Formation ofintramolecular triplex inhomopurine- homopyrimidine mirror repeats withpoint substitutions

Wehaveusedtwo-dimensional gelelectrophoresis to study thestructural transition tothetriplex Hformof sequences5'-AAGGGAGAAXGGGGTATAGGGGYAAGAGGGAA-3' whereXandYareanyDNAbases. The transition was observed atacidpHundersuperhelical stress. ForX = Y = A orX = Y = Gthesequences corresponded tohomopurine-homopyrimidine mirror repeats (H-palindrome) which areknowntoadoptthe HformunderacidpHandsuperhelical stress. Wehave shownthattheHformisactually formed forall Xand Y,though incasesother thanX = Y = AandX = Y = Gthetransition requires larger negative superhelical stress. Different substitutions require different superhelicity levels forthetransition to occur. Theoretical analysis ofthedataobtained madeit possible toestimate theenergycostoftriplex formation duetoallpossible mismatched basetriads.