MOLECULAR-DYNAMICS AND NMR-STUDIES OF SINGLE-STRANDED PNAS

Proton NMR spectroscopy and molecular dynamics simulations are employed to investigate the conformations of PNA monomers, a dimer and an octamer. The monomers exist as a 70:30 mixture of two amide rotamers interconverting slowly on the NMR time scale at 20 degrees C. In the major form, the side chain carbonyl soup points toward the glycine, which places the methylene protons in proximity to the 2-aminoethyl protons. The minor form places its side chain carbonyl soup away from the glycine, and the methytene protons are close in space to the glycine a protons. ?he PNA CT-dimer has multiple rotamers at 20 degrees C. In contrast, a NOESY spectrum taken from an octamer indicates only a single conformer in solution at 40 degrees C.