PKa of cytosine on the third strand of triplex DNA: Preliminary Poisson–Boltzmann calculations
✍ Scribed by George R. Pack; Linda Wong; Gene Lamm
- Publisher
- John Wiley and Sons
- Year
- 1998
- Tongue
- English
- Weight
- 346 KB
- Volume
- 70
- Category
- Article
- ISSN
- 0020-7608
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✦ Synopsis
The energetics of formation of a triple-helical structure in homopurine᎐homopyrimidine mixtures has been modeled using Poisson᎐Boltzmann Ž . Ž . calculations. Oligomers with the sequence d TC and d AG form hydrogen-bonded n n Ž . Ž . Ž q . triple-helical structures of the form d TC и d AG и d TC . The third base, a n n n pyrimidine in this case, forms Hoogsteen-type hydrogen bonds with the purine, requiring that the cytosine residues of the third strand protonate at N3. The p K of cytosine, 4.3 in a the isolated solvated molecule, is raised by the strong electrostatic field in the triple helix.
We have done calculations of the effective p K of this cytosine and compared the results a with experimental studies of triple-helix formation as a function of pH. This provides a test of various models of the dielectric constant for triplex DNA and its local environment.