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. 1988 Dec 23;16(24):11795–11809. doi: 10.1093/nar/16.24.11795

DNA stem-loop structures in oligopurine-oligopyrimidine triplexes.

S C Harvey 1, J Luo 1, R Lavery 1
PMCID: PMC339111  PMID: 3211749

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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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

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