 dna repair enzymes are essential for maintaining the integrity of the dna sequence . 
 unfortunately , very little is known about how these enzymes recognize damaged regions along the helix . 
 structural analysis of cellular repair enzymes bound to dna reveals that these enzymes are able to recognize dna in a variety of conformations . 
 however , the prevalence of these deformations in the absence of enzymes remains unclear , as small populations of dna conformations are often difficult to detect by nmr and x - ray crystallography . here , we used time - resolved fluorescence spectroscopy to examine the conformational dynamics of linear , nicked , gapped , and bulged dna in the absence of protein enzymes . 
 this analysis reveals that damaged dna is polymorphic in nature and able to adopt multiple individual conformations . 
 we show that dna repair intermediates that contain a one - nucleotide gap and bulge have a significant propensity to adopt conformations in which the orphan base resides outside the dna helix , while dna structures damaged by a nick or two - nucleotide gap favor intrahelical conformations . because changes in dna conformation appear to guide the recognition of dna repair enzymes 
 , we suggest that the current approach could be used to study the mechanism of dna repair . 
Supplementary Material