SEQUENCE DEPENDENCE OF 4',6-DIAMIDINO-2-PHENYLINDOLE (DAPI) DNA INTERACTIONS

We have characterized the interaction of 4',6-diamidino-2-phenylindole (DAPI) with a series of DNA oligonucleotides containing a varying num ber of contiguous alternating AT base pairs in the center of a GC-stre tch. The binding affinity of DAPI to the oligonucleotides increases wi th the number of contiguous AT base pairs. When entropy effects are ta ken into account, the microscopic affinity reaches a maximum value whe n 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 lo w binding ratios. With none or only a single AT base pair in the cente r of a GC dodecamer, the spectral properties of bound DAPI are very si milar 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 com plexed with [poly(dG-dC)]2, while the circular dichroism spectrum rese mbles that of DAPI bound to [poly(dA-dT)]2.