Antiparallel DNA duplex formation between alternating alpha d(GA)n and beta d(GA)n sequences.
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.
Kalisch
B W
BW
Department of Medical Biochemistry, Faculty of Medicine, The University of Calgary, Alta, Canada.
Germann
M W
MW
van de Sande
J H
JH
D000225:Adenine / Q000737:chemistry; D001482:Base Composition; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D018900:Dinucleotide Repeats; D006147:Guanine / Q000737:chemistry; D006358:Hot Temperature; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry
D009838:Oligodeoxyribonucleotides; D006147:Guanine; D004247:DNA; D000225:Adenine