RELATIVE STABILITY OF AT AND GC PAIRS IN PARALLEL DNA DUPLEX FORMED BY A NATURAL SEQUENCE

The low-cooperative melting of parallel DNA formed by a natural 40 bp long sequence from Drosophila: 5'-d(TGATTGATCGATTGTTTGCATGCACACGTTTTTG TGAGCG)-3' 5'-d(ACTAACTAGCTAACAAACGTACGTGTGCAAAAACACTCGC)-3' that poss esses a normal nucleotide content was studied by using the special met hod of measuring the fluorescence of its complex with acriflavine as w ell as by conventional thermal denaturation. Acriflavine allows discri mination of the melting of AT and GC pairs because its fluorescence is quenched by neighbouring G bases. We have observed that about 40% of AT pairs melt at 14-degrees-C while the remainder melt at 42-degrees-C . The GC pairs remain stable up to approximately 40-degrees-C and melt at 54-degrees-C. The higher stability of GC pairs suggests the format ion of cis Watson-Crick pairs in parallel DNA.