Sequence dependence of 4',6-diamidino-2-phenylindole (DAPI)-DNA interactions

Abstract

We have characterized the interaction of 4',6-diamidino-2-phenylindole (DAPI) with a series of DNA oligonucleotides containing a varying number of contiguous alternating AT base pairs in the center of a GC-stretch. The binding affinity of DAPI to the oligonucleotides increases with the number of contiguous AT base pairs. When entropy effects are taken into account, the microscopic affinity reaches a maximum value when the oligonucleotides contain three AT base pairs. Three is also the minimum number of base pairs that provides a binding site with all the characteristics of binding observed with DNA and [poly(dA-dT)]2 at low binding ratios. With none or only a single AT base pair in the center of a GC dodecamer, the spectral properties of bound DAPI are very similar to those of DAPI bound to [poly(dG-dC)]2. When DAPI is complexed with an oligonucleotide containing two AT base pairs, the absorption and fluorescence properties of DAPI closely resemble those of DAPI complexed with [poly(dG-dC)]2, while the circular dichroism spectrum resembles that of DAPI bound to [poly(dA-dT)]2.