RECOGNITION OF THE 4 WATSON-CRICK BASE-PAIRS IN THE DNA MINOR-GROOVE BY SYNTHETIC LIGANDS

The design of synthetic ligands that read the information stored in th e DNA double helix has been along-standing gal at the interface of che mistry and biology(1-5). Cell-permeable small molecules that target pr edetermined DNA. sequences offer a potential approach for the regulati on of gene expression(6). Oligodeoxy-nucleotides that recognize the ma jor groove of double-helical DNA via triple-helix formation bind to a broad range of sequences with high affinity and specificity(3,4), Alth ough oligonucleotides and their analogues have been shown to interfere with gene expression(7,8), the triple-helix approach is limited to re cognition of purines and suffers from poor cellular uptake. The subseq uent development of pairing rules for minor-groove binding polyamides containing pyrrole (Py) and imidazole (Im) amino acids offers a second code to control sequence specificity(9-11). An Im/Py pair distinguish es G.C from C.G and both of these from A.T/T.A base pairs(9-11). A Py/ Py pair specifies A.T from G.C but does not distinguish A.T from T.A(9 -14). To break this degeneracy, we have added a new aromatic amino aci d, 3-hydroxypyrrole (Hp), to the repertoire to test for pairings that discriminate A.T from T.A. We find that replacement of a single hydrog en atom with a hydroxy group in a Hp/Py pairing regulates affinity and specificity by an order of magnitude. By incorporation of this third amino acid, hydroxy pyrrole-imidazole-pyrrole polyamides form four rin g-pairings (Im/Py, Py/Im Hp/Py and Py/Hp) which distinguish all four W atson-Crick base pairs in the minor groove of DNA.