Stable DNA triple helix formation

Abstract

Triplex-forming oligonucleotides bind in the major groove of duplex DNA, generating three stranded structures containing T.AT and C+.GC triplets. Their sequence specific binding has potential uses in gene targeting but is limited by their low affinity, the requirement for low pH and the need for oligopurine targets. We have prepared nucleotide analogues to overcome these limitations and can now target some sequences that contain pyrimidine interruptions at physiological pH. We have tested the biological activity of these modified oligonucleotides. TFOs that contain multiple substitutions with positively charged groups bind with high affinity and we have explored how they interact with secondary sites.