Long‐range interactions between DNA‐bound ligands

Abstract

We have studied the interaction of the A:T specific minor-groove binding ligand 4',6-diamidino-2-phenylindole (DAPI) with synthetic DNA oligomers containing specific binding sites in order to investigate possible long-range interactions between bound ligands. We find that DAPI binds cooperatively to the oligomers. The degree of cooperativity increases with increasing number of binding sites and decreases with the separation between them. This dependence is paralleled by changes in the induced circular dichroism spectrum of DAPI, which decreases in intensity at 335 nm and increases at 365 nm. These results are consistent with an allosteric interaction of DAPI with DNA, where bound ligands cooperatively alter the structure of the DNA molecule. This structural change seems possible to induce under various conditions, including physiological. One consequence of allosteric binding is that ligands bound at a distance from each other sense each other's presence and influence each others' properties. If some regulatory proteins induce the same conformational change as DAPI, novel mechanisms for controlling gene expression can be anticipated.

Cooperativity in the Binding of Echinomycin to DNA Fragments Containing Closely Spaced CpG Sites

“…Cooperativity mediated via conformational changes in DNA has been envisaged with monointercalating drugs such as daunomycin (Krugh et al, 1981;Chaires, 1983;Correia & Chaires, 1994), ethidium (Winkle et al, 1982), actinomycin, and certain anthracenedione derivatives. Cooperative binding of distamycin and DAPI into the minor groove of DNA and synthetic polynucleotides has also been reported (Samuelson et al, 1994). It is entirely possible that cooperative binding of drugs to DNA may be an underlying principle for enhancing their effect on DNA structure and metabolism.…”

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

“…The binding of a protein to a single site on nucleosomal DNA is usually not sufficient to promote displacement since it is energetically favorable for the adjacent DNA in the nucleosome to remain bound to histones (57)(58)(59). Protein-induced disruption may occur by ATP-dependent processes or by an energy-independent mechanism when multiple factor binding sites are clustered on the nucleosomal DNA (57)(58)(59)(60)(61)(62). The results in Fig.…”

Identification of Preferred Distamycin−DNA Binding Sites by the Combinatorial Method REPSA

“…For a series of (A/T) 4 sequences, distamycin demonstrated binding affinities ranging from 0.1 to 1.0 µM (9). Numerous studies have shown that distamycin effectively inhibits DNA cleavage by both nonspecific endonucleases and restriction endonucleases (reviewed in ref 10) and that higher-affinity, multimeric distamycin binding sites exist in heterogeneous DNA (11). Taken together, these findings suggest that distamycin would provide an ideal test for REPSA.…”

“…This length of random sequence is many times that of an individual distamycin binding site (5 bp). Thus, ST3 allows screening for multimeric distamycin binding sites, which are believed to have higher affinities (11). The flanking sequences were designed to allow interconversion of the IISRE sites, from BpmI to BsgI or Eco57I, depending on the primers used.…”