Photo-cross-linked oligonucleotide duplex as a decoy-DNA for inhibition ofrestriction endonuclease activity

As a novel type of regulator molecule for DNA-recognizing proteins, a photo -cross-linked oligonucleotide duplex was designed and synthesized, The mole cule regulated the activity of a restriction endonuclease by being recogniz ed as a substrate. This type of regulating molecule is regarded as a decoy- DNA. 4,5 ' ,8-[4-Aminoethylaminomethyl]-trioxaten (aeAMT) was conjugated wi th art oligodeoxyribonucleotide (ODN) at the 5 ' -end and the aeAMT was cro ss-linked with the thymine residue of the complementary oligonucleotide upo n UVA irradiation. The terminally cross-linked oligonucleotides, singly cli pped (SC) decoy-DNA, acquired thermal stability, An oligonucleoside phospho rothioate (OPT) was also introduced as one or both components, yielding thr ee types of decoy-DNAs, SC-ODN-ODN (SC.DD), SC-OPT-ODN (SC.SD). and SC-OPT- OPT (SC.SS). The SC decoy-DNAs inhibited the function of the restriction en donuclease, AatII, in a sequence-specific and concentration-dependent manne r with an appreciable IC50 value (1.3 muM for SC.DD, 0.016 muM for SC.SD. 0 .002 muM for SC.SS). The SC decoy-DNAs were found to be effective for regul ating the DNA recognizing proteins. (C) 2001 Academic Press.