Circular dichroism spectroscopy analysis of conformational transitions of a 54 base pair DNA duplex composed of alternating CGCGCG and TATATA blocks

dCD spectroscopy was used to analyze conformational properties of a self-co mplementary 54-mer DNA composed of alternating (CG)(3) and (TA)(3) hexamers . NaCl induced the Z-form in poly(GC), but the 54-mer remained the B-form u nder the same conditions. The B-Z transition was induced only after the add ition of NiCl2. However, the Z-form was adopted by the whole molecule, not by the (CG)(3) blocks alone. Two orders of magnitude higher concentrations of NiCl2 were required to induce the Z-form in poly(AT). The Z-form was als o induced in poly(GC) by CsF that switched poly(AT) into the X-form, which seems to be a solution counterpart of D-DNA. Under these conditions the CD spectrum of the 54-mer was consistent with the (TA), blocks being in the X- form and the (CG)(3) blocks in the B-form. At high concentrations of ethano l or trifluoroethanol, poly(AT) was an A-form, while poly(GC) adopted eithe r Z-form, A-form or Z'-form. At the high trifluoroethanol concentrations th e 54-mer cooperatively switched into a conformation whose CD spectrum was : most consistent with the A-form in the (TA)(3) blocks and the Z'-form in th e (CG)(3) blocks. This suggests that the base pairs are tilted in the Z'-fo rm as in the A-form. The present article illustrates that CD spectroscopy c an provide interesting pieces of information about conformational isomeriza tions and coexistence of multiple conformations in DNA molecules containing blocks of different simple sequence repeats. (C) 1999 John Wiley & Sons, I nc.