title: Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system.
abstract: An experimental rationalization of the structure type encountered in DNA and RNA by systematically investigating the chemical and physical properties of alternative nucleic acids has identified systems with a variety of sugar-phosphate backbones that are capable of Watson-Crick base pairing and in some cases cross-pairing with the natural nucleic acids. The earliest among the model systems tested to date, (4' --> 6')-linked oligo(2',3'-dideoxy-beta-d-glucopyranosyl)nucleotides or homo-DNA, shows stable self-pairing, but the pairing rules for the four natural bases are not the same as those in DNA. However, a complete interpretation and understanding of the properties of the hexapyranosyl (4' --> 6') family of nucleic acids has been impeded until now by the lack of detailed 3D-structural data. We have determined the crystal structure of a homo-DNA octamer. It reveals a weakly twisted right-handed duplex with a strong inclination between the hexose-phosphate backbones and base-pair axes, and highly irregular values for helical rise and twist at individual base steps. The structure allows a rationalization of the inability of allo-, altro-, and glucopyranosyl-based oligonucleotides to form stable pairing systems.
authors.affiliation: Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA. martin.egli@vanderbilt.edu
authors.forename: Martin
authors.initials: M
authors.lastname: Egli
authors.forename: Pradeep S
authors.initials: PS
authors.lastname: Pallan
authors.forename: Rekha
authors.initials: R
authors.lastname: Pattanayek
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Wilds
authors.forename: Paolo
authors.initials: P
authors.lastname: Lubini
authors.forename: George
authors.initials: G
authors.lastname: Minasov
authors.forename: Max
authors.initials: M
authors.lastname: Dobler
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Leumann
authors.forename: Albert
authors.initials: A
authors.lastname: Eschenmoser
mesh_terms: D004247:DNA / Q000737:chemistry*; D006601:Hexoses / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010429:Pentoses / Q000737:chemistry*
chemical_list: D006601:Hexoses; D010429:Pentoses; D004247:DNA