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Quantifying changes in DNase I-sensitivity with qrt-PCR. qrt-PCR was used to detected small changes in DNase I-sensitivity in two reciprocally expressed genes (redD and rlpA) at the earliest and latest time points. In vivo digestions were performed as described in Figure 1; qrt-PCR is described elsewhere (6). DNase I sensitivity was estimated by the percentage loss of copy number after the rate of digestion had reached a steady level (commonly after 4 U of enzyme had been used).
