Figure 1. (A)Repeat sequences of the three CRISPR loci in H. volcanii. The repeat sequences of the three different CRISPR RNAs differ by one nucleotide (at position 23). The sequence of the CRISPR locus C repeat is shown. Positions that are identical in the P1 and P2 locus repeats are indicated with a dot. The pre-crRNA is processed in the repeat region directly upstream of nucleotide 23 (marked by the arrow). (B) Structure of the crRNA in Haloferax. The product of the pre-crRNA processing reaction is shown. It contains the spacer sequence and an eight-nucleotide 5′ handle, which originates from the upstream repeat. Because position 23 varies between the three CRISPR repeats, the first nucleotide of the 5′ handle is either a G (locus C), an A (locus P1) or a U (locus P2). Downstream of the spacer are the remaining 22 nucleotides of the downstream repeat, which can fold into a minimal stem loop.