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Nucleic Acids Symposium Series 2006 50(1):39-40; doi:10.1093/nass/nrl020
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© 2006 Oxford University Press

Multiplex formation of repetitive sequences d([G]nA)m through non-WC pairings: Crystal structure of d(gcGAGGGAgc)

Yoshiteru. Sato1, Kenta Mitomi1, Hiromu Sugiyama1, Satoru Shimizu1, Ella C. M. Juan1, Jiro Kondo2 and Akio Takénaka1

1 Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan, 2 IBMC-CNRS, Université Louis Pasteur, Strasbourg, France

The crystal structure of a DNA fragment with the sequence d(gcGA[G]3Agc), a shortened and mutated derivative of the VNTR sequence d(ccGA[G]4Agg), has been determined by X-ray analyses at 1.8 Å resolution to investigate structures and mechanisms of a non-coding DNA. This sequence forms an antiparallel duplex with two WC pairings at the both ends and six consecutive non-WC pairings in the major part. Based on this structure, d(GA[G]nA) (n=3–6) and d([G]nA)m (n>1 and m>1) were designed. It is expected that all bases form non-WC pairs when the DNA fragments adapt antiparallel duplex. Electrophoresis experiments showed that these DNA fragments form not only duplexes, but also multiplexes such as quadruplexes, octaplexes, and so on.


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