Revised Manuscript ReceivedSeptember 29, 1995® abstract: A 1.5 ns long molecular dynamics simulation was conducted to compare the structure and stability of a model DNA triplex in saline solution with that found from experiments. The model DNA was an antiparallel py-pu-pu (CG-G) 7-mer structure which contained a GC-T mismatch triplet at the middle of the sequence. The local conformation of the mismatch triplet and the effects of this triplet on the global helical structure suggest that the GC-T triplet forms stable hydrogen bonds and showsdistortions from an in-plane alignment. The overall rms deviation of the triplex is similar to one without a mismatch, although the thymine base in the mismatch triplet shows significantly higher mobility. A high coordination probability for water between the G and T bases in the mismatch triplet was observed to have an effect on the stability of non-hydrogen-bonded base pairs. Average helical parameters, sugar pucker, and backbone dihedral angles indicate that the CG-G triplets on the 3'side of the mismatch triplet possess different structural and dynamical properties than that of the 5'side. These observations are consistent with recently available experimental results and provide an interpretation of the observed experimental structure. They also suggest that inclusion of explicit water molecules is necessary in order to understand and predict the interaction between the third strand and duplex DNA.

There has been significant progress in both experimental (Greenberg & Dervan, 1995; Radhakrishnan & Patel, 1993; Beal & Dervan, 1991; Durland et al., 1991; Moser & Dervan, 1987; Rajagopal & Feigon, 1989) and theoretical (Weera-singhe et al., 1995; Piriou et al., 1994; Cheng & Pettitt, 1992a; Laughton & Neidle, 1992) studies toward the understanding of the structure, stability, and thermodynamics of triplex formation. Findings from these studies have given insight into the possibleapplications in sequencingand the control of gene expressionthrough binding of a third strand to duplex DNA (Sun & Helene, 1993; Wilson et al „1993; Helene & Toulme, 1990; Letai et al., 1988). Most of the theoretical studies have focused on the binding of a third strand to a homopolymer purine—pyrimidine (pu-py) duplex (Cheng & Pettitt, 1992b). These early assessments were important in the understanding of the nature of binding of a third strand to a duplex sequence. In order to further our knowledge of the formation of triplexes, one has to under-stand the factors behind the stability of different triplexes especially with nonhomo-pu-pyduplexes in solution. The molecular dynamics (MD) simulationmethod has been used successfullyin studies of a variety of biological systems, including proteins (McCammon & Harvey, 1987), duplex DNA (Swaminathan et al., 1991; Forester & Mc-Donald, 1991), and triplex DNA (Mohan et al., 1993b; Weerasinghe et al., 1995) in aqueous solutions. In principle, comparison of the simulation with experiments should be able to provide evidence regarding the quality of the initial structure of the triplex and the force field/protocol, as well as a structural and dynamical description of the behavior of the triplex DNA in salt solutions. A previous simulation of