Table 1.
Alignment of DNA cleavage sites for S. pneumoniae gyrase induced by clerocidin
| Sites involving cleavage on complementary DNA strands | ||
| −1 +5 | ||
|---|---|---|
| CCCCAGCC CAAT CTAAGAAT | Site 1 | S fragment |
| TAAGAATG AACT CTATCTAG | 2 | S fragment |
| AGTTGAGG GGGA CTCTGCCG | 3 | S fragment |
| TTGAGGGG GACT CTGCCGGT | 4 | S fragment |
| CAAGGTCG TGAC CGCAAGTT | 5 | S fragment |
| TTCCAGGC TATT CTACCTCT | 6 | S fragment |
| CAGGCTAT TCTA CCTCTTCG | 7 | S fragment |
| AGGCTATT CTAC CTCTTCGT | 8 | S fragment |
| ATTCTACC TCTT CGTGGTAA | 9 | S fragment |
| CCAAGATG GCGG ATATCCTC | 10 | S fragment |
| CAAAAATG AAGA GATCAATA | 11 | S fragment |
| GGTAGATG ACGA CCATCAGG | Site 1 | pBR322-1073 |
| GCAGGTAG ATGA CGACCATC | 2 | pBR322-1070 |
| GTAGATGA CGAC CATCAGGG | 3 | pBR322 |
| GAGGCTGG ATGG CCTTCCCC | 4 | pBR322 |
| CGCTTCCG GCGG CATCGGGA | 5 | pBR322 |
| AGGCCATG CTGT CCAGGCAG | 6 | pBR322 |
| CATCAGGG ACAG CTTCAAGG | 7 | pBR322 |
| TTACCAGC CTAA CTTCGATC | 8 | pBR322 |
| Sites with cleavage on one DNA strand | ||
| AGATAGAG TTCA TTCTTAGC | Site 12 | S fragment |
| GCCGGTGG TTCT GCCAAACA | 13 | S fragment |
| TTTGGCAG AACC ACCGGCAG | 14 | S fragment |
| AGCCAAGG CCAA GATGGCGG | 15 | S fragment |
| GACCGCTG ATCG TCACGGCG | 9 | pBR322 |
| CGGAAGCG AGAA GAATCATA | 10 | pBR322 |
| ATAATGGG GAAG GCCATCCA | 11 | pBR322 |
DNA sequences surrounding the breakage point are shown for one strand of each double-stranded breakage site or for sites of single-stranded breakage promoted by clerocidin in the parE S fragment (31) and in pBR322 (905–1200 nt region). The central four nucleotides (+1 to +4) correspond to those in the 4-bp overhang produced by DNA breakage by gyrase. Preferred guanines at –1 and cytosines at +5 (indicating guanine at –1 on the complementary strand) are shown in boldface.