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Published May 1, 1995 | public
Journal Article

Energetics of Formation of Sixteen Triple Helical Complexes Which Vary at a Single Position Within a Purine Motif


The association constants for the formation of sixteen purine purine pyrimidine triple helical complexes which vary at a single common position (Z . XY where Z = A, G, C, T and XY = AT, GC, CG, TA) were determined by quantitative DNAse I footprint titration. The sequence context in which the sixteen pairings Z . XY were studied is 5'-d(AGGGGAGGGGXGGGA)-3' within a 648 base pair DNA fragment. The association constants for the purine-rich oligonucleotides 5'-d(TGGGZGGGGTGGGGT)-3' ranged from 2.7 x 10^5 (Z . XY = G . TA) to 8.9 x 10^7 M^(-1) (Z . XY = T . AT) at 37 degrees C, pH 7,4, 50 mM tris acetate, 10 mM NaCl, and 3 mM MgCl_2. For the sequences studied, T . AT is more stable than T . CG, T . GC, and T . TA by greater than or equal to 1.2 kcal mol^(-1); A . AT is more stable than A . CG, A . GC, and A . TA by greater than or equal to 1.2 kcal mol^(-1); and G . GC is more stable than G . AT, G . CG, and G . TA by greater than or equal to 2.1 kcal mol^(-1). The triplet T . CG is greater than or equal to 1.5 kcal mol^(-1) more stable than the other three bases opposite a CG base pair.

Additional Information

© 1995 American Chemical Society. Received December 12, 1994. Publication Date: May 1995. Abstract published in Advance ACS Abstracts, April 15, 1995. We thank Dr. Peter Bed for the plasmids used in this study and for helpful discussions. We are grateful for generous support from the National Institutes of Health (GM35724) and the Office of Naval Research and for a National Science Foundation predoctoral fellowship to W.A.G.

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