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

The crystal structure of a DNA fragment with the sequence d(gcGA[G](3)Agc), a shortened and mutated derivative of the VNTR sequence d(ccGA[G](4)Agg), has been determined by X-ray analyses at 1.8 A 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](n)A) (n=3-6) and d([G](n)A)(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.