9-Anthracene methyl ammonium chloride (AMAC) cleaves supercoiled pUC18
DNA with a marked preference for 3'-AG-5' sites when the reaction mix
ture is irradiated with blue light (390 nm) in the presence of hexammi
necobalt(III) chloride (CoHA). Irradiation of pUC18 DNA in the presenc
e of either CoHA or AMAC alone, led to poor photocleavage, establishin
g a strong synergistic effect for the DNA nicking reaction. Irradiatio
n of a mixture of AMAC and CoHA in the absence of DNA led to the photo
oxidation of AMAC to anthraquinone. Time resolved fluorescence studies
show that AMAC fluorescence is quenched by DNA in a base sensitive ma
nner. AMAC emission is quenched by CoHA at diffusion controlled rate,
and the quenching events may involve electron transfer from AMAC to Co
HA. The DNA may facilitate bimolecular electron transfer between the D
NA-bound AMAC, and CoHA. The cation radical resulting from AMAC oxidat
ion by CoHA is suggested to result in DNA cleavage. DNA sequencing exp
eriments reveal preferential cleavage at 3'-AG-5' sites. Among these c
leavage sites, 3'-AGG-5' sequences were associated with higher intensi
ties. Only one out of 9 observed cleavage sites is not a 3'-AGG-5' seq
uence, instead it was a 3'-TGC-5' site, containing a central G flanked
by T/C instead of A/G. Little or no cleavage is observed at 3'-GCA-5'
, or 3'-TGT-5' sites. Several visible light absorbing agents bind to D
NA at specific sites, and current observations may open the possibilit
y of using these binding agents for sequence dependent photo-cleavage
of DNA. (C) 1997 Elsevier Science Inc.