title: DNA stem-loop structures in oligopurine-oligopyrimidine triplexes.
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.
authors.affiliation: Department of Biochemistry, University of Alabama, Birmingham 35294.
authors.forename: S C
authors.initials: SC
authors.lastname: Harvey
authors.forename: J
authors.initials: J
authors.lastname: Luo
authors.forename: R
authors.initials: R
authors.lastname: Lavery
mesh_terms: D004247:DNA; D003855:Deoxyribose; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011685:Purine Nucleotides; D011742:Pyrimidine Nucleotides; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D011685:Purine Nucleotides; D011742:Pyrimidine Nucleotides; C051802:triplex DNA; D003855:Deoxyribose; D004247:DNA