BASE DYNAMICS OF LOCAL Z-DNA CONFORMATIONS AS DETECTED BY ELECTRON-PARAMAGNETIC RESONANCE WITH SPIN-LABELED DEOXYCYTIDINE ANALOGS

Conformational detection and base dynamics of spin-labeled Z-DNA have been investigated by electron paramagnetic resonance (EPR) spectroscopy. The two synthesized and characterized probes used in this study were C(5)-nitroxide-labeled 2′-deoxycytidine 5′-triphosphates, pppDCAT and pppDCAVAT, which serve as suitable substrates for Micrococcus luteus DNA polymerase. Enzymatic incorporation of these probes into (dG-dC) n yields the EPR-active alternating copolymers (dG-dC,DCAT)n and (dG-dC,- DCAVAT) n. These polymers assume typical B- and Z-DNA conformations under respective low (0.1 M NaCl) and high (4.5 M NaCl) salt conditions, as evidenced by their UV-circular dichroism spectra. The EPR line shape of (dG-dC,DCAT) n in Z-form is unique and significantly different from the B-form EPR spectrum. A similar observation is made for (dG-dC,DCAVAT) n. Thus, the EPR line shapes of these spin-labeled DNAs are indicative of their local conformations. The EPR spectra, analyzed with a previously published motional model [Kao, S.-C., Polnaszek, C. F., Toppin, C. R., & Bobst, A. M. (1983) Biochemistry 22, 5563-5568], indicate τ⊥ values of 4 and 7 ns for the B- and Z-forms, respectively. Therefore, the base dynamics of Z-DNA are about two times slower than in B-DNA.© 1990, American Chemical Society. All rights reserved.