Table 3.

Observed errors during TT dimer and AP site bypass by exonuclease-deficient T7 DNA polymerase

Dark blue plaques	Colorless plaques
GATT
10/11: Single base substitution in ambera codon (4 G → C, 3 T → C, 1 G → T, 1 A → G, 1 T → A)	1/16: Single base deletion in amber codon (CGATT → CATT)
1/11: Single base substitution outside amber codon (C → A)	13/16: Single base deletion outside amber codon (6 CTGAG → CTAG, 2 GGCCA → GGCA, 2 TGGGC → TGGC, 1 TGGCT → TGCT, 1 GGCTC → GGTC, 1 AGGTT → AGTT)
	2/16: Single base substitution outside amber codon (C → A, T → G)
GATT
25/28: Single base substitution in amber codon (T → C)	15/16: Single base deletion outside amber codon (1 CTGAG → CTAG, 14 TTGGGC → TTGGC)
2/28: Single base substitution outside amber codon (T → G, C → G)	1/16: Single base substitution outside amber codon (T → G)
1/28: Separate single base insertion (TGGG → TGGGG) and deletion (TGAGG → TGGG)b flanking amber codon
xATT
15/15: dAMP insertion opposite AP site	5/16: dAMP insertion opposite AP site with single base insertion outside amber codon (2 TGGC → TGGGC, GGCT → GGCCT, GTTTC → GTTTTC, TCGA → TCGGA)
	4/16: dAMP insertion opposite AP site with single base deletion outside amber codon (AGGGT → AGGT, CGGAC → CGAC, TTGGG → TTGG, CATGG → CAGG)
	4/16: Deletion of AP site (CCxATT → CCATT)
	2/16: dAMP insertion opposite AP site coupled with potential single base deletion in amber codon (TCCxATTG → TCCTATG)
	1/16: Four base deletion including AP site (TTCCxATT → TATT)
GxTT
9/14: dAMP insertion opposite AP site	16/16: Deletion of AP site (CGxTT → CGTT)
5/14: Deletion of AP site coupled with single base insertion (3 TGGG → TGGGG, 2 CCAT → CCAAT)
GAxT
2/8: dTTP insertion opposite AP site	13/15: dAMP insertion opposite AP site with single base deletion outside amber codon (GAxTGGGC → GATTGGC)
2/8: Coupled single base deletion (TGGGC → TGGC) and insertion in amber codon (CGATT → CGGATT, CGATT → CGAATT)	1/15: Single base deletion of either the AP site or the adjacent T (GAxTGG → GATGG)
1/8: Three base deletion of AP site and flanking bases (CGAxTG → CGG)	1/15: Two distinct single base deletions (GAxTGG → GATGG, TTTCCG → TTTCG)
1/8: Coupled single base deletion (TTGGGC → TTGGC) and insertion outside amber codon (GCCA → GCCCA)
1/8: Single base substitution outside amber codon (G → C)
1/8: Three base deletion outside amber codon (GGCCAT → GAT)

^aThe amber codon (shown in italics in the left-most column) is the target sequence in which each lesion is located. All sequence information is of the template strand in the 3′ → 5′ orientation (see Fig. 1 for full sequence).

^bChanges occurring in the primer:template duplex region are shown in italics in the main table body and are assumed to be caused by errors during chemical synthesis of the oligonucleotides.