Unusual conformation of (dA)n.(dT)n-tracts as revealed by cyclobutane thymine-thymine dimer formation

Cyclobutane dimer formation has been used to probe conformation of (dA)n.(dT)n-tracts cloned in plasmid DNA. The observed dimer probability patterns for (dA)n.(dT)n-tracts with n greater than or equal to 4 exhibit maximum intensity at the 3'-terminal TT site of Tn-tract, whereas photoreactivity at all the other TT sites is inhibited. Both the temperature and dimethyl sulfoxide increase dimer formation within Tn-tracts and result in an even dimer pattern. The data obtained have been interpreted in terms of an unusual structure adopted by (dA)n.(dT)n-tracts. An influence of flanking base pairs, ethidium bromide binding and ionic strength has also been studied.