Spin-labeled nucleotide substrates for DNA-dependent RNA polymerase from Escherichia coli

New spin-labeled analogs of nucleoside triphosphates, 8-amino(2,2,6,6-tetramethylpiperidine-N-oxyl)adenosine 5'-triphosphate ((8-AmTEMPO)ATP) and 5-amino(2,2,6,6-tetramethylpiperidine-N-oxyl)uridine 5'-triphosphate ((5-AmTEMPO)UTP), with the probe 4-amino(2,2,6,6-tetramethylpiperidine-N-oxyl) (4-AmTEMPO) attached to C-8 of ATP and C-5 of UTP via a secondary amine bond, were synthesized in 50 and 40% yield, respectively. These analogs showed a single spot by thin layer chromatographic analysis. The absorption spectra of (8-Am-TEMPO)ATP and (5-AmTEMPO)UTP exhibit maxima at 310 and 265 nm, respectively; their X-band EPR spectra have a typical three-line pattern with lines at 3,221, 3,239, and 3,257 Gauss. The intensity ratios for mid to high field lines of the EPR derivative lines were found to be 1.03 +/- 0.02, 1.08 +/- 0.04, and 1.15 +/- 0.07 for 4-AmTEMPO, (8-AmTEMPO)ATP, and (5-AmTEMPO)UTP, respectively. The immobilization of 4-AmTEMPO bound to C-8 of ATP or bound to C-5 of UTP was observed to be 5 and 11%, respectively, as compared with free 4-AmTEMPO. The initial velocity (s-1) of [3H]UMP incorporation into RNA in the presence of [3H]UTP, CTP, GTP, and (8-AmTEMPO)ATP or ATP was measured. The percent incorporation of (8-AmTEMPO)ATP into RNA product by Escherichia coli RNA polymerase using various DNA templates is 68, 66, and 61% for pAR1435 (plasmid containing A1 promoter from T7 DNA), calf thymus DNA, and poly(dA-dT) respectively, as compared with ATP incorporation. The polymerase-catalyzed reaction of (8-AmTEMPO)ATP with (3'-OCH3)UTP yielded 5'-triphosphate delta-amino(2,2,6,6-tetramethylpiperidine-N-oxyl)adenylyl (3'-5')3'-methoxy uridine in the presence of poly(dA-dT). The structure of this spin-labeled dinucleotide was identified by paper chromatographic analysis of the products of phosphodiesterase digestion. These analogs also can be used for the study by EPR spectroscopy of the dynamics of gene transcription catalyzed by RNA polymerases or of other nucleotide-utilizing enzymes.