Synthesis and properties of triple helix-forming oligodeoxyribonucleotidescontaining 7-chloro-7-deaza-2 '-deoxyguanosine

Multiple incorporations of 7-chloro-7-deaza-2'-deoxyguanosine in place of 2 '-deoxyguanosine have been performed into a triple helix-forming oligodeoxy ribonucleotide involving a run of six contiguous guanines designed to bind in a parallel orientation relative to the purine strand of the DNA target. The ability of these modified oligodeoxyribonucleotides to form triple heli ces in a buffer containing monovalent cations was studied by UV-melting cur ves analysis, gel shift assay and restriction enzyme protection assay. In t he presence of Na+, the incorporation of two, three or five modified nucleo sides in the third strand has improved the efficacy of formation of the tri pler as compared to that formed with the unmodified oligonucleotide. The st abilities of the three modified triplexes were similar. The coupling of 6-c hloro-2-methoxy-9-(omega -hexylamino)-acridine to the 5'-end of the oligonu cleotides containing modified nucleosides led to an increase in tripler sta bility similar to that observed when the acridine was added to the 5'-end o f the unmodified oligonucleotide. In the presence of KC, only the oligodeox yribonucleotides containing modified G retained the ability to form triple helices with the same efficiency. The incorporation of the modified nucleos ide has two effects: (i) it decreases TFO self-association, and (ii) it sli ghtly increases tripler stability. The enhanced ability of the modified oli gonucleotides containing 7-chloro-7-deaza-2'-deoxyguanosine over the parent oligomer to form triple helices was confirmed by inhibition of restriction enzyme cleavage using a circular plasmid containing the target sequence. ( C) 2001 Elsevier Science Ltd. All rights reserved.