Binding specificity of a nuclear scaffold: supercoiled, single-stranded, and scaffold-attached-region DNA

Scaffold-attached-region (SAR) elements of DNA enhance transcriptional rates, and this has been correlated with their ability to undergo separation into single strands (ssDNA) under conditions of negative superhelicity (Bode et al., 1992). The competition studies presented here suggest that the SAR-scaffold interaction is based, in part, on the recognition of single strands, while about one-half of SAR sites are inaccessible to ssDNA. Conversely, since there are 20,000 SAR sites but more than 60,000 sites for ssDNA per nuclear equivalent, not all ssDNA sites are open for SARs. In addition, a completely separate set of binding centers recognizing and enzymatically converting DNA of superhelical density below -0.04 can be titrated. These findings reflect multiple binding specificities for scaffold preparations that are routinely used for screening scaffold-attached regions.