Three-dimensional Structure Of DNA Research Articles

Modelling the probability distribution of the number of DNA double-strand breaks due to sporadic alkylation of nucleotide bases

Metabolites and certain chemical agents (for example methyl methanesulfonate) can induce nucleotide bases on chromosomal strands to become alkylated. These alkylated sites have the potential to become single-strand chromosomal breaks, a form of DNA damage, if they are exposed to a sufficient temperature in vitro. It has been proposed that a single-strand break (SSB) sufficiently close to another SSB on the opposite chromosomal strand will form a double-strand break (DSB). DNA repair mechanisms are less able to repair DSBs compared to SSBs. Because of the complex three-dimensional structure of DNA, some chromosomal regions are more susceptible to alkylation than others. A question of interest is therefore whether these alkylated bases are randomly distributed or tend to be clustered. Pulsed-field gel electrophoresis allows the number of DNA fragments (and hence the number of DSBs) to be observed directly. The randomness of alkylation events can therefore be tested using the standard statistical hypothesis-testing framework. Under the null hypothesis, that the SSBs are randomly distributed on each of the strands, we can calculate the probability of observing a number of DSBs at least as large as that observed and hence the associated p-value. Previously, the probability distribution of the number of DSBs has been determined by Monte Carlo simulations; when considering the whole genome this can be very time consuming. In this paper, we theoretically derive an approximation to the distribution enabling appropriate probabilities to be calculated quickly. Based on previous findings we assume that the number of breaks on each strand is small compared to the number of nucleotide bases. We show that our method can give the correct probability distribution when alkylation events are relatively rare, discuss how rare these events have to be and suggest potential extensions to the model when a greater proportion of bases are alkylated.

Epigenetic mechanisms: a common theme in vertebrate and invertebrate memory formation.

In this review we address the idea that conservation of epigenetic mechanisms for information storage represents a unifying model in biology, with epigenetic mechanisms being utilized for cellular memory at levels from behavioral memory to development to cellular differentiation. Epigenetic mechanisms typically involve alterations in chromatin structure, which in turn regulate gene expression. An emerging idea is that the regulation of chromatin structure through histone acetylation and DNA methylation may mediate long-lasting behavioral change in the context of learning and memory. We find this idea fascinating because similar mechanisms are used for triggering and storing long-term 'memory' at the cellular level, for example when cells differentiate. An additional intriguing aspect of the hypothesis of a role for epigenetic mechanisms in information storage is that lifelong behavioral memory storage may involve lasting changes in the physical, three-dimensional structure of DNA itself.

Writhe of DNA induced by a terminal twist

This paper considers the three-dimensional structure of B-form DNA. The molecule may be open or covalently closed. For the former, its two ends are not allowed to move or rotate freely in space unless the molecule is under the influence of rigid body motions of the ambient space. Implied by the elastic rod model for DNA, the molecule writhes immediately when subject to a terminal twist as long as its axis is none of the following curves: lines, circular arcs, circular helices. This result is remarkably different from well-known results about DNA of other conformations. For example, if a DNA is regarded as an elastic rod whose axis is a circle, then it has no induced writhe when subject to a terminal twist until the latter meets a critical extent.

Self-assembly of irregular graphs whose edges are DNA helix axes.

A variety of computational models have been introduced recently that are based on the properties of DNA. In particular, branched junction molecules and graphlike DNA structures have been proposed as computational devices, although such models have yet to be confirmed experimentally. DNA branched junction molecules have been used previously to form graph-like three-dimensional DNA structures, such as a cube and a truncated octahedron, but these DNA constructs represent regular graphs, where the connectivities of all of the vertexes are the same. Here, we demonstrate the construction of an irregular DNA graph structure by a single step of self-assembly. A graph made of five vertexes and eight edges was chosen for this experiment. DNA branched junction molecules represent the vertexes, and duplex molecules represent the edges; in contrast to previous work, specific edge molecules are included as components. We demonstrate that the product is a closed cyclic single-stranded molecule that corresponds to a double cover of the graph and that the DNA double helix axes represent the designed graph. The correct assembly of the target molecule has been demonstrated unambiguously by restriction analysis.

A unique loop in the DNA-binding crevice of bacteriophage T7 DNA polymerase influences primer utilization.

The three-dimensional structure of bacteriophage T7 DNA polymerase reveals the presence of a loop of 4 aa (residues 401-404) within the DNA-binding groove; this loop is not present in other members of the DNA polymerase I family. A genetically altered T7 DNA polymerase, T7 polDelta401-404, lacking these residues, has been characterized biochemically. The polymerase activity of T7 polDelta401-404 on primed M13 single-stranded DNA template is one-third of the wild-type enzyme and has a 3'-to-5' exonuclease activity indistinguishable from that of wild-type T7 DNA polymerase. T7 polDelta401-404 polymerizes nucleotides processively on a primed M13 single-stranded DNA template. T7 DNA polymerase cannot initiate de novo DNA synthesis; it requires tetraribonucleotides synthesized by the primase activity of the T7 gene 4 protein to serve as primers. T7 primase-dependent DNA synthesis on single-stranded DNA is 3- to 6-fold less with T7 polDelta401-404 compared with the wild-type enzyme. Furthermore, the altered polymerase is defective (10-fold) in its ability to use preformed tetraribonucleotides to initiate DNA synthesis in the presence of gene 4 protein. The location of the loop places it in precisely the position to interact with the tetraribonucleotide primer and, presumably, with the T7 gene 4 primase. Gene 4 protein also provides helicase activity for the replication of duplex DNA. T7 polDelta401-404 and T7 gene 4 protein catalyze strand-displacement DNA synthesis at nearly the same rate as does wild-type polymerase and T7 gene 4 protein, suggesting that the coupling of helicase and polymerase activities is unaffected.

Topoisomerase I inhibition and cytotoxicity of 5-Bromo- and 5-Phenylterbenzimidazoles

Topoisomerase I is an enzyme that is essential for maintaining the three-dimensional structure of DNA during the processes of transcription, translation and mitosis. With the introduction of new clinical agents that are effective in poisoning topoisomerase I, this enzyme has proved to be an attractive molecular target in the development of anticancer drugs. Several terbenzimidazoles have been identified as potent topoisomerase I poisons. Structure–activity data on various terbenzimidazoles have revealed that the presence of lipophilic substituents at the 5-position of various terbenzimidazoles correlates with enhanced cytotoxicity. While the effect of having substituents at both the 5- and 6-positions had not been evaluated, previous studies did indicate that the presence of a fused benzo-ring at the 5,6-position results in a significant decrease in topoisomerase I poisoning activity and cytotoxicity. In the present study we investigated whether substituents at both the 5- and 6-positions of varied terbenzimidazoles would allow for retention of topo I poisoning activity. The 6-bromo, 6-methoxy, or 6-phenyl derivatives of both 5-bromo- and 5-phenylterbenzimidazole were synthesized and evaluated for topo I poisoning activity, as well as their cytotoxicity toward human lymphoblastoma cells. The data indicate that such derivatives do retain similar topo I poisoning activity and possess cytotoxicity equivalent to either 5-bromo- or 5-phenylterbenzimidazole. Significant enhancement in the topoisomerase I poisoning activity and cytotoxicity of 5-phenylterbenzimidazole is observed when the 2″-position is substituted with either a chloro or trifluoromethyl substituent. The influence of such substituents on the biological activity of 5,6-dibromoterbenzimidazole (6a) was also explored. In the case of either 2″-chloro-5,6-dibromoterbenzimidazole (6b) or 2″-trifluoromethyl-5,6-dibromoterbenzimidazole (6c), topoisomerase I poisoning was not enhanced relative to 6a. While cytotoxicity toward RPMI 8402 was also not significantly affected, comparative studies performed against several solid human tumor cell lines did reveal a significant increase in cytotoxicity observed for 6c as compared to 6a.

DNA loop domain organization: the three-dimensional genomic code.

It is well known that aberrations in the nuclear matrix contribute to the development of cancer, but many aspects of this process remain unknown. The mammalian sperm nuclear matrix serves as a distinctive model of DNA loop domain organization by the nuclear matrix since the integrity of the DNA structure can be measured by the ability of the paternal chromosomes to participate in embryogenesis. The structure of the nuclear matrix is known to be important for normal cellular functions such as transcriptional regulation and DNA replication. Even small aberrations in DNA structural organization in the sperm cell could have disastrous consequences for the embryo if they were essential for function. Recent work from our laboratory suggests that sperm nuclei with disrupted nuclear matrix structures but intact DNA cannot participate fully in embryogenesis, suggesting that the structural organization of DNA may provide important, heritable information that is necessary for development. We term the DNA sequence together with its three-dimensional organization the "genomic code." We suggest that the sperm nucleus is an ideal model for understanding the principles of the involvement of the three-dimensional structure of DNA in normal cellular function. Finally, the implications for cancer about what we can learn using sperm DNA as a model about the "genomic code" are discussed. J. Cell. Biochem. Suppl. 35:23-26, 2000.

Sequence-dependent DNA structure.

The three-dimensional structure of DNA depends subtly on its sequence, and this property is used by the proteins that regulate gene expression to locate their target sequences. Despite the large body of experimental data that has been accumulated on the relationship between sequence and DNA structure, we still do not fully understand the molecular basis for these properties, nor can we predict a three-dimensional structure from a given sequence. We have been using computer modelling to tackle these problems. Some of our results and the implications for understanding the biological role of key sequences are discussed here.

In vitro selection of optimal AbrB-binding sites: comparison to known in vivo sites indicates flexibility in AbrB binding and recognition of three-dimensional DNA structures.

The AbrB protein of Bacillus subtilis regulates expression of numerous genes, primarily through specific binding interactions to DNA regions containing transcriptional promoters. Although over 15 target regions for AbrB binding to chromosomally located sequences have been analysed by DNase I footprinting, no obvious consensus sequence or motif has yet emerged from their examination. Using in vitro selection techniques, we have isolated optimal AbrB-binding sites from oligonucleotides containing 22 or 44 random base pairs. The best of these sites have an apparent in vitro Kd which is fivefold lower than a similar-sized DNA fragment containing the sequence corresponding to the AbrB-binding site on the spo0E gene. We tested one of the sites in vivo and found that it confers AbrB-mediated control upon a promoter not normally regulated by AbrB. In each of four separate trials, the selected sites possess motifs that converge to a simple consensus. It is argued that the nature and spacing of these motifs produce a type of three-dimensional DNA structure recognizable by AbrB, and that known in vivo sites, which lack these motifs, possess an approximation of the optimal structural determinant.

A sequence-induced superhelical DNA segment serves as transcriptional enhancer

The initiation of transcription at the sigma 54-dependent promoter glnAp2 of Escherichia coli is activated by the protein NR1(NTRC)-phosphate, which binds to two sites located upstream of the promoter that together constitute an enhancer. The cooperative binding facilitates the oligomerization of NR1-phosphate endowing it with the ATPase activity required for its ability to serve as transcriptional activator. We show here that these sites can be replaced by sequence-dependent superhelical inserts, lacking any homology to the nucleotide sequence of the enhancers. These superhelical inserts, irrespective of their chirality, are as effective as the paired sites in binding NR1-phosphate and in stimulating its oligomerization. We conclude that a specific sequence of nucleotides and the three-dimensional structure of DNA can determine its affinity for the NR1 activator protein capable of binding to DNA.

Crystallographic studies of DNA helix structure

X-ray crystallography can reveal the three-dimensional structure of short fragments of DNA or RNA with unique precision. It provides information concerning both the global helical structure and the geometry of local features such as base-pair stacking patterns and backbone conformation. An analysis of the structures of a family of DNA decamers with related sequences, crystallizing in a number of different lattices, defines the ranges in which conformational parameters can vary in B-DNA helices and shows the correlations between them. Thus, these studies show the static structures and give insight into the mechanics of DNA helices by showing how a change of one local conformational parameter will influence others. Crystal structures are also used to assess the competing influences of nucleotide sequence and environment on the three-dimensional DNA structure. To extrapolate from DNA crystal structures to physical characteristics and function of these molecules in solution or embedded into a defined sequence context remains a major challenge.

Nucleic Acid Structure Analysis: Mathematics for Local Cartesian and Helical Structure Parameters That Are Truly Comparable Between Structures

Analyzing nucleic acid structures in a comparable manner has become increasingly important as the number of solved structures has increased. This paper presents the concepts, mathematics, theorems, and proofs that form the basis of a new program to analyze three-dimensional DNA and RNA structures. The approach taken here provides numerical data in accordance with guidelines set at a 1988 EMBO workshop. Mathematical definitions are provided for all local structural parameters described in the guidelines. The definitions satisfy the guideline requirements while preserving the original physical intuition of the parameters. In particular, the rotational parameters are true rotations based on a simple physical model (net rotation at constant angular velocity), not Euler angles or angles between vectors and planes as is the case with other approaches. As a result, the mathematical definitions are symmetrical with the property that a 5° tilt is the same as a 5° roll and a 5° twist, except that the rotations take place about different axes. In other approaches, a 5° tilt can mean a different amount of net rotation than a 5° roll or a 5° twist. A second unique feature of the mathematics is that it explicitly incorporates the concept of a pivot point, which is the point about which a base in a base-pair rotates as it buckles, propeller twists, and opens. Pivot points enable one to model the physical motion of bases more accurately. As a result, they greatly reduce and/or eliminate the statistical correlations between rotational and translational parameters that arise as mathematically induced artifacts in other approaches. This paper, together with the statistical analysis in the companion paper for determining the locations of the pivot points, provides everything needed to understand the output of the program as it relates to individual structures.

Topoisomerases, New Targets in Cancer Chemotherapy

The enzymes involved in the regulation of the three-dimensional structure of DNA, topoisomerase I and II, are important for the handling of DNA during vital cellular processes such as translation, transcription and mitosis. The enzymes are currently being studied intensively, they are being biochemically characterized and their mechanism of action is now better understood. Empirically discovered antitumor drugs appear to interfere with these enzymes, especially topoisomerase II. The DNA-topoisomerase II complex, which is an intermediate in the normal enzyme pathway, is stabilized by the drug and forms a 'cleavable complex', which appears to be cytotoxic. The drugs involved are, e.g. anthracyclines, epipodophyllotoxins and acridines. The central role of this enzyme offers the cell an opportunity for the development of resistance by down-regulation of this enzyme or the production of resistant mutants, provided the adaptation does not hamper other vital cell functions. Knowledge of the working mechanism and the cellular regulation of the topoisomerases might lead to the selection of most effective drugs and treatment schedules, and to circumvention of drug resistance.

1 New Approaches to DNA in the Crystal and in Solution

I. INTRODUCTION We review here the progress that has been made concerning the role of DNA in biology during the years 1979–1988. The first part of this chapter will deal with the use of X-ray crystallography to study the three-dimensional structure of DNA in single crystals at near-atomic resolution. This method led to the discovery of left-handed DNA (Pohl and Jovin 1972; Drew et al. 1978, 1980; Wang et al. 1979; Crawford et al. 1980) and also to the realization that the structure of normal, right-handed DNA depends on its nucleotide sequence (Dickerson and Drew 1981; Wang et al. 1982a; Shakked et al. 1983; McCall et al. 1985; Nelson et al. 1987). The second part of this chapter will describe how the results from X-ray crystallography made it possible to improve on the methods of studying DNA in solution using enzymes, chemicals, topological methods, “statistical sequencing,” and gel electrophoresis. Such solution studies turned out to be essential in learning more about the properties of DNA at a length of 50–200 bp for which it is difficult if not impossible to form single crystals. In brief, it was found that (1) most of the X-ray structures of short pieces of DNA are relevant to long DNA in solution (Lomonossoff et al. 1981; Drew and Travers 1984, 1985a; Johnston and Rich 1985; Burkhoff and Tullius 1987), (2) the ability of DNA to fold into a tightly curved shape about proteins depends on its nucleotide sequence (Drew and Travers 1985b; Satchwell...

Supercoils in plant DNA: nucleoid sedimentation studies.

Plant nuclei have been studied with respect to the three-dimensional structure of DNA. Nucleoids derived from nuclei by non-ionic detergent and high salt treatment were analysed by sedimentation in a series of sucrose gradients containing increasing amounts of the intercalating agent ethidium bromide. In addition the nucleoid sedimentation behaviour was investigated following gamma irradiation. The results show that plant DNA is supercoiled, as is the DNA from the other eukaryotes studied, and contains approximately the same concentration of superhelical turns but probably relatively fewer DNA superhelical loops. The plant nuclear populations in all cases studied give rise to two distinct nucleoid bands. These have been characterized by electron microscopy and by their DNA and protein content. The possible origin of the two bands is discussed.

Sequence-dependent anisotropic flexibility of B-DNA. A conformational study.

Bending flexibility of the six tetrameric duplexes was investigated d(AAAA):d(TTTT), d(AATT)2, d(TTAA)2, d(GGGG):d(CCCC), d(GGCC)2 and d(CCGG)2,. The tetramers were extended in the both directions by regular double helices. The stiffness of the B-DNA double helix when bent into the both grooves proved to be less than that in the perpendicular direction by an order of magnitude. Such an anisotropy is a property of the sugar-phosphate backbone structure. The calculated fluctuations of the DNA bending along the dyad axis, 5-7 degree, are in agreement with experimental value of the DNA persistence length. Anisotropy of the double helix is sequence-dependent: most easily bent into the minor groove are the tetramers with purine-pyrimidine dimer (RY) in the middle. In contrast, YR dinucleotides prefer bending into the major groove. Moreover, they have an equilibrium bend of 6-12 degree into this groove. The above inequality is caused by stacking interaction of the bases. The bend in the central dimer is distributed to some extent between the adjacent links, though the main fraction of the bend remains within the central link. Variation of the sugar-phosphate geometry in the bent helix is inessential, so that DNA remains within the B-family of forms: namely, when the helical axis is bent by 20 degree. the backbone dihedral angles vary by no more than 15 degree. The obtained results are in accord with x-ray structure of the B-DNA dodecamer; they further substantiate our early model of DNA wrapping in the nucleosome by means of "mini-kinks" separated by a half-pitch of the double helix, i.e. by 5-6 b.p. Sequence-dependent anisotropy of DNA presumably dictates the three-dimensional structure of DNA in solution as well. We have found that nonrandom allocation of YR dimers leads to the systematic bends in equilibrium structure of certain DNA fragments.

DNA: sequence, structure and supercoiling. The twentieth Colworth medal lecture.

DNA structures It is now 30 years since Watson & Crick (1953) proposed the base-paired double helical structure for DNA. Although the details of the structure in terms of the precise torsion angles adopted along the deoxyribose-phosphate backbone have undergone considerable revision and refinement, the essential nature of the structure was of course correct, and has subsequently stimulated the growth of the new science of molecular biology to an almost incalculable degree. Clearly, a molecule with the central importance of D N A must equally be of recurrent interest to structural biologists, and indeed the area has undergone something of a renaissance in recent years. This has been a result chiefly of the advent of X-ray crystallographic studies of oligonucleotides of defined sequence. Previous structural studies were limited to fibre diffraction measurements of high molecular weight DNA, and was therefore limited both by the nature of the sample and the manner of the collection of the data. Recent single-crystal studies have allowed for the first time atomic, or nearly atomic, resolution structures to be elucidated, giving information on each nucleotide in a molecule rather than an averaged structure. Both A (Conner et al., 1982) and B (Wing et al., 1980) forms of DNA structure have been solved at this resolution without presenting any great surprises, but the solution of a d(CpG)3 high salt structure by Rich and coworkers (Wang et al. 1979) turned out to be very much less conventional. The most obvious difference was that the new structure, termed Zform DNA, was left-handed, achieved by a CpG dinucleotide symmetrical unit in which the deoxyguanosine has unusual glycosidic bond angle (syn) and deoxyribose pucker (C3’-endo) compared with R-DNA. This was really the first indication that the three-dimensional structure of DNA might reflect its base sequence. Another example of this behaviour emerged from the refined structure of a d(CGCGAATTCGCG) dodecamer by Dickerson and colleagues (Dickerson & Drew, 1981). Whilst the overall structure is clearly recognizable as the B-form, the variation in individual torsion angles is considerable. Each nucleotide differs in its detailed ‘geometry from the others of the dodecamer. The underlying message is very clear: DNA structure exhibits a large element of sequence dependence. Proteins are capable of DNA sequence recognition with exquisite precision, obvious to anyone who has ever performed a restriction enzyme reaction. The problem of understanding the specificity of DNA-protein interaction is fundamental to molecular biology, and the basis may well reside in the fine details of base-specific backbone structure. These interactions may well give clues as to such structural variation, and enzyme probing has been used with considerable success in revealing structural polymorphism in DNA. Experiments of this kind have been performed at varying levels of precision, and with various aims. DNase I has been used as a probe of DNA bound to solid supports such as calcium phosphate, in order to measure helical periodicity, and the results obtained have indicated that this parameter may vary with the sequence of the DNA studied (Rhodes & Klug, 1980, 1981). An alternative endonuclease,

The three-dimensional structure of DNA.

The three-dimensional structure of DNA.

Regulation of Cell Cycles

Of the major achievements in cell biology during the last 25 years, none is more important than the understanding of regulation of cell cycles. In 1953 two fundamental observations concerning DNA were made. Watson and Crick suggested that the three-dimensional structure of DNA exists as a double helix with specific base pairings, and Howard and Pelc observed that DNA is replicated during a specific phase in the mitotic cycle. Thus developed the theory of cell cycles. Next, investigators explored which events occur during each phase of the cycle and what controls the readout of the genes of proliferation or differentiation. In 1961, Jacob and Monod proposed that for prokaryotic cells the operon is the mechanism which controls the readout of the genes; and by the end of the 1960s, several investigators had defined the role of cyclic AMP and its mechanism of action at the gene level. The control mechanisms of eukaryotic cells are less well defined. Basically there are two types of regulatory molecules: those that arrive at the cell surface and send messages inside the cell; and those that enter the cell, bind to receptors, and then enter the nucleus to interact with the genes. During the past five to ten years, the cell surface and its receptors have received considerable attention as the recognition and control areas for cell proliferation and differentiation, and currently the role of the cyclic nucleotides and prostaglandins is being investigated. Various model systems are now available for detailed studies of these control mechanisms.

X-RAY DIFFRACTION STUDY OF A DNA WHICH CONTAINS URACIL.

Three-dimensional structure of DNA from PBS2 bacteriophage, which contains uracil in place of the more usual thymine, is the same as that of "normal" DNA. The difference in secondary structure between DNA and RNA thus appears to be due to the 2'-hydroxyl group alone.