Parallel-Stranded DNA with Mixed Sequence. Evidence for Conformational Transition in Solution at Low Water Activity

Abstract

Parallel-stranded deoxyoligonucleotide 5′d(CTATAGGGAT)3′/5′d(GATATCCCTA)3′ (III) was shown to be stable in solution at 3°-5°C, 0.1−0.25 M NaCl, 10⁻² M phosphate buffer, pH 7.0 by means of a set of fluorescent techniques as well as of conventional optical methods. A cooperative change in the CD spectra is observed in trifluoroethanol (TFE) solutions at decreased water activity (relative humidity, r.h.). This distinctive change is supposed to stem from a cooperative conformational transition of parallel double helix from a B-like form with C2′endo sugar conformation to an A-like form designated as A_p. The 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-III). The ability of parallel helix to transit into A_p form is important for DNA-RNA parallel double helix formation.