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Journal of Biochemistry Advance Access originally published online on October 24, 2006
Journal of Biochemistry 2006 140(6):759-762; doi:10.1093/jb/mvj213
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© 2006 The Japanese Biochemical Society.

Rapid Communication

DNA Octaplex Formation with an I-Motif of Water-Mediated A-Quartets: Reinterpretation of the Crystal Structure of d(GCGAAAGC)

Yoshiteru Sato1, Kenta Mitomi1, Tomoko Sunami1, Jiro Kondo2 and Akio Takénaka1,*

1 Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuda, Midori-ku, Yokohama 226-8501 and 2 Institut de Biologie Moléculaire et Cellulaire du CNRS, Université Louis Pasteur, 15 rue René Descartes, Strasbourg F-67084, France

* To whom correspondence should be addressed. Tel: +81-45-924-5709, Fax: +81-45-924-5748, E-mail: atakenak{at}bio.titech.ac.jp


  Abstract

The crystal structure of the tetragonal form of d(gcGAAAgc) has been revised and reasonably refined including the disordered residues. The two DNA strands form a base-intercalated duplex, and the four duplexes are assembled according to the crystallographic 222 symmetry to form an octaplex. In the central region, the eight strands are associated by I-motif of double A-quartets. Furthermore, eight hydrated-magnesium cations link the four duplexes to support the octaplex formation. Based on these structural features, a proposal that folding of d(GAAA)n, found in the non-coding region of genomes, into an octaplex can induce slippage during replication to facilitate length polymorphism is presented.

1 Lowercase characters indicate that they can form a Watson-Crick G:C or C:G pair when the two fragments are aligned in an anti-parallel fashion.

2 Asterisk represents the counter strand of the duplex around the two-fold axis.


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