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Published February 1995 | public
Journal Article

Energetics of Formation of Sixteen Triple Helical Complexes Which Vary at a Single Position within a Pyrimidine Motif


The association constants for the formation of 16 pyrimidine•purine•pyrimidine triple helical complexes which vary at a single common position (Z.XY where Z = A, G, ^(Me)C, T and XY = AT, GC, CG, TA) were determined by quantitative affinity cleavage titration. The sequence context in which the 16 pairings Z•XY were studied is 5'-d(AAAAAGAGAXAGAGA)-3' within a 242 base pair DNA fragment. The association constants of four pyrimidine rich oligodeoxyribonucleotides, 5'-d(TTTTT^(Me)CT^(Me)CTZT^(Me)CT^(Me)CT)-3', ranged from 3.8 x 10^4 M^(-1) (Z•XY = A.CG) to 5.6 x 10^7 M^(-1) (Z•XY = T•AT) at 22 °C, pH 7.0; 10 mM bis-tris, 100 mM NaCl, 250 µM spermine. For the sequences studied, T.AT is more stable than T•GC, T•CG, or T•TA by greater than or equal to 2.3 kcal mol^(-1); ^(Me)C•GC is more stable than ^(Me)C•AT, ^(Me)C•CG, or ^(Me)C•TA by greater than or equal to 1.4 kcal mol^(-1); G•TA is more stable than G•AT, G•CG, or G•GC by greater than or equal to 0.8 kcal mol^(-1).

Additional Information

© 1995 American Chemical Society. Received September 12, 1994. Publication Date: February 1995. Abstract published in Advance ACS Abstracts, January 1, 1995. We are grateful to the National Institutes of Health (GM 35724) for support and the Fannie and John Hertz Foundation for a predoctoral fellowship to G.C.B. We thank S. Priestley for careful reading of the manuscript.

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