Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system

Martin Egli*, Pradeep S. Pallan, Rekha Pattanayek, Christopher J. Wilds, Paolo Lubini, George Minasov, Max Dobler, Christian J. Leumann, Albert Eschenmoser

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

86 Scopus citations


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-β-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 30-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.

Original languageEnglish (US)
Pages (from-to)10847-10856
Number of pages10
JournalJournal of the American Chemical Society
Issue number33
StatePublished - Aug 23 2006

ASJC Scopus subject areas

  • Catalysis
  • General Chemistry
  • Biochemistry
  • Colloid and Surface Chemistry


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