Structural polymorphism of d(GA.TC)n DNA sequences. Intramolecular and intermolecular associations of the individual strands.

Alternating d(GA.TC)n sequences are highly structurally polymorphic. Most of their conformational flexibility is likely to reside in the structural properties of the individual strands themselves. In this paper the conformational behaviour of the d(GA)20 and d(TC)20 oligonucleotides was analysed. Formation of d(GA)20 intramolecular duplexes is observed at any pH value, from 8.3 to 4.6. On the other hand, intramolecular d(TC)20 duplexes are formed only under acidic conditions. The acid d(TC)20 intramolecular duplex is likely to be stabilized through the formation of C+C pairs, the thymine residues remaining unpaired. The d(GA)20 oligonucleotide also forms intermolecular duplexes which coexist with the intramolecular forms at any pH, from 8.3 to 4.6. The structural conformation adopted by the d(TC)20 oligonucleotide at neutral pH is uncertain. Under these conditions, this oligonucleotide shows an electrophoretic apparent molecular weight consistent with the formation of a bimolecular complex. However, no hydrogen bonding was observed to occur under these conditions. Implications of these results for an understanding of the molecular principles behind the conformational flexibility of alternating d(GA.TC)n sequences are discussed. The possible biological significance of these results is also discussed.