Singleton, Scott F. and Dervan, Peter B. (1992) Influence of pH on the equilibrium association constants for oligodeoxyribonucleotide-directed triple helix formation at single DNA sites. Biochemistry, 31 (45). pp. 10995-11003. ISSN 0006-2960. https://resolver.caltech.edu/CaltechAUTHORS:20160510-142113533
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Abstract
The energetics of oligodeoxyribonucleotide-directed triple helix formation for the pyrimidine.purine.pyrimidine structural motif were determined over the pH range 5.8-7.6 at 22 degrees C (100 mM Na^+ and 1 mM spermine) using quantitative affinity cleavage titration. The equilibrium binding constants for 5'-TTTTTCTCTCTCTCT-3' (1) and 5'-TTTTTm^5CTm^5CTm^5CTm^5CTm^5CT-3' (2, m^5C is 2'-deoxy-5-methylcytidine) increased by 10- and 20-fold, respectively, from pH 7.6 to 5.8, indicating that the corresponding triple-helical complexes are stabilized by 1.4 and 1.7 kcal.mol-1, respectively, at the lower pH. Replacement of the five cytosine residues in 1 with 5-methylcytosine residues to yield 2 affords a stabilization of the triple helix by 0.1-0.4 kcal.mol^(-1) over the pH range 5.8-7.6. An analysis of these data in terms of a quantitative model for a general pH-dependent equilibrium transition revealed that pyrimidine oligonucleotides with cytidine and 5-methylcytidine form local triple-helical structures with apparent pKa's of 5.5 (C+GC triplets) and 5.7 (m^5C+GC triplets), respectively, and that the oligonucleotides should bind to single sites on large DNA with apparent affinity constants of ~10^6 M^(-1) even above neutral pH.
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| Additional Information: | © 1992 American Chemical Society. Received July 10, 1992. This research was supported by National Institutes of Health Grant GM-35724 and by a Ralph M. Parsons Foundation prcdoctoral fellowship to S.F.S. | |||||||||
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| Issue or Number: | 45 | |||||||||
| Record Number: | CaltechAUTHORS:20160510-142113533 | |||||||||
| Persistent URL: | https://resolver.caltech.edu/CaltechAUTHORS:20160510-142113533 | |||||||||
| Official Citation: | Influence of pH on the equilibrium association constants for oligodeoxyribonucleotide-directed triple helix formation at single DNA sites Scott F. Singleton and Peter B. Dervan Biochemistry 1992 31 (45), 10995-11003 DOI: 10.1021/bi00160a008 | |||||||||
| Usage Policy: | No commercial reproduction, distribution, display or performance rights in this work are provided. | |||||||||
| ID Code: | 66940 | |||||||||
| Collection: | CaltechAUTHORS | |||||||||
| Deposited By: | Victoria Brennan | |||||||||
| Deposited On: | 18 May 2016 22:18 | |||||||||
| Last Modified: | 26 Nov 2019 11:15 |
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