Table 1.

Ligation error rate on two specific template regions. We tested for the ligation of a matched 10-nt oligomer to a possibly matched, adjacent 7-nt oligomer (of the form NNNXNN_rN) at the sequences: AATCAGG (43% GC content) or GAGCGGA (71% GC content). The hairpin was periodically opened for a time t and the ligation was confirmed during the rezipping phase by the presence of a long blockage time. We tested more than 500 ligation runs and counted the number of successful ligations for each possible specific nucleotide (X). We fitted the measured probability of ligation P(t) to an exponential form: 1 − exp(−t/τ). We thus determined the ligation time τ_match and τ_mismatch for matched and mismatched oligonucleotides. The error rate for a ligation time τ_trial is then computed as ε = P_mismatch(τ_trial)/P_match (τ_trial).

oligonucleotide	Expected: GAGCGGA	Lifetime (τlig)	Error rate (ttrial = 40s)
NNNGNNrN	Mismatch	2235 s	1.77%
NNNCNNrN	Matching	6 s	-
NNNTNNrN	Mismatch	8459 s	0.47%
NNNANNrN	Mismatch	27302 s	0.15%

oligonucleotide	Expected: AATCAGG	Lifetime (τlig)	Error rate (ttrial = 50s)
NNNGNNrN	Mismatch	19825 s	0.25%
NNNCNNrN	Matching	45 s	-
NNNTNNrN	Mismatch	3091 s	1.60%
NNNANNrN	Mismatch	22275 s	0.22%