John Kiely

Molecular dynamics and NMR studies of single-stranded PNAs

Abstract 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 °C. In the major form, the side chain carbonyl group points toward the glycine, which places the methylene protons in proximity to the 2-aminoethyl protons. The minor form places its side chain carbonyl group away from the glycine, and the methylene protons are close in space to the glycine α protons. The PNA CT-dimer has multiple rotamers at 20 °C. In contrast, a NOESY spectrum taken from an octamer indicates only a single conformer in solution at 40 °C.

Decapitation of a 5' capped RNA by an antisense copper complex conjugate

Abstract This report presents the synthesis and 5 cap reactivity of an antisense oligodeoxynucleotide equipped with two equivalents of an analog of N-(2-mercaptopropionyl)glycine (MPG). MPG is a peptide derivative which coordinates to copper(II) in solution as a monomeric species via the thiol, amide, and carboxylate groups. Decapitation of a complementary 5 capped RNA was observed for the oligonucleotide-ligand conjugate coordinated to copper.

Chapter 30. Recent Advances in Antisense Technology

Publisher Summary The treatment of disease, by the modulation of biological processes, can be undertaken at the level of the gene, the messenger RNA (mRNA) or the protein. Since the 1970s, proteins associated with disease pathology have been the major focus of drug discovery efforts. More recently, however, the goal of creating specific drugs to act directly on the mRNA is now the focus of significant research and development efforts. This paradigm is a method of affecting the expression of a gene, by interfering with the translation of the genes mRNA into a functional protein. This exploits the susceptibility of formally single stranded mRNA to undergo sequence-specific high-affinity binding to a complementary oligonucleotide sequence called the anti-sense sequence, via Watson-Crick hydrogen bonding. By binding to the mRNA, the anti-sense oligomer can, by any one of the several mechanisms, interfere with and arrest cytosolic translation of the mRNA into protein. Each mechanism assumes that the anti-sense oligomer has found and bound to the target mRNA. The first is translational (ribosomal) blockade, where the antisense strand hybridizes to the sense strand and prevents the ribosome from completely reading the mRNA message, resulting in the synthesis of truncated nonfunctional protein. The second is binding of a DNA-like anti-sense oligonucleotide to the mRNA and activation of RNase H, an enzyme that specifically cleaves the RNA strand of a RNA-DNA duplex. The cleavage, by RNase H of the RNA strand, results in the destruction of the message and arrest of protein production.