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DNA stem-loop structures in oligopurine-oligopyrimidine triplexes.

S C Harvey·J Luo·R Lavery
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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 and (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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DNADeoxyriboseModels, MolecularNucleic Acid ConformationPurine NucleotidesPyrimidine NucleotidesStructure-Activity RelationshipThermodynamicsJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, P.H.S.

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S C Harvey, J Luo, R Lavery. 1988-12-23. DNA stem-loop structures in oligopurine-oligopyrimidine triplexes.. https://doi.org/10.1093/nar%2F16.24.11795

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