Structure and mechanism of formation of the H-y5 isomer of an intramolecular DNA triple helix

H-DNA, thought to play a regulatory role in transcription, exists in two is omeric forms, H-y3 and H-y5. We present the first solution structure of a D NA fragment representing the H-y5 fold. The structure shows the H-y5 triple helix, and for the First time how in an H-DNA isomer the purine strand ext ension interacts with the tripler loop. It gives direct insight into the me chanism of H-DNA formation, and explains a host of biochemical and biophysi cal data on the relative stability of the H-DNA isomers, in addition, the o bserved interaction of the purine strand extension and the tripler loop pro vides new dues to the design of damp-type triple helix-forming oligonucleot ides.