The Triplex-Hairpin Transition in Cytosine-Rich DNA
Anton S. Petrov 1, Gene Lamm 1 and George R. Pack 1*
1 University of Louisville
* To whom correspondence should be addressed. E-mail: george.pack{at}louisville.edu.
Submitted on March 29, 2004
Revised on July 4, 2004
Accepted on 3 September 2004
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Abstract |
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We present a theoretical study of the self-complementary single-stranded 30-mer d (TC*TTC*C*TTTTCCTTCTC*CCGAGAAGGTTTT) (PDB ID: 1b4y) that was designed to form an intramolecular triplex by folding back twice on itself. At neutral pH the molecule exists in a duplex hairpin conformation, while at acidic pH the cytosines labeled by * are protonated, forming Hoogsteen hydrogen bonds with guanine of a GC Watson-Crick base pair to generate a triplex. As a first step in an investigation of the energetics of the triplex-hairpin transition, we applied the Bashford-Karplus multiple site model of protonation to calculate the titration curves for the two conformations. Based on these data, a two-state model is used to study the equilibrium properties of transition. Although this model properly describes the thermodynamics of the protonation-deprotonation steps that drive the folding-unfolding of the oligomer, it cannot provide insight into the time-dependent mechanism of the process. A series of MD simulations using the ff94 force field of the AMBER 6.0 package was therefore run to explore the dynamics of the folding/unfolding pathway. The MD method was combined with Poisson-Boltzmann calculations to determine when a change in protonation state was warranted during a trajectory. This revealed a sequence of elementary protonation steps during the folding/unfolding transition and suggests a strong coupling between ionization and folding in cytosine-rich triple helical triplexes.
Key Words:
Poisson-Boltzmann, cytosine protonation, electrostatics, pKa calculations, triple helix
