Bacteria are surrounded by a cell wall containing layers of peptidoglycan, the integrity of which is essential for bacterial survival. In the final stage of peptidoglycan biosynthesis, peptidoglycan glycosyltransferases (PGTs; also known as transglycosylases) catalyze the polymerization of Lipid II to form linear glycan chains. PGTs have tremendous potential as antibiotic targets, but the potential has not yet been realized. Mechanistic studies have been hampered by a lack of substrates to monitor enzymatic activity. We report here the total synthesis of heptaprenyl-Lipid IV and its use to study two different PGTs from E. coli. We show that one PGT can couple Lipid IV to itself whereas the other can only couple Lipid IV to Lipid II. These in vitro differences in enzymatic activity may reflect differences in the biological functions of the two major glycosyltransferases in E coli.
The sequence-specific inhibition of essential protein-DNA contacts in the promoter of a gene is a central issue for the regulation of gene expression by chemical methods. Hairpin polyamides have been shown to inhibit protein-DNA complexes in some but not all cases. For example, polyamides co-occupy the same DNA sequence in the minor groove in the presence of major-groove binding bZip proteins. Four hairpin polyamide-acridine conjugates were synthesized and shown to bind the minor groove of DNA with high affinity in a sequence-specific manner. The polyamide-acridine conjugates were shown to unwind DNA (phi = 14-15 degrees), evidence for intercalation by the acridine moiety. Importantly, the polyamide-intercalator conjugates, which combine sequence-specific groove binding with proximal local unwinding, inhibit major-groove DNA binding by the GCN4 bZip protein. This class of DNA binding molecules creates a sequence-specific allosteric change in DNA structure and has the potential to be a general inhibitor of transcription factor binding independent of the specific protein-DNA structure.
Programmable bisintercalators: Symmetric synthetic DNA bisintercalators (see picture) based on the H‐pin polyamide motif afford high affinity and programmable sequence specificity.
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