Distribution of histone F1 on calf thymus nucleohistone DNA

Melting of cross-linked DNA v. cross-linking effect caused by local stabilization of the double helix

DNA interstrand cross-links are usually formed due to bidentate covalent or coordination binding of a cross-linking agent to nucleotides of different strands. However interstrand linkages can be also caused by any type of chemical modification that gives rise to a strong local stabilization of the double helix. These stabilized sites conserve their helical structure and prevent local and total strand separation at temperatures above the melting of ordinary AT and GC base pairs. This local stabilization makes DNA melting fully reversible and independent of strand concentration like ordinary covalent interstrand cross-links. The stabilization can be caused by all the types of chemical modifications (interstrand cross-links, intrastrand cross-links or monofunctional adducts) if they give rise to a strong enough local stabilization of the double helix. Our calculation demonstrates that an increase in stability by 25 to 30 kcal in the free energy of a single base pair of the double helix is sufficient for this "cross-linking effect" (i.e. conserving the helicity of this base pair and preventing strand separation after melting of ordinary base pairs). For the situation where there is more then one stabilized site in a DNA duplex (e.g., 1 stabilized site per 1000 bp), a lower stabilization per site is sufficient for the "cross-linking effect" (18 - 20 kcal). A substantial increase in DNA stability was found in various experimental studies for some metal-based anti-tumor compounds. These compounds may give rise to the effect described above. If ligand induced stabilization is distributed among several neighboring base pairs, a much lower minimum increase per stabilized base pair is sufficient to produce the cross-linking effect (1 bp- 24.4 kcal; 5 bp- 5.3 kcal; 10 bp- 2.9 kcal, 25 bp- 1.4 kcal; 50 bp- 1.0 kcal). The relatively weak non-covalent binding of histones or protamines that cover long regions of DNA (20- 40 bp) can also cause this effect if the salt concentration of the solution is sufficiently low to cause strong local stabilization of the double helix. Stretches of GC pairs more than 25 bp in length inserted into poly(AT) DNA also exhibit properties of stabilizing interstrand cross-links.

Differences in the binding of methylated albumin to non-replicating, replicating and denatured DNA from Ehrlich ascites cells

The binding of methylated albumin to DNA, the basis of the chromatography on columns of kieselguhr coated with methylated albumin (MAK chromatography), was investigated. Scatchard plots revealed only one mode of interaction with fully double-stranded DNA. The complexes should be completely dissociated by raising the NaCl concentration of the solution to 0.8 M, indicating a binding by electrostatic attraction between the oppositely charged protein and DNA molecules. In complexes with denatured and partially single-stranded replicating DNA an additional kind of binding was found which made these complexes more stable against salt dissociation. These secondary interactions were stronger at 23 degrees C than at 0 degrees C and could be weakened by the addition of 6 M urea. It was therefore concluded that apolar forces were involved in these interactions.

Transition from noncooperative to cooperative and selective binding of histone H1 to DNA

A transition from noncooperative to cooperative binding of DNA and histone h1 occurs between 20 and 40mMNaCI in 5 mM Tris-HCI, pH 7.5. Below 20mM NaCI in mixtures in H1 and excess DNA, H1 binds to all of the DNA molecules, causing them to sediment faster, and does not distinguish between DNA molecules that differ in size or base composition. However, at NaCI concentrations above the narrow transition range, H1 binds to only some of the DNA molecules and leaves the rest free. If the DNA molecules in a mixture are the same size, H1 selectively binds those that have the highest content of adenosine (A)+thymidine (T). By means of competion experiments at salt concentrations spanning the transition range, it is demonstrated that H1 selectivity requires cooperativity. A high degree of selectivity based on A + T content can be produced by cooperative binding: for average DNA sizes of 2 X10(6) daltons, more than ten molecules of calf lymphocyte DNA (57% a+ t) are chosen per molecule of Escherichia coli DNA (50% A+T).