Evaluation of the Base-Pairing Properties of 5-(5-Indolylethynyl) and 5-(5-Indolyl)-2′-deoxyuridine Modified Triplex and Duplex

Indole was conjugated to deoxyuridine either directly or via ethynyl linkage to synthesize two new DNA monomers. Due to the high reactivity of indole toward electrophilic substitution reactions, unwanted iodination was observed during the oxidation step with iodine oxidizer in automated DNA synthesizer leading to an additional oligonucleotide having extra 126 mass unit beside the desired oligonucleotide. On the other hand, using CSO oxidizer ensured the formation of the wanted oligonucleotide. Oligonucleotide synthesis was confirmed by MALDI-TOF-MS analysis. Polypyrimidine strands containing non-iodinated indole nucleoside were able to form parallel triplexes, antiparallel RNA and DNA duplexes. The thermal denaturation experiments showed higher triplex stabilization for 5-(5-indolylethynyl)-2′-deoxyuridine over 5-(5-indolyl)-2′-deoxyuridine as the triple bond allows twisting to put the indole into a proper position within the triplex encouraging better π-π stacking.