Selective inhibition of sequence-specific protein-DNA interactions by incorporation of 6-thioguanine: cleavage by restriction endonucleases. 
Incorporation of the antileukemic agent 6-thioguanine (TG) into cellular DNA has been demonstrated to be a major determinant of its cytotoxicity.  We have previously shown that complete replacement of G by TG within one DNA strand of the SV40 origin of replication can completely inhibit sequence-specific binding of the viral replication protein T antigen.  The aim of the present study was to determine the effect of more selective TG substitutions on DNA-protein interactions, by utilizing the simpler base recognition sequence motifs of restriction endonucleases.  In the first part of our study, we replaced G with TG in one or two of four possible sites within the duplex hexameric recognition sequence of BamHI (5'-G decreases GATCC-3'), by enzymatic extension of primed oligonucleotides.  This extension was stalled, but not completely inhibited, at locations where insertion of consecutive TG moieties was required.  Both strands of molecules containing a single substitution were cleaved by BamHI at reduced rates, with the substituted strand inhibited to a greater degree.  In molecules containing two substitutions, neither strand was cut by BamHI.  In contrast, we found that scission of these same mono- and disubstituted substrates by the less stringent isoschizomer MboI (5'-N decreases GATCN-3') was inhibited only slightly.  In the second part of our study, we investigated the effect of analog substitution on scission by the type II-S enzymes AlwI and FokI, in order to separately determine the effects of restriction site modification versus scission site modification.  We found that the reactivity of these enzymes was completely abolished by TG substitution within the recognition site, whereas substitution at the scission site had no effect.  Our results demonstrate that infrequent TG substitutions within symmetric DNA sequences can inhibit sequence-specific interactions in an asymmetric fashion.  In addition, although previous reports have shown that TG forms a relatively weak base pair with cytosine, it appears that the inhibition of restriction endonuclease-mediated cleavage resulting from TG incorporation is a function of the sequence requirements of the protein and not a general consequence of disrupted base-pairing at the recognition locus.  These data support the idea that the cytotoxic consequences of TG incorporation may be due to inhibition of sequence-specific protein-DNA interactions.