PARALLEL-STRANDED DNA WITH MIXED SEQUENCE - EVIDENCE FOR CONFORMATIONAL TRANSITION IN SOLUTION AT LOW WATER ACTIVITY

Parallel-stranded deoxyoligonucleotide 5'd(CTATAGGGAT)3'/5'd(GATATCCCT A)3' (I-II) was shown to be stable in solution at 3 degrees -5 degrees C, 0.1-0.25 M NaCl, 10(-2) M phosphate buffer, pH 7.0 by means of a s et of fluorescent techniques as well as of conventional optical method s. A cooperative change in the CD spectra is observed in trifluoroetha nol (TFE) solutions at decreased water activity (relative humidity, r. h.). This distinctive change is supposed to stem from a cooperative co nformational transition of parallel double helix from a B-like form wi th C2'endo sugar conformation to an A-like form designated as A(p). Th e free energy difference between the A(p) and B-like conformation for the parallel duplex is 7.35 kcal/mol which is close to the value 7.40 kcal/mol for the antiparallel 5'd(CTATAGGGAT)3'/3'd(GATATCCCTA)5' (I-I II). The ability of parallel helix to transit into A(p) form is import ant for DNA-RNA parallel double helix formation.