Heterogeneous DNA binding modes of berenil

Isothermal titration calorimetry (ITC) profiles of berenil bound to different DNAs show that, despite the strong preference of berenil for AT-rich regions in DNA, it can bind to other DNA sequences significantly. The ITC results were used to quantify the binding of berenil, and the thermodynamic profiles were obtained using natural DNAs as well as synthetic polynucleotides. ITC binding isotherms cannot be simply described when a single set of identical binding sites is considered, except for poly[d(A-T)2]. Ultraviolet melting of DNA and differential scanning calorimetry were also used to quantify several aspects of the binding of berenil to salmon testes DNA. We present evidence for secondary binding sites for berenil in DNA, corresponding to G+C rich sites. Berenil binding to poly[d(G-C)2] is also observed. Circular dichroism experiments showed that binding to GC-rich sites involves drug intercalation. Using a molecular modeling approach we demonstrate that intercalation of berenil into CpG steps is sterically feasible.

Crystal structure of a DNA Holliday junction

DNA recombination is a universal biological event responsible both for the generation of genetic diversity and for the maintenance of genome integrity. A four-way DNA junction, also termed Holliday junction, is the key intermediate in nearly all recombination processes. This junction is the substrate of recombination enzymes that promote branch migration or catalyze its resolution. We have determined the crystal structure of a four-way DNA junction by multiwavelength anomalous diffraction, and refined it to 2.16 A resolution. The structure has two-fold symmetry, with pairwise stacking of the double-helical arms, which form two continuous B-DNA helices that run antiparallel, cross in a right-handed way, and contain two G-A mismatches. The exchanging backbones form a compact structure with strong van der Waals contacts and hydrogen bonds, implying that a conformational change must occur for the junction to branch-migrate or isomerize. At the branch point, two phosphate groups from one helix occupy the major groove of the other one, establishing sequence-specific hydrogen bonds. These interactions, together with different stacking energies and steric hindrances, explain the preference for a particular junction stacked conformer.

The identification of nuclear proteins that bind the homopyrimidine strand of d(GA.TC)n DNA sequences, but not the homopurine strand

Alternating d(GA.TC)(n)DNA sequences, which are abundant in eukaryotic genomes, can form altered DNA structures. Depending on the environmental conditions, the formation of (GA.GA) hairpins or [C+T(GA.TC)] and [GA(GA.TC)] intramolecular triplexes was observed in vitro. In vivo, the formation of these non-B-DNA structures would likely require the contribution of specific stabilizing factors. Here, we show that Friend's nuclear extracts are rich in proteins which bind the pyrimidine d(TC)(n)strand but not the purine d(GA)n strand (NOGA proteins). Upon chromatographic fractionation, four major proteins were detected (NOGA1-4) that have been purified and characterized. Purified NOGAs bind single-stranded d(TC)n with high affinity and specificity, showing no significant affinity for either d(GA)n or d(GA.TC)nDNA sequences. We also show that NOGA1, -2 and -3, which constitute the three most abundant and specific NOGA proteins, correspond to the single-stranded nucleic acid binding proteins hnRNP-L, -K and -I, respectively. These results are discussed in the context of the possible contribution of the NOGA proteins to the stabilization of the (GA.GA) and [GA(GA.TC)] conformers of the d(GA.TC)n DNA sequences.

Crystallization and preliminary structural results of catalase from human erythrocytes

Catalase (hydrogen peroxide:hydrogen peroxide oxidoreductase, E.C. 1. 11.1.6) is present in most aerobic prokaryotic and eukaryotic cells. Despite a large number of studies on catalases, the only mammalian catalase structure available is that from beef liver, in which about 50% of the haem groups are degraded to bile pigments. Three different crystal forms of human erythrocyte catalase were obtained by the hanging-drop vapour-diffusion technique using PEG as precipitant. Monoclinic crystals, with space group P21 and unit-cell parameters a = 102.9, b = 140.0, c = 173.6 A and beta = 103.2 degrees, require NADP(H) in the crystallization solution. Two types of hexagonal packing, with unit-cell parameters of either a = b = 86. 9, c = 255.5 A or a = b = 90.0, c = 521.2 A, were obtained under identical crystallization conditions in the absence of NADP(H). Only one diffraction data set could be collected: this was obtained from the hexagonal crystals with the smaller c axis using synchrotron radiation, with resolution to 2.65 A. A molecular-replacement solution, determined using a modified beef-liver catalase model as a search structure, corresponds to space group P6422 and contains a single subunit in the asymmetric unit, with an estimated solvent volume of about 50%. The packing determined suggests how minor rearrangements might allow the transition between both hexagonal crystal forms and provides an explanation for the anisotropic character of the corresponding diffractions.

The interaction of zinc(II) ions with antiparallel-stranded d(GA)n DNA homoduplexes

In the presence of specific metal-ions (namely zinc but also cadmium, cobalt and manganese), d(GA x TC)n DNA sequences can form non-B-DNA conformations. At low metal-ion concentration they form [GA(GA x TC)] intramolecular triplexes but, upon increasing the metal concentration, the formation of (GA x GA) intramolecular hairpins is detected. In this paper we address the question of the specific effects of zinc on the structure of the d(GA x TC)n sequences. In the presence of zinc, the DMS-reactivity of the (GA x GA) hairpins is strongly reduced suggesting a direct interaction of the metal-ion with the N7-group of the guanines. This effect is specific for antiparallel-stranded d(GA)n homoduplexes. No such strong decrease in DMS-reactivity is observed in B-DNA duplexes or in d(GGA)n and d(GGGA)n homoduplexes. In addition, the thermal stability of antiparallel-stranded d(GA)n homoduplexes increases in the presence of zinc. On the contrary, the melting temperature of similar B-DNA molecules decreases upon increasing the zinc concentration. Altogether, these result indicate that zinc plays an specific role on the stabilization of the (GA x GA) intramolecular hairpins.

Tandem 5'-GA:GA-3' mismatches account for the high stability of the fold-back structures formed by the centromeric Drosophila dodeca-satellite

The centromeric dodeca-satellite of Drosophila forms unusual DNA structures in which its purine-rich strand (GTACGGGACCGA)n folds into very stable intramolecular hairpins. These intramolecular hairpins contain groups of tandem 5'-GA:GA-3' mismatches that, as judged by gel electrophoresis analysis and UV-melting studies, have a determinant contribution to their stability. Duplexes of the dodeca-satellite purine-rich strand, carrying tandem 5'-GA:GA-3' mismatches, are as stable as equivalent fully Watson-Crick duplexes containing tandem 5'-TA:TA-3' Watson-Crick pairs in place of the non-Watson-Crick G.A pairs. On the other hand, duplexes carrying any of the other three possible tandem combinations of purine.purine mismatches, including G.A pairs on the opposite orientation 5'-AG:AG-3', are very unstable. The high stability of the dodeca-satellite hairplus suggests that the tandem G.A pairs are on the sheared configuration although they are found within the less favourable 5'-G-(G-A)-C-3' sequence context. Other centromeres DNA sequences, including the AAGAG satellite of Drosophila and the mammalian CENP-B box sequence, have the potential of forming intramolecular hairpins stabilised by similar purine.purine interactions.

Divalent zinc cations induce the formation of two distinct homoduplexes of a d(GA)20 DNA sequence

Homopurine DNA sequences are highly structurally polymorphic. In particular, d(GA)n DNA sequences are known to be capable of forming intramolecular foldbacks, bimolecular homoduplexes, and tetrastranded complexes. Counterions play a determinant role on the equilibria between the different structural conformers of d(GA)n sequences. In this paper, the effect of divalent zinc cations on the structure of a d(GA)20 oligonucleotide has been analyzed by CD spectroscopy and polyacrylamide gel electrophoresis. Depending on the precise experimental conditions at which zinc is added, two distinct conformations of the d(GA)20 oligonucleotide are stabilized. At neutral pH in the absence of zinc, d(GA)20 is partially organized into intramolecular foldbacks and bimolecular homoduplexes [Casasnovas et al. (1993) J. Mol. Biol. 233, 671-681]. Under these conditions, addition of zinc results in the stabilization of the bimolecular homoduplex which is nonspecific for zinc since it is also stabilized by divalent magnesium cations, increasing ionic strength, or decreasing pH. Its CD spectrum is identical to that reported earlier for parallel-stranded d(GA)n homoduplexes [Rippe et al. (1992) EMBO J. 11, 3777-3786]. On the other hand, if zinc is added under conditions where the d(GA)20 oligonucleotide is exclusively single-stranded, a different bimolecular homoduplex appears which is only observed in the presence of zinc. The zinc-specific duplex melts cooperatively, and, in contrast to the nonspecific duplex, its thermostability is high. Transition from the nonspecific to the zinc-specific duplex is observed at high zinc concentrations or at high temperatures. The transition is cooperative. These results are discussed in the context of the specific cation effects on the formation of intramolecular R.R.Y triplexes at d(GA.TC)n DNA sequences.

Structural polymorphism of d(GA.TC)n DNA sequences. Intramolecular and intermolecular associations of the individual strands

Alternating d(GA.TC)n sequences are highly structurally polymorphic. Most of their conformational flexibility is likely to reside in the structural properties of the individual strands themselves. In this paper the conformational behaviour of the d(GA)20 and d(TC)20 oligonucleotides was analysed. Formation of d(GA)20 intramolecular duplexes is observed at any pH value, from 8.3 to 4.6. On the other hand, intramolecular d(TC)20 duplexes are formed only under acidic conditions. The acid d(TC)20 intramolecular duplex is likely to be stabilized through the formation of C+C pairs, the thymine residues remaining unpaired. The d(GA)20 oligonucleotide also forms intermolecular duplexes which coexist with the intramolecular forms at any pH, from 8.3 to 4.6. The structural conformation adopted by the d(TC)20 oligonucleotide at neutral pH is uncertain. Under these conditions, this oligonucleotide shows an electrophoretic apparent molecular weight consistent with the formation of a bimolecular complex. However, no hydrogen bonding was observed to occur under these conditions. Implications of these results for an understanding of the molecular principles behind the conformational flexibility of alternating d(GA.TC)n sequences are discussed. The possible biological significance of these results is also discussed.