title: Side chain homologation of alanyl peptide nucleic acids: pairing selectivity and stacking.
abstract: Alanyl peptide nucleic acids (alanyl-PNAs) are oligomers based on a regular peptide backbone with alternating configuration of the amino acids. All side chains are modified by covalently linked nucleobases. Alanyl-PNAs form very rigid, well defined, and linear double strands based on hydrogen bonding of complementary strands, stacking, and solvation. Side chain homology was examined by comparing a methylene linker (alanyl-PNA) with an ethylene linker (homoalanyl-PNA), a trimethylene linker (norvalyl-PNA), and PNA sequences with mixed linker length between nucleobase and backbone. Side chain homology in combination with a linear double strand topology turned out to be valuable in order to selectively manipulate pairing selectivity (pairing mode) and base pair stacking.
authors.affiliation: Institut fur Organische und Biomolekulare Chemie, Tammannstrasse 2, D-37077 Gottingen, Germany. udieder@gwdg.de
authors.forename: Ulf
authors.initials: U
authors.lastname: Diederichsen
authors.forename: Daniel
authors.initials: D
authors.lastname: Weicherding
authors.forename: Nicola
authors.initials: N
authors.lastname: Diezemann
mesh_terms: D020029:Base Pairing; D002942:Circular Dichroism; D006860:Hydrogen Bonding; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D020135:Peptide Nucleic Acids / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D020135:Peptide Nucleic Acids