Guiding the Design of Synthetic DNA-Binding Molecules with Massively Parallel Sequencing

Genomic applications of DNA-binding molecules require an unbiased knowledge of their high affinity sites. We report the high-throughput analysis of pyrrole-imidazole polyamide DNA-binding specificity in a 10^(12)-member DNA sequence library using affinity purification coupled with massively parallel sequencing. We find that even within this broad context, the canonical pairing rules are remarkably predictive of polyamide DNA-binding specificity. However, this approach also allows identification of unanticipated high affinity DNA-binding sites in the reverse orientation for polyamides containing β/Im pairs. These insights allow the redesign of hairpin polyamides with different turn units capable of distinguishing 5′-WCGCGW-3′ from 5′-WGCGCW-3′. Overall, this study displays the power of high-throughput methods to aid the optimal targeting of sequence-specific minor groove binding molecules, an essential underpinning for biological and nanotechnological applications

Diastereo- and Enantioselective Iridium-Catalyzed Allylation of Cyclic Ketone Enolates: Synergetic Effect of Ligands and Barium Enolates

We report asymmetric allylic alkylation of barium enolates of cyclic ketones catalyzed by a metalla­cyclic iridium complex containing a phosphor­amidite ligand derived from (<i>R</i>)-1-(2-naphthyl)­ethylamine. The reaction products contain adjacent quaternary and tertiary stereocenters. This process demonstrates that unstabilized cyclic ketone enolates can undergo diastereo- and enantio­selective Ir-catalyzed allylic substitution reactions with the proper choice of enolate counter­cation. The products of these reactions can be conveniently transformed to various useful poly­carbo­cyclic structures