TABLE 3

Characteristics of deletion mutations produced by wild-type and mutant RB69 DNA polymerases in vitro without and with accessory proteins

PolymeraseAPsNo. of
bases
deleted
Location
in lacZαa
Flanking
repeats
Pol+ Exo+-436All lacZαCTGGC
111(144-150)→AGCTGGC
+201→(-7)None
276→(94-102)ACCCTGGCG
Pol+ Exo--260→(57-58)TC
3753-92GAA
363→146Noneb
13165-181GCCC
160(97-101)→CTGGC
152→(64-68)CCGTC
427→(137-143)TTTCGCC
315→(134-137)CCCT
7-(37-26)CTTTA
317→(166-170)CCCGC
317→(166-170)CCCGC
317→(166-170)CCCGC
317→(166-170)CCCGC
+81(-15)-70TCGT
52131-186TCCC
317→(166-170)CCCGC
PolM Exo--276→(94-102)ACCCTGGCG
38(-8)-30None
286→85None
66115-180atcgccc
+4997-152CTGGCGT
  • a Arrows from the left indicate that the deletion approaches the terminal repeat or the flanking base from the left from outside the lacZα sequence, while arrows to the right indicate that the deletion extends outside the lacZα sequence from the terminal repeat to the right. All listed flanking repeats are direct repeats.

  • b In this deletion, the left end has the sequence AAGGG CAATCagctgttgcccg and the right end has the sequence tcgccagCTGGCGT where lowercase letters indicate deleted bases. These two sequences are replete with repeats, including the direct repeat CAGCTG that overlaps the deletion ends, the nearly perfect palindromic reverse repeat GGGCAA(t)Cag/ctgttgccc surrounding the left end of the deletion, and the perfect palindrome cgccagCTGGCG precisely surrounding the right end of the deletion. For ways in which combinations of direct and palindromic repeats can enhance deletion formation, see Glickman and Ripley (1984).

  • c In this deletion, the left end has the sequence ACCCAACT TAatcgcct and the right end has the sequence gatcgccCTTCC CAACA where lowercase letters indicate deleted bases. Here, both atcgcc repeats were deleted instead of the usual loss of only one repeat. Two additional repeats, CCCAAC and CCT, are separated from the deletion on one or both sides by intervening bases, but their contribution to the formation of the deletion is not obvious and their presence may be fortuitous. No reverse repeats occur near the ends of this deletion.