2H9S

Crystal Structure of Homo-DNA and Nature's Choice of Pentose over Hexose in the Genetic System

Summary for 2H9S

• Entry DOI: 10.2210/pdb2h9s/pdb
• Descriptor: 5'-D(*(XCT)P*(XGU)P*(XAD)P*(XAD)P*(XTH)P*(XTH)P*(XCT)P*(XGU))-3', MAGNESIUM ION (3 entities in total)
• Functional Keywords: homo-dna, homo-dna crystal structure, 2', 3'-di-deoxy-beta- d-glucopyranose, hexose nucleic acid, glucopyranosyl nucleic acid, dideoxyglucopyranose octamer, dna
• Total number of polymer chains: 2
• Total formula weight: 5101.97

Authors

Egli, M.,Pallan, P.S. (deposition date: 2006-06-11, release date: 2006-12-12, Last modification date: 2024-02-14)

Primary citation

Egli, M.,Pallan, P.S.,Pattanayek, R.,Wilds, C.J.,Lubini, P.,Minasov, G.,Dobler, M.,Leumann, C.J.,Eschenmoser, A.
Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system.
J.Am.Chem.Soc., 128:10847-10856, 2006

PubMed 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.

PubMed: 16910680
DOI: 10.1021/ja062548x

Experimental method

X-RAY DIFFRACTION (1.75 Å)