Water mediated Dickerson-Drew-type crystal of DNA dodecamer containing 2'-deoxy-5-formyluridine.
To investigate the role of divalent cations in crystal packing, a Dickerson-Drew-type dodecamer with the sequence d(CGCGAATXCGCG), containing 2'-deoxy-5-formyluridine at X, was crystallized under several conditions with Ba(2+) ion instead of Mg(2+) ion. The crystal structure is isomorphous with the original Dickerson-type crystal containing Mg(2+) ion. In the Mg(2+)-free crystals, however, a five-membered ring of water molecules occupies the same position as the magnesium site found in the Mg(2+)-containing crystals, and connects the two duplexes similarly to the hydrated Mg(2+) ion. It has been concluded that the five-membered water molecules can take the place of the hydrated magnesium cation in crystallization. The 5-formyluracil residues form the canonical Watson-Crick pair with the opposite adenine residues.
Tsunoda
Masaru
M
Department of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan.
Kondo
Jiro
J
Karino
Naoko
N
Ueno
Yoshihito
Y
Matsuda
Akira
A
Takenaka
Akio
A
D001464:Barium / Q000494:pharmacology; D020029:Base Pairing; D002413:Cations, Divalent / Q000494:pharmacology; D003460:Crystallization; D018360:Crystallography, X-Ray; D003857:Deoxyuridine / Q000031:analogs & derivatives* / Q000737:chemistry*; D008274:Magnesium / Q000494:pharmacology; D009690:Nucleic Acid Conformation / Q000187:drug effects; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D014867:Water / Q000737:chemistry* / Q000494:pharmacology
D002413:Cations, Divalent; D009838:Oligodeoxyribonucleotides; D014867:Water; D001464:Barium; C061519:5-formyl-2'-deoxyuridine; D008274:Magnesium; D003857:Deoxyuridine