Hoogsteen versus Reversed-Hoogsteen Base Pairing: DNA Triple Helices

Recently, oligonucleotides have been shown to inhibit transcription in genes by triple helix or triplex formation in vitro and in vivo. A better understanding of the forces that stabilize triplex structures will be important in developing applications of this method of genetic medication to arbitrary sequences. Therefore, base pairings and strand orientations for homogeneous d(T·A·T)₂₇ and d(C·G·G)₂₇ triplexes were examined. The method was extended to triplex models formed by c-myc gene promoter region and complementary oligonucleotides. Templates of a single plane with three bases were constructed and used in a simple geometric replication based on experimental geometric parameters. Minimizations and quenched molecular dynamics simulations were performed on the model systems. The estimated accessibility of the major groove for countercation coordination was obtained by calculating the effective accessible surface areas of backbone phosphate oxygen atoms. Free energy calculations of the solvation/desolvation penalty on single strands, duplexes, and the stereoisomeric triplexes have been performed. They were combined with corresponding enthalpic terms so that the results could be discussed in a more realistic aspect. For d(T·A·T)₂₇ triplexes, results from both the internal potential energy and solvation free energy calculations contribute to the experimentally known base pairing and strand orientation. Solvation is found to determine the strand orientation for d(C·G·G)₂₇ triplexes with either Hoogsteen or reversed-Hoogsteen base pairing between the two purine strands being possible. We have compared the d(C·G·G)₂₇ triplexes by computing the hydrogen-hydrogen distances which may be useful in verifying these models by future NMR/NOE studies. Using these homopolymers the orientation of oligonucleotides bound to the c-myc gene promoter site is shown to also be dominated by the forces of solvation.