Table 2. Summary of vector repair and mRNA quantification shows low levels of expansions/contractions at DNA stem loops, and significant deletions of unpaired loops.
| Cell line | Extrahelical DNA | Location in vector | Extrahelical DNA deleted | mRNA indicating deletion1 | Extrahelical DNA expanded | mRNA indicating expansion2 |
|---|---|---|---|---|---|---|
| Normal human fibroblasts | DNA stem–loop | Transcribed strand | <7% | 51 ± 14% | <4% | Not applicable |
| Nontranscribed strand | <7% | Not applicable | <6% | 12 ± 6% | ||
| Unpaired DNA loop | Transcribed strand | 19 ± 5%* | 93 ± 1% | <1% | Not applicable | |
| Nontranscribed strand | 10 ± 5%* | Not applicable | <6% | 3 ± 2% | ||
| XPA(−/−) human fibroblasts | DNA stem–loop | Transcribed strand | <7% | 52 ± 3% | <4% | Not applicable |
| Nontranscribed strand† | 9%† | Not applicable | 6%† | 9 ± 1% | ||
| Unpaired DNA loop | Transcribed strand | 20 ± 5%* | 91 ± 4% | <1% | Not applicable | |
| Nontranscribed strand | 10 ± 2%* | Not applicable | <6% | 6 ± 1% | ||
| CSB(−/−) human fibroblasts | DNA stem–loop | Transcribed strand | <7% | 55 ± 7% | <4% | Not applicable |
| Nontranscribed strand | <7% | Not applicable | < 6% | 8 ± 0.4% | ||
| Unpaired DNA loop | Transcribed strand | 23 ± 4%* | 85 ± 2% | < 1% | Not applicable | |
| Nontranscribed strand | 8 ± 5%* | Not applicable | < 6% | 6 ± 6% |
*P < 0.05 for deletions or expansions in DNA repair assay.†No replicate data. Percent repair is reported observed repair over background. 1For extrahelical structures on the non-transcribed strand, mRNA bands would not detect deletions as the mRNA length would be the same in the case of deletion and retention of the structure. 2For extrahelical structures on the transcribed strand, mRNA bands would not detect expansions as the mRNA length would be the same in the case of expansion and retention of the structure. Statistical significance was estimated using ANOVA followed by Tukey's HSD to get individual P-values, testing for significance over background.