Sequence-selective binding to DNA of bis(amidinophenoxy)alkanes related to propamidine and pentamidine

Abstract

The DNA sequences targeted by a complete homologous series of aromatic diamidines have been determined at single-nucleotide resolution via protection from cutting by the endonucleases DNase I, DNase II and micrococcal nuclease. Propamidine, pentamidine and to a lesser extent hexamidine bind selectively to nucleotide sequences composed of at least four consecutive A-T base pairs. In contrast, the binding to DNA of butamidine, heptamidine, octamidine and nonamidine is poorly sequence-selective. Sequences composed of only three consecutive A-T base pairs do not afford a potential binding site for propamidine or the longer homologues, and none of the drugs tolerate the presence of a G-C base pair within the binding site. Experiments with DNA molecules containing inosine in place of guanosine and 2,6-diaminopurine in place of adenine reveal that the lack of binding of propamidine to GC-containing sites is attributable to an obstructive effect of the exocyclic 2-amino group of guanosine. The present data support the view that the local conformation of the double helix (in particular the width of the minor groove) plays a dominant role in the binding reaction and that the capacity of diamidines to recognize AT-rich sequences selectively varies considerably depending on the length of the alkyl chain. The evidence indicates that binding to AT-tracts in DNA must play a role in the biological activity of these diamidines, but there is no simple correlation between binding and pharmacological efficacy.

Design of DNA Minor Groove Binding Diamidines That Recognize GC Base Pair Sequences: A Dimeric-Hinge Interaction Motif

“…10,19,[46][47][48][49] The fit of the compounds into the minor groove was visualized in molecular detail in the x-ray structure by Dickerson and coworkers of netropsin bound to the same-AATT-sequence of the self-complementary duplex, d(CGCG-AATT-CGCG) 2 . 49 Neidle and coworkers have provided highly informative x-ray structures for pentamidine, berenil, DB75 and a number of other diamidines bound at the -AATT-site.…”

Propamidine decreas mitochondrial complex III activity of Botrytis cinerea

“…The mechanism of aromatic diamidine compounds has been studied, the precise mechanism is unclear and its major macromolecular targets have not been identified unequivocally (1). The results from a broad array of methods (DNase I footprinting, surface plasmon resonance, X-ray crystallography, and molecular dynamics) showed that aromatic diamidines bind in the minor groove of duplex DNA by forming hydrogen bonds and van der Waals contacts between its amidinium groups and adenine N3 or thymine O2, bridging 4 or 5 base pairs in AT-rich sequences (2)(3)(4). AT-selective DNA recognition by a series of diamidines can not be simply correlated with their potency of antimicrobial action, and can be explained as being only the first step in a multiple-step process (2,5).…”

“…The results from a broad array of methods (DNase I footprinting, surface plasmon resonance, X-ray crystallography, and molecular dynamics) showed that aromatic diamidines bind in the minor groove of duplex DNA by forming hydrogen bonds and van der Waals contacts between its amidinium groups and adenine N3 or thymine O2, bridging 4 or 5 base pairs in AT-rich sequences (2)(3)(4). AT-selective DNA recognition by a series of diamidines can not be simply correlated with their potency of antimicrobial action, and can be explained as being only the first step in a multiple-step process (2,5). The pharmacological effects are based on specific complex formations between propamidine or its analogs and AT-rich sequences in DNA (6)(7)(8)(9)(10)(11)(12)(13).…”

Silencing of endo-exonuclease expression sensitizes mouse B16F10 melanoma cells to DNA damaging agents

“…The small molecular compound pentamidine, however, has pleiotropic effects in the cell. The pleiotropic effects of pentamidine include: (1) ability to bind to the minor groove of the DNA [50], (2) inhibition of other protein such as PRL phosphatase [51], and (3) inhibition of the endo-exonuclease [52]. In our previous report, we clearly showed that the recombinant yeast homologue of the protein truly possess endo-exonuclease activity in vitro with demonstrated insufficiency in repairing DSBs in mutants without the activity of the yeast homologue of the endo-exonuclease alone or in combination with other DNA DSB repair proteins.…”