Selective inhibition of DNA gyrase in vitro by a GC specific eight‐ring hairpin polyamide at nanomolar concentration

Abstract

The influence of an eight-ring hairpin DNA minor groove binder on the gyrase mediated DNA supercoiling and cleavage reaction step of the enzyme was investigated. The results demonstrate that supercoiling is affected by the hairpin polyamide in the millimolar concentration range while the enzyme catalyzed cleavage of a 162 bp fragment of pBR322 containing a single strong gyrase site is effectively inhibited at nanomolar concentration. As demonstrated by footprint analysis the latter effect is caused by a specific binding of the hairpin forming polyamide to the enzyme recognition site (GGCC), which indicates that the gyrase activity to produce a double strand break is blocked at this site. The pyrrole^imidazole hairpin polyamide is the most potent inhibitor of the gyrase mediated cleavage reaction compared to other known anti-gyrase active DNA binding agents.z 2000 Federation of European Biochemical Societies.

The pivot point arginines identified in the β-pinwheel structure of C-terminal domain from Salmonella Typhi DNA Gyrase A subunit

“…The intermediate length of 162 bp from pBR322 has been reported to bind to GyrA-CTD. The 162 bp DNA contains a strong gyrase binding site in pBR322 plasmid 28 and hence was considered for this study. The studies with the 37 bp DNA, aided in the determination of the DNA binding ability of GyrA-CTD protein.…”

“…(2020) 10:7817 | https://doi.org/10.1038/s41598-020-64792-w www.nature.com/scientificreports www.nature.com/scientificreports/ be distinctly identified in the EMSA. The assay was performed using 37 bp and 162 bp DNA sequences reported in previous studies 17,24,28 . The EMSA illustrated that wild type StGyrA-CTD binds efficiently with both 37 bp and 162 bp DNA (Figs.…”

1-Methyl-N-(2-{[(1-methyl-4-nitro-1H-pyrrol-2-yl)carbonyl]amino}ethyl)-4-nitro-1H-pyrrole-2-carboxamide dimethylformamide disolvate

“…Dervan and co-workers have discovered that polyamides with certain numbers of N-methylpyrrole-and N-methylimidazolecarboxamides can recognize and bind in the minor groove of predetermined DNA sequences with high af®nity, and with a speci®city comparable with that of naturally occurring DNA-binding proteins, and further regulate gene expression (Dervan & Bu È ril, 1999;Simon et al, 2000). These properties prompted the present synthesis and structure determination of the title compound, (I).…”

Biological Applications of Foldamers

“…Oligoamides have been designed to target GC rich regions flanking CRE sites to inhibit Tax protein binding and Tax transactivation in vitro [200]. Other oligoamides targeting GC rich sequences bound to a 4 base pair site typically cleaved by bacterial gyrase, thus preventing strand cleavage at nanomolar concentrations [201]. The NF-kB heterodimer, a transcription factor which binds in the DNA major groove, has been inhibited by oligoamides that bind the minor groove opposite one of the monomers [202].…”