CONFORMATIONAL PROPERTIES OF DNA DODECAMERS CONTAINING 4 TANDEM REPEATS OF THE CNG TRIPLETS

We studied DNA dodecamers (CAG)(4), (CCG)(4), (CGG)(4) and (CTG)(4) by CD spectroscopy and polyacrylamide gel electrophoresis, Each dodecame r adopted several ordered conformers which denatured in a cooperative way, Stability of the conformers depended an the dodecamer concentrati on, ionic strength, temperature and pH, The dodecamers, having a pyrim idine base in the triplet center, generated foldbacks at low ionic str ength whose stem conformations were governed by the GC pairs, At high salt, (CCG)(4) isomerized into a peculiar association of two strands, The association was also promoted by high oligonucleotide concentratio ns, No similar behavior was exhibited by (CTG)(4). At low salt, (CGG)( 4) coexisted in two bimolecular conformers whose populations were stro ngly dependent on the ionic strength. In addition, (CGG)(4) associated into a tetraplex at acidic pH, A tetraplex was even observed at neutr al pH if the (CGG)(4) concentration was sufficiently high, (CAG)(4) wa s very stable in a monomolecular conformer similar to the known extrem ely stable foldback of the (GCGAAGC) heptamer, Nevertheless, even this very stable conformer disappeared if (CTG)(4) was added to the soluti on of (CAG)(4). Association of the complementary strands was also stro ngly preferred to the particular strand conformations by the other cou ple, (CCG)(4) and (CGG)(4).