Structural constraints regulating triple helix formation by A-tracts

The study concerns the propensity of triple helix formation by different DN A oligonucleotides containing long A-tracts with and without flanking G(.)C base pairs in order to probe the role of length of the A-tract and the fla nking sequences. From nuclear magnetic resonance (NMR) studies of imino pro ton spectra and circular dichroism (CD) spectroscopy of samples composed of potential tripler forming strand sequences in correct stoichiometries, we have concluded that 8-mer A-tracts flanked by G(.)C base pairs exert signif icant steric hindrance to triple helix formation. When as much as 50 mM Mg2 + was added, no triple helix: formation was observed in these samples. In c ontrast, open-ended 8-mer A-tracts formed tripler with the corresponding tw o T-8 strands under relatively mild ionic conditions (100 mM Na+). Moreover , the shorter the length of the A-tract, the less is the hindrance to form a triple helix. (C) 2000 Elsevier Science B.V. All rights reserved.