Sequence composition and mismatch effects on triple helix formation

Citation

Best, George C. (1995) Sequence composition and mismatch effects on triple helix formation. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/kj1w-5c31. https://resolver.caltech.edu/CaltechETD:etd-09062007-134504

Abstract

NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.

The association constants for the formation of sixteen triple helical complexes which vary at a single common position (Z•XY where Z = A, G, [...], T and XY = AT, GC, CG, TA) were determined by quantitative affinity cleavage titration. The association constants ranged from 9.5 x [...] (A•CG) to 5.6 x [...] (T•AT) at 22 °C, pH 7.0, 10 mM bis-tris, 100 mM NaCl, 250 [...] spermine. For the sequences studied, T•AT is more stable than T•GC, T•CG, or T•TA by [...] 2.3 kcal mol[...]; [...]+GC is more stable than [...]•AT, [...]•CG, or [...]•TA by [...] 1.4 kcal mol[...]; G•TA is more stable than G•AT, G•CG, or G•GC by [...] 0.8 kcal mol[...]. Under the conditions used in these experiments, none of the natural bases form triplets which offer means of recognizing the Watson-Crick CG base pair in a clearly energetically preferred manner.

The association constants for the formation of nine triple helical complexes of varying length and sequence composition were determined by quantitative DNase footprint titration. The association constants ranged from 2.0 x [...] to 3.1 x [...] at 22 °C, pH 7.0, 10 mM bis-tris, 100 mM NaCl, 250 [...]M spermine. The free energy of formation of the various triple helices was expressed as the linear combination of the free energy contributions of the various dinucleotide components of the oligonucleotide, and the value of each energetic contribution was determined. The 5'-TT-3' dinucleotide makes the greatest contribution to the stability of the triple helix, -1.2 kcal•mol[...] dinucleotide[...], while the inclusion of a [...] dinucleotide requires the payment of an energetic penalty of 0.5 kcal•mol[...] dinucleotide[...].

Thesis Files