There is a wealth of crystallographic information on model drug-nucleic acid crystalline complexes contributed over the years by our laboratory and other laboratories around the world. From these data, it is possible to divide intercalators into two general classes -- simple and complex.


Simple intercalators (shown in Figure 1 and in Table 1) bind to the beta-structural element in both DNA and RNA model dinucleotide systems (i.e., this contains the C3' endo (3'-5') C2' endo mixed-pucker geometry). The interactions are "simple" in the sense that they involve stacking interactions with the base pairs and electrostatic interactions with the sugar-phosphate chains.

Figure 1. Chemical structures of simple intercalators.

Figure 1. Chemical structures of simple intercalators.

Simple intercalators demonstrate a sequence binding preference, CpG and TpA, in these model solid-state studies, and in related solution studies (Krugh and Reinhardt, 1975). This reflects the ease of unstacking pyrimidine-purine sequences versus purine-pyrimidine sequences -- an important consideration in understanding how simple intercalators bind to synthetic DNA- (and RNA-) like polymers such as poly d (A-T) and poly d (G-C). Other effects predominate, however, when simple intercalators bind to long chain naturally occurring DNA molecules (see later discussions).

Table 1

A typical study that demonstrates the beta-structural element is ethidium: cytidylyl (3'-5') guanosine (Jain and Sobell, 1984b). See Figure 2. This complex consists of an intercalated ethidium molecule (shown with dark covalent bonds) and stacked ethidium molecules (shown with light covalent bonds) above and below the intercalated complex. Sugar-phosphate conformations contain the mixed sugar-puckering pattern: cytidylyl [C3' endo (3'-5') C2' endo] guanosine.

Figure 2. Structure of a 2:2 ethidium: CpG crystalline complex.

Figure 2. Structure of a 2:2 ethidium CpG crystalline complex.

Cytidylyl residues are C3' endo and in the low anti conformation, while guanosine residues are C2' endo and in the high anti conformation. Base pairs above and below the intercalator are twisted (using as a reference the angle relating interglycosidic (C1') vectors projected on the plane of the ethidium chromophore) by about 9 degrees, and are separated 6.7 Angstroms. The planes of the G-C base pairs above and below the intercalator are not exactly parallel. They are inclined by about 10 degrees, opening into the narrow groove direction. This reflects the steric presence of the phenyl- and ethyl- groups on the intercalated ethidium molecule.

The beta-structural element is observed in 15 separate crystallographic determinations. These involve seven different intercalators complexed to a variety of DNA-like and RNA-like self-complementary dinucleoside monophosphates (see Table 1). Four structures [5-iodocytidylyl (3'-5') guanosine complexed to ellipticine, acridine orange, tetramethyl-N-methylphenantrolinium, and N, N-dimethylproflavine] are isomorphous and therefore demonstrate a guest-host relationship. The remaining 11 structures crystallize in different lattice environments that contain variable numbers of water molecules. The invariance of the beta- geometry in this series of studies argues that the beta-structural element is a particularly stable structure that can accommodate a large variety of heterocyclic ring systems without significant alterations in its geometry, and that this geometry forms equally well with either DNA- or RNA-like dinucleotides.

Two key predictions arise if one uses this information to understand how simple intercalators bind to DNA. The first is that simple intercalators unwind DNA at the immediate intercalation site by about 26 degrees (i.e., 36 - 10 = 26) (see Wang, 1974). The second is that simple intercalators bind DNA sequentially, giving rise to expanding domains of neighbor-exclusion structure. The presence of this structure is most easily detected at saturating drug/DNA-binding ratios (see Bond et al., 1975). See Figure 3.

Figure 3. Ethidium-DNA Neighbor Exclusion Binding Model

Figure 3. Ethidium-DNA Neighbor-Exclusion Binding Model.

  This helical complex is calculated with information obtained from X-ray crystallographic studies of the ethidium dinucleoside monophosphate complexes, using the technique of linked atom least squares. The beta-structural element plus ethidium form the asymmetric unit of the helix. Repeated twist (47.2 degrees) and translation (9.8 Angstroms) of this asymmetric unit along the helix axis generates the helical complex shown.

It should be noted that intercalation occurs between every other base pair, since binding is restricted to neighboring beta-structural elements. This feature explains the magnitude of DNA stretching and unwinding accompanying neighbor-exclusion binding. Notice that the stereochemistry connecting neighboring beta-structural elements is different (i.e., C2' endo (3'-5') C3' endo). There is no significant stretching or unwinding in this region.

Since DNA in this helical complex contains the beta-structural element as its underlying asymmetric unit, we have called this structure beta-DNA. As explained earlier, beta-DNA is a metastable and hyperflexible DNA form that exists in variety of energy states. Its highest energy state (found in this ethidium-DNA complex) corresponds to a transition state intermediate in DNA melting. Being unstable, this state must be "pinned" by ethidium in order to be visualized.

We envision the intercalation process to involve the following steps:
  1. Simple intercalators (i.e., ethidium) begin by "pinning" premeltons that arise spontaneously in DNA ("nucleation").

  2. As the drug/DNA binding-ratio increases, ethidium continues to bind to DNA sequentially to form expanding domains of neighbor-exclusion structure, surrounded by moving (kink-antikink) phase boundaries on either side ("propagation").

  3. At saturation, practically all the DNA is complexed with ethidium, DNA being held in an elongated and unwound (high-energy) beta-DNA form.

  4. The above process is most easily understood as being a structural phase transition, in which the ethidium: (high-energy) beta-DNA complex emerges as the dominant phase.
A similar mechanism can explain how simple intercalators bind to double-stranded RNA.