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Nucleic Acids Research, 1988, Vol. 16, No. 24 11795-11809
© 1988

CHEMISTRY

DNA stem-loop structures in oligopurine-oligopyrimidine triplexes

Stephen C. Harvey*,, Jia Luo and Richard Lavery1

Department of Biochemistry, University of Alabama Birmingham, AL 35294, USA 1Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild 13 rue Pierre et Marie Curie, 75005 Paris, France

*To whom correspondence should be addressed

Received July 1, 1988. Revised November 13, 1988. Accepted November 13, 1988.

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.


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