Left-handed Z-DNA structure is favored by the alternating (dC-dG)(n) sequence. Many Z-potentiating sequences are found in genome and they often do not have a perfect alternating (dC-dG)(n) sequence. When a single base pair is removed from the alternating (dC-dG)(n) sequence, a Z-Z junction is created. A Z-Z junction is energetically less favorable by 3.5 kcal/mol than a perfect Z-DNA sequence. We designed special sequences to probe the structural perturbation at the Z-Z junction. Four DNA oligomers, d(*CG*CGT*CG*CG) and d(*CG*CGA*CG*CG) (*C = C or br5C), have been synthesized and analyzed by NMR. The two br5C-modified DNA nonamers are in the Z-DNA conformation in 50% methanol solution. The T and the A nucleotides are in the anti and syn conformation, respectively, in the two br5C nonamers. The NOE-restrained molecular dynamics refinement demonstrated that T-T and A-A bases in the two Z-DNA duplexes are dynamic and adopt a range of conformations. Mixing the br5C-d(*CG*CGT*CG*CG) and br5C- d(*CG*CGA*CG*CG) nonamers together converts a fraction of the two nonamer populations into a hetero duplex as evident from the presence of the imino proton (at 13.70 ppm) of an A:T base pair. A model has been generated for the br5C-d(*CG*CGT*CGΓG)+br5C-d(*CG*CGA*CG*CG) duplex which incorporates a Z-Z junction. Previous biophysical and biochemical data associated with the Z-Z junction are discussed in the context of the present model.
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