SYNTHETIC NUCLEASES CRAFTED FROM L-LYSINE

A central strategy fdr the design of chemical nucleases is presented. This involves the utilization of the cc-amino carboxylate unit of L-ly sine to form Cu(II) templates to function as the cleaving centre on th e one hand and sigma-amino group for the attachment of DNA recognition elements on the other, thus giving rise to a duplex recognition termi ni, harbouring a centrally placed Cu(II) for potentiation of oxidative scission. The recognition element studied encompasses a spectrum of s tructures ranging from quinazolines and purine residues to specificall y crafted peptide segments that have potential to form secondary struc tures. These could be represented as R-K-Cu-K-R wherein R is the recog nition system and K-Cu-K, a composite crafted from lysine, consisting of the cleaving centre from metal complexation of cl-amino acid unit a nd the spacer consisting of the four methylene groups of the side chai n. The binding and DNA scission profile of the sixteen chemical nuclea ses thus prepared and fully characterized have been probed by UV, fluo rescence quenching and electrophoretic studies. Their binding to, calf thymus DNA is associated with a decrease in epsilon and an similar to 10-15 nm red shift. The involvement of GC sequence in binding is indi cated from studies with poly[d(G-C).d(G-C)] and poly[d(A-T).d(A-T)], w herein the hypochromicity and red shift were found to be quite pronoun ced in the former. Fluorescence quenching studies with Bz-Trp-Trp-K-Cu -K-Trp-Trp-Bz demonstrated the binding of one ligand at approximately every stretch of 112bp and approximately a stretch of 80 bp in the pre sence of salt. The DNA cleaving properties of all the nucleases were d emonstrated with pBR 322 and p blue script 11KS using standard protoco ls. In all cases, covalently closed supercoiled (form I DNA) is conver ted largely into open circular (form II) suggesting nicking of the sin gle strand at binding sites. Sequence specificity experiments with the nuclease. Bz-Ala-Gly-K-Cu-K-Gly-Ala-Bz in a P-32 3'-end labeled 117bp restriction fragment (Eco RI/Hind III) of pUC-18 showed almost exclus ive attacks at thymidylate residues in particular, thymines correspond ing to 5'T of the CTAT(3'-5') box. Whilst the most preferred site of a ttack is found at T of 3'-ATC-5' at the trinucleotide level, cleavage studies at low concentration have shown that at pentanucleotide level, the lone sequence 3'-GATCT-5' (a part of the inverted repeat -GAGATCT C-) is favoured (fragment 92) over the more frequently occurring 3'-TA TCT-5' segment.