-substituted 2'-deoxyuridines

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Abstract
Two series of modified oligonucleotides based on the self-complementary dodecamer d(CGCTAATTAGCG) were synthesized. The first contained the -C≡CCH2R linker at C5 of deoxyuridine at position 4 (T*) of d(CGCT*AATTAGCG) and the second contained the -SR linker. The goal of the study was to evaluate and compare these two types of side chains for suitability as tethers for linking reporter groups to oligonucleotides. Our primary concern was how these tethers would effect duplex stability. The modified nucleosides were synthesized by palladium-mediated coupling reactions between the substituted alkyne and 5′-(4,4′-dimethoxytrityl)-5-iodo-2′-deoxyuridine and between a disulfide and 5-chloromercurio-2′-deoxyuridine. The C5 deoxyuridine side chains evaluated included C≡CCH3, C≡CCH2NHC(O)CH3, C≡CCH2N(CH3)2, C≡CCH2N-HC(O)C5H4N, C≡CCH2NHC(O)C10H15, SCH3, SC6H5 and SCH2CH2NHC(O)CH3. The nucleosides containing these substituents were incorporated into oligodeoxyribonucleotides by standard phosphoramidite methodology. Melting studies demonstrated that the sequence containing the C≡CCH3 side chain had the highest Tm value (59.1°C) in comparison with the control sequence (Tm = 55.2°C) and that any additional substituent on C3 of the propynyl group lowered the Tm value relative to propynyl. Nevertheless, even the most destabilizing substituent, adamantylcarbamoyl, yielded an oligodeoxyribonucleotide that dissociated with a Tm of 54°C, which is only 1.2°C less than the control sequence. In contrast, the thioether substituents led to lower Tm values, ranging from as low as 45.1°C for SPh up to 52.2°C for SMe. Replacing the methyl of the SMe substituent with a CH2CH2NHC(O)CH3 tether led to no further reduction in melting temperature. The Tm value of the CH2CH2NHC(O)CH3-containing oligonucleotide was less than the natural sequence by 1.6°C/substituent. This is sufficiently small that it is anticipated that the C5 thioether linkage may be as useful as the acetylenic linkage for tethering reporter groups to oligonucleotides. More importantly, the thioether linkage provides a means to position functional groups to interact specifically with opposing complementary (target) sequences.

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