Structural characterization of ultra-stable higher-ordered aggregates generated by novel guanine-rich DNA sequences

Guanine-rich oligonucleotides (GROs) often show a strong tendency of self-aggregation based on G-quartets and thus form a family of stable higher-ordered structures such as G-wire. Such a structure is specially high-lighted due to the connection with the telomere structure, which is well known to be related with the regeneration mechanism of shortened chromosomal DNAs and to contain GRO repeats such as d(TTAGGG). In this paper, we analyze a new series of GROs by gel electrophoresis and circular dichroism and report a finding of a novel GRO sequence, d(G(11)T), which forms ultra-stable aggregates of higher-ordered structures. The structure of these aggregates was durable against the exposure to denaturants (8 M urea and 40% formamide) at the boiling temperature and even the treatment with an excess amount of nucleases, which was confirmed by assay of electrophoretic mobility. Systematic substitution of nucleotides was introduced to this sequence in order to examine the sequence effect on this phenomenon. Based on the facts thus revealed, we constructed a model for the aggregation phenomenon: successively attaching of a unitary G-quartet block through a switching of Hoogsteen-type pairing like a modular toy 'lego'. Whatever the true structure is, the unusual bonding characteristics and properties of the self-assembling of GROs must be exploited for various purposes related to nano-technology and thus worthy of further investigation from both scientific and technological interest.