DAPI (4',6-DIAMIDINO-2-PHENYLINDOLE) BINDS DIFFERENTLY TO DNA AND RNA- MINOR-GROOVE BINDING AT AT SITES AND INTERCALATION AT AU SITES

The interaction of DAPI and propidium with RNA (polyA.polyU) and corre sponding DNA (polydA.polydT) sequences has been compared by spectrosco pic, kinetic, viscometric, T(m), and molecular modeling methods. Spect ral changes of propidium are similar on binding to the AT and AU seque nces but are significantly different for binding of DAPI. Spectral cha nges for DAPI with the DNA sequence are consistent with the expected g roove-binding mode. All spectral changes for complexes of propidium wi th RNA and DNA and for DAPI with RNA, however, are consistent with an intercalation binding mode. When complexed with RNA, for example, DAPI aromatic protons signals shift significantly upfield, and the DAPI UV -visible spectrum shows significantly larger changes than when complex ed with DNA. Slopes of log k(d) (dissociation rate constants) versus - log [Na+] plots are similar for complexes of propidium with RNA and DN A and for the DAPI-RNA complex and are in the range expected for an in tercalation complex. The slope for the DAPI-DNA complex, however, is m uch larger and is in the range expected for a groove-binding complex. Association kinetics results also support an intercalation binding mod e for the DAPI-RNA complex. The viscosity of polyA-polyU solutions inc reases significantly on addition of both propidium and DAPI, again in agreement with an intercalation binding mode for both molecules with R NA. Molecular modeling studies completely support the experimental fin dings and indicate that DAPI forms a very favorable intercalation comp lex with RNA. DAPI also forms a very stable complex in the minor groov e of AT sequences of DNA, but the stabilizing interactions are conside rably reduced in the wide, shallow minor groove of RNA. Modeling studi es, thus, indicate that DAPI interaction energetics are more favorable for minor-groove binding in AT sequences but are more favorable for i ntercalation in RNA.