Base dynamics of local Z-DNA conformations as detected by electron paramagnetic resonance with spin-labeled deoxycytidine analogues.
Conformation 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 tau perpendicular 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.
Strobel
O K
OK
Department of Chemistry, University of Cincinnati, Ohio 45221.
Keyes
R S
RS
Bobst
A M
AM
D002942:Circular Dichroism; D003497:Cyclic N-Oxides; D004247:DNA / Q000737:chemistry*; D003845:Deoxycytosine Nucleotides; D004578:Electron Spin Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry; D013056:Spectrophotometry, Ultraviolet; D013113:Spin Labels
D003497:Cyclic N-Oxides; D003845:Deoxycytosine Nucleotides; D009838:Oligodeoxyribonucleotides; D013113:Spin Labels; C066939:5-(3-(2,2,6,6-tetramethyl-1-oxy-piperidine-4-carboxamido)prop-1-enyl)-2'-deoxycytidine 5'-triphosphate; C066941:5-(3-(5-(2,2,6,6-tetramethyl-1-oxypiperidine-4-carboxamido)pentanamido)prop-1-enyl)-2'-deoxycytidine 5'-triphosphate; D004247:DNA