Highly Stable Pyrimidine-Motif Triplex Formation at Physiological pH Values by a Bridged Nucleic Acid Analogue

Formation of a stable triplex DNA molecule at physiological pH values is a highly desirable phenomenon in molecular biology and medicinal chemistry because of its great importance in regulation of gene expression, site-specific cleavage of DNA, gene mapping and isolation, maintenance of folded chromosome conformations, and gene-targeted mutagenesis.[ 1] In a pyrimidine-motif triplex DNA, the (homopyrimidine) triplex-forming oligonucleotide (TFO) binds with the homopurine tract of the target duplex DNA in a sequencespecific manner through Hoogsteen hydrogen bonds to form T·A:T and C+·G:C triads. However,  formation of the C+·G:C triad is dependent on the cytosine protonation, which is only favorable at acidic pH values (pKa=4.5) and, therefore, homopyrimidine-motif triplexes are extremely unstable at physiological pH values, which severely restricts their biological application.