Alternating polypurine d(GA)n, sequences exhibit a considerable polymorphism. 
Here we report that alpha d(GA) x d(GA) sequences form an antiparallel stranded 
duplex DNA at neutral pH. The spectroscopic, electrophoretic and thermodynamic 
properties of the alpha/beta chimeric oligodeoxynucleotide, 5'-d(GA)4(T)4 alpha 
d(AG)4T-3', support the formation of a hairpin structure with antiparallel 
strands in the stem. The optical properties of this novel antiparallel structure 
are different from the parallel stranded homoduplex formed by d(GA)G7. This 
alpha/beta hairpin has a remarkably high Tm of 44.5 degrees C in 0.4 M NaCl with 
a van't Hoff enthalpy comparable to that of a parallel d(GA)n duplex. Base 
pairing was confirmed by T4 polynucleotide ligase catalyzed joining of the 
alpha/beta hairpin to an antiparallel bimolecular duplex and by non-denaturing 
gel electrophoresis using duplexes containing sequence constraints. Both support 
the presence of alphaG-G and alphaA-A base pairing in the antiparallel 
5'-d(GA)4(T)4 alpha d(AG)4T-3' intramolecular duplex. This study adds to the 
polymorphic nature of alternating d(GA)n sequences as well as providing novel 
homopurine base pairing approaches for probing polypurine polypyrimidine 
sequences.