Selective Nucleosome Disruption by Drugs That Bind in the Minor Groove of DNA

Abstract

Previous studies have shown that drugs which bind in the DNA minor groove reduce the curvature of bent DNA. In this article, we examined the effects of these drugs on the nucleosome assembly of DNA molecules that display different degrees of intrinsic curvature. DAPI (4,6-diamidino-2-phenylindole) inhibited the assembly of a histone octamer onto a 192-base pair circular DNA fragment from Caenorhabditis elegans and destabilized a nucleosome that was previously assembled on this segment. The inhibitory effect was highly selective since it was not seen with nonbent molecules, bent molecules with noncircular shapes, or total genomic DNA. This marked template specificity was attributed to the binding of the ligand to multiple oligo A-tracts distributed over the length of the fragment. A likely mechanism for the effect is that the bound ligand prevents the further compression of the DNA into the minor groove which is required for assembly of DNA into nucleosomes. To further characterize the effects of the drug on chromatin formation, a nucleosome was assembled onto a 322-base pair DNA fragment that contained the circular element and a flanking nonbent segment of DNA. The position of the nucleosome along the fragment was then determined using a variety of nuclease probes including exonuclease III, micrococcal nuclease, DNase I, and restriction enzymes. The results of these studies revealed that the nucleosome was preferentially positioned along the circular element in the absence of DAPI but assembled onto the nonbent flanking sequence in the presence of the drug. DAPI also induced the directional movement of the nucleosome from the circular element onto the nonbent flanking sequence when a nucleosome preassembled onto this template was exposed to the drug under physiologically relevant conditions.

Replication timing of two human common fragile sites: FRA1H and FRA2G

“…In our case, both FRA1H and FRA2G are induced by DAPI as well as by other compounds (see above) (Limongi et al, 2003;Curatolo et al, 2007). DAPI preferentially binds to AT-rich DNA and acts in G2 phase as an undercondensing agent (Prantera et al, 1981;Fitzgerald and Anderson, 1999). The combination of late replication with the presence of sequences receptive to DAPI may make some fragile sites available for binding with this compound and thus no longer capable of undergoing normal condensation.…”

Dicationic DNA Minor Groove Binders as Antimicrobial Agents

“…Several different enzymes from different organisms have been implicated as possible targets [92,96,116,129,130]. It is also possible that the dications may act by direct inhibition of transcription [3,131]. Despite the fact that no unifying mechanism across organisms has yet emerged, the potent and broad-spectrum activity of furamidine and related dicationic molecules and their selective DNA affinity has stimulated us to The hydrogen bonds between the DB75 amidines and the T carbonyl groups can be identified on the left and the twist of the DB75 structure is seen on the right.…”

Nucleosome Positioning Determinants

“…However, nucleosome formation occurs at multiple positions along these circular DNA fragments, presumably because of the monotonous bending along these segments. 34,35 Likewise, the repeating TG reference standard described by Crothers and co-workers displays a high affinity for the histone octamer but fails to position a nucleosome at a single translational site in vitro or in vivo. 19,36 More likely, translational positioning results from signals that occur at unique locations within the nucleosome.…”