The long repetitive polypurine/polypyrimidine sequence (TTCCC)48 forms DNA triplex with PU-PU-PY base triplets in vivo

Abstract

Polypurine/polypyrimidine repetitive sequences occur with high frequency in eucaryotic genomes, particularly around transcription units. Since such sequences are known to adopt triple stranded-structures under appropriate conditions in vitro, it is of major interest to know if they occur in vivo, and thus if they can have some biological importance by inducing structural constraints in the genomic DNA. To this end, we have isolated a (TTCCC)48 sequence, present in the promoter of an avian gene, and tested its ability to form PU-PY-PY and PU-PU-PY triple helices in vitro, through the oligonucleotide gel shift technique and single strand-specific nuclease footprinting. We have then developed an oligonucleotide protection assay, which can be adapted to in vivo investigations. This strategy leads us to conclude that in vivo conditions allow preponderant formation of triplex of the PU-PU-PY class.