Visualization of drug-nucleic acid interactions at atomic resolution

The neighbor-exclusion principle is one of the most general and interesting rules describing intercalative DNA binding by small molecules. It suggests that such binding can only occur at every other base-pair site, reflecting a very large negative cooperativity in the binding process. We have carried out molecular mechanics and molecular dynamics simulations to study intercalation complexes between 9-amino acridine and the base-paired heptanucleotide d(CGCGCGC) d(GCGCGCG), in which the neighbor-exclusion principle was both obeyed and violated. Our studies find no stereochemical preference that favors the neighbor-exclusion-obeying structures over the neighbor-exclusion-violating structures. Alternative explanations for the existence of the neighbor-exclusion principle are vibrational entropy effects that we calculate to favor the more flexible neighbor-exclusion models over the more rigid neighbor-exclusion-violating models and polyelectrolyte (counterion release) effects.The neighbor-exclusion principle proposed by Crothers (1) is one of the most general rules for intercalative binding of planar drugs to DNA. According to this principle, every second (next-neighbor) intercalation site along the length of the DNA double helix remains unoccupied. Experimental evidence for this principle has been found in fiber diffraction studies on nucleic acid fibers bound to metallointercalative agents (2, 3), in single-crystal studies (4-8) on complexes between dinucleoside monophosphates complexed with intercalating drugs, and solution studies on binding of ethidium ion to oligonucleotides of ribose and deoxyribose sugars (9). Based on earlier crystallographic studies (4-6) that suggested mixed sugar puckering at the intercalation site, a stereochemical basis for the neighbor-exclusion principle was proposed. However, this mixed sugar puckering scheme has not been shown to be essential for creating intercalating sites in double-helical DNA through several crystal structure and model building studies (7-11).The first evidence suggesting violation of the neighborexclusion model was obtained from viscometric studies (12-14) on interactions between bi-and triderivatives of acridine and DNA, where it was suggested that a single base pair was sandwiched between two acridines. 1H NMR studies on the binding of a series of bis(acridine) compounds to d(AT)5d(AT)5, in which the two acridine rings were linked through linker chains of various lengths, found no evidence of violation of the neighbor-exclusion principle (15,16).However, it was also noted that these studies have not ruled out violation of the neighbor-exclusion principle under different salt conditions and temperatures or a different nucleotide sequence (15). It has been postulated (17) that the anticooperativity of ethidium binding to DNA could be explained without reference to the neighbor-exclusion rule and is solely due to polyelectrolyte effects.Why do some simple monofunctional intercalators such as 9-amino acridine not intercalate at neighboring sites and viol...

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Molecular mechanical simulations on double intercalation of 9-amino acridine into d(CGCGCGC) X d(GCGCGCG): analysis of the physical basis for the neighbor-exclusion principle.

Rao¹,

Kollman²

1987

“…It unwinds the DNA helix by 260 (25), and induces changes in sugar pucker, glycosidic torsional angle, and phosphodiester torsional angles in DNA and RNA (26)(27)(28). These changes in winding angle and conformation produce a slight bending of the DNA helix towards the major groove (28). In general, intercalation of planar molecules causes lengthening and stiffening of the helix (4).…”

Section: Discussionmentioning

confidence: 99%

Binding of ethidium bromide causes dissociation of the nucleosome core particle.

McMurray¹,

Holde²

1986

The binding of ethidium bromide to chicken erythrocyte core particles results in a step-wise dissociation of the structure that involves the initial release of one copy each of histones H2A and H2B. Quantitation of the dissociated DNA reveals that a critical amount of drug is required for the dissociation. Above the critical value, the dissociation is time dependent, reversible, and independent of DNA concentration.

“…Helical alterations in DNA of the type we have proposed would also involve an angular unwinding (26) at the site of the ribonucleotide. Possibly both of these effects in concert account for the surprising ability of even a single ribo residue in DNA to impair nucleosome formation.…”

mentioning

confidence: 99%

Ribonucleotide-induced helical alteration in DNA prevents nucleosome formation.

Hovatter¹,

Martinson²

1987

Several polynucleotides that assume an Aform helical structure in solution are unable to form nucleosomes. We attempted to establish a relationship between the ease of the A-form -+ B-form helix transition and ease of nucleosome formation by reconstituting nucleosomes using ribosubstituted DNA containing various levels of ribonucleotides. Instead we discovered that, when riboadenosine is substituted for deoxyriboadenosine, even one ribonucleotide per 125 base pairs of DNA reduces nucleosome formation and that DNA containing >5% ribonucleotide is completely unable to form nucleosomes. Ribosubstituted DNA restriction fragments exhibited altered mobility on native 6% polyacrylamide gels, indicating an altered helical structure (probably bending).The effects on both nucleosome formation and gel mobility are nucleotide specific and are correlated, being greatest for riboadenosine and decreasing in the order riboadenosine > riboguanosine > ribocytosine. The results are consistent with the hypothesis that the rate of nucleosome formation can be drastically reduced by isolated local perturbations, such as kinking or bending, in the helical structure of DNA.We are interested in the manner by which DNA helix structure modulates its own mode of packaging by histones in chromatin. In some cases the effects on packaging have obvious physiological implications. For example, the positioning of artificial nucleosomes on Escherichia coli lac operator DNA (1) constrains the DNA in such a way that the repressor binding surface of the DNA always faces outward to bind repressor (2). Eukaryotic examples include the specific positioning of nucleosomes on 5S gene DNA (3) so as to facilitate binding by transcription factor IIIA (4) and the avoidance by nucleosomes of poly(dA)-poly(dT) tracts in DNA (5, 6), which probably accounts for the promoteractivating properties of this sequence in chromatin (7).It now appears that the sequence-specific positioning of nucleosomes and the sidedness with which DNA binds the histone core may be explained by the tendency of certain short sequence elements (8) The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.