Localization of the arginine tRNA gene to the D segment of T5 bacteriophage DNA. A new procedure for producing duplex DNA fragments.

The tRNA genes of bacteriophage T5 are located in four clusters on the continuous heavy DNA strand (Chen, M.-J., Locker, J., and Weiss, S.B. (1976) J. Biol. Chem. 251, 536--547). Three of the four clusters are within the DNA C segment; the fourth cluster, to which only tRNAArg has been localized, maps in a 3.02 kilobase (kb) region of which 1.99 kb are at the right end of the C segment and 1.03 kb at the left end of the D segment. In order to localize the tRNAArg gene further and to define its relationship to the C-D nick, we devised a suitable method for preparing T5 DNA fragments whose ends correspond to the position of the T5 DNA nicks contained in the light DNA strand. In this method, DNA is denatured, partially renatured, and digested with low concentrations of S1 nuclease. Agarose-gel electrophoresis of these digests gives a pattern of bands which correlate in size with the pattern expected from the nicked structure of T5 DNA. Annealing of individual purified T5 [35P]tRNA species to the T5 DNA fragments transferred to nitrocellulose filters shows that tRNAArg hybridizes exclusively to the D fragment and is therefore localized to 1.03 kb at the 5' (left) end of the heavy strand of the D segment. This finding suggests that the promotor for this early gene is to the right of the C-D nick in T5 DNA; hence, the C-D nick does not coincide with this early promotor.