DNA stem-loop structures in oligopurine-oligopyrimidine triplexes

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Abstract
Closed circular DNA containing polypurine-polypyrimidine sequences can adopt a triple helical stem-loop structure under supercoiling pressure. We describe an automated procedure for building model loops and its application to the investigation of the polypyrimidine loop at the end of such a triple helical stem. All possible combinations of 3′-stacked and 5′-stacked structures have been examined for loops containing three, four, five, and six nucleotides. The lowest energy conformation is a four-membered loop with all bases stacked on the strand at the 3′ end of the loop. The model predicts that sequences (GA) n (GGGA) n arid (GAAA) n should form the stem-loop structure more easily than (GGA) n and (GAA) n It is also predicted that when a polypurine polypyrimidine sequence converts from a double stranded structure to a triple stranded stem-loop, the most favorable conditions are those where an even number of basepairs makes the transition. Experimental tests of these predictions are also described.