The relation of single-stranded regions in bacteriophage PM2 supercoiled DNA to the early melting sequences

Dinuclear complex-induced DNA melting

Dinuclear copper complexes have been designed for molecular recognition in order to selectively bind to two neighboring phosphate moieties in the backbone of double strand DNA. Associated biophysical, biochemical and cytotoxic effects on DNA were investigated in previous works, where atomic force microscopy (AFM) in ambient conditions turned out to be a particular valuable asset, since the complexes influence the macromechanical properties and configurations of the strands. To investigate and scrutinize these effects in more depth from a structural point of view, cutting-edge preparation methods and scanning force microscopy under ultra-high vacuum (UHV) conditions were employed to yield submolecular resolution images. DNA strand mechanics and interactions could be resolved on the single base pair level, including the amplified formation of melting bubbles. Even the interaction of singular complex molecules could be observed. To better assess the results, the appearance of treated DNA is also compared to the behavior of untreated DNA in UHV on different substrates. Finally, we present data from a statistical simulation reasoning about the nanomechanics of strand dissociation. This sort of quantitative experimental insights paralleled by statistical simulations impressively shade light on the rationale for strand dissociations of this novel DNA interaction process, that is an important nanomechanistic key and novel approach for the development of new chemotherapeutic agents.

Evidence Falsifying the Double Helix Model

Through more than 40 years of reading, thinking, searching, and experimentation, we have found that the double helix model carries some defects or incorrect information. Evidence gleaned from the literature clearly indicates that the two strands of DNA are coiled ambidextrously, rather than plectonemically. It is likely that the linking number of native chromosomal Escherichia coli (E. coli) DNA is less than 960. Presently, a clear voice is necessary to break the ice formed from decades of misleading media, questionable textbooks, and expediency. For the sake of science, we are responsible and willing to share our hard-earned knowledge, experience, and knack with the public. A promising research plan is provided for the additional falsification of the right-handed double helix model. It would be a precision hit at the Achilles’ heel of the double helix model. An appropriate conceptual shift will hopefully lead to new knowledge on the secondary structure of DNA and improve understanding of its biological functions.

Probing hyper-negatively supercoiled mini-circles with nucleases and DNA binding proteins

It is well accepted that the introduction of negative supercoils locally unwinds the DNA double helix, influencing thus the activity of proteins. Despite the use of recent methods of molecular dynamics simulations to model the DNA supercoiling-induced DNA deformation, the precise extent and location of unpaired bases induced by the negative supercoiling have never been investigated at the nucleotide level. Our goals in this study were to use radiolabeled double-stranded DNA mini-circles (dsMCs) to locate the unpaired bases on dsMCs whose topology ranged from relaxed to hyper-negatively supercoiled states, and to characterize the binding of proteins involved in the DNA metabolism. Our results show that the Nuclease SI is nearly ten times more active on hyper-negatively supercoiled than relaxed DNA. The structural changes responsible for this stimulation of activity were mapped for the first time with a base pair resolution and shown to be subtle and distributed along the entire sequence. As divalent cations modify the DNA topology, our binding studies were conducted with or without magnesium. Without magnesium, the dsMCs topoisomers mostly differ by their twist. Under these conditions, the Escherichia coli topoisomerase I weakly binds relaxed dsMCs and exhibits a stronger binding on negatively and hyper-negatively supercoiled dsMCs than relaxed dsMCs, with no significant difference in the binding activity among the supercoiled topoisomers. For the human replication protein A (hRPA), the more negatively supercoiled is the DNA, the better the binding, illustrating the twist-dependent binding activity for this protein. The presence of magnesium permits the dsMCs to writhe upon introduction of negative supercoiling and greatly modifies the binding properties of the hRPA and Escherichia coli SSB on dsMCs, indicating a magnesium-dependent DNA binding behavior. Finally, our experiments that probe the topology of the DNA in the hRPA-dsMC complexes show that naked and hRPA-bound dsMCs have the same topology.

Supercoiling induces denaturation bubbles in circular DNA

We present a theoretical framework for the thermodynamic properties of supercoiling-induced denaturation bubbles in circular double-stranded DNA molecules. We explore how DNA supercoiling, ambient salt concentration, and sequence heterogeneity impact on the bubble occurrence. An analytical derivation of the probability distribution to find multiple bubbles is derived and the relevance for supercoiled DNA discussed. We show that in vivo sustained DNA bubbles are likely to occur due to partial twist release in regions rich in weaker AT base pairs. Single DNA plasmid imaging experiments clearly demonstrate the existence of bubbles in free solution.

Activity of single-stranded DNA endonucleases in mung bean is associated with cell division

A single-strand-specific endonuclease from mung bean sprouts is widely used in molecular biology. However, the biological role of this enzyme is unknown. We studied the spatial and temporal activity of single-stranded DNA endonucleases in mung bean seedling by following enzyme activity that linearizes supercoiled plasmid DNA, a characteristic of this type of enzyme. The formation of a linear molecule from supercoiled DNA was found to occur in two distinguishable steps. The first, which involves introducing a nick into the supercoiled DNA and relaxing it, is very rapid and complete within a few seconds. The second step of cleaving the opposite strand to generate a unit-length linear duplex DNA is a relatively slow process. Analysis of the DNA cleavage sites showed the nuclease preferentially cuts supercoiled DNA at an AT-rich region. Varying levels of nuclease activity could be detected in different tissues of the mung bean seedling. The highest activity was in the root tip and was correlated with histone H1 kinase activity. This implies a link between nuclease activity and cell division. Induction of cell division in mung bean hypocotyls with auxin promoted formation of root primordia and considerably increased the activity of single-stranded DNA endonucleases. The nuclease activity and histone H1 kinase activity were reduced in mung bean cuttings treated with hydroxyurea, but not in cuttings treated with oryzalin. The potential function of single-stranded DNA endonucleases is discussed.

Evidence for a salt-induced conformational transition in UV-irradiated superhelical PM2 DNA

Upon treatment with UV irradiation, native (supercoiled) PM2 DNA undergoes an increase in electrophoretic mobility relative to the nicked circular form in the presence of 1 M NaCl or 5 mM CaCl2 or MgCl2. This effect is dependent upon supercoiling in that the relative electrophoretic mobility decreases with decreasing superhelical density of the molecule. These findings indicate that supercoil-dependent aspects of the secondary and tertiary structure of nonirradiated PM2 DNA can be altered by a combination of UV irradiation and any of the ionic environments above. We show that the alteration is not the result of a conversion of Z-DNA segments to a right-handed helix or to a renaturation of denatured regions in PM2 DNA. Circular dichroism studies do not support a simple model in which A-form DNA induced by superhelical stress is converted to B-form DNA by UV-induced photodamage and salt. We, therefore, present three alternative explanations for these observations two of which invoke conformational transitions in secondary structure and a third which requires a change in tertiary structure due to an increase in flexibility.

Low concentrations of acridine dimers inhibit micrococcus AP endonuclease through interaction with apurinic sites in DNA

The effect of dimeric DNA intercalating compounds was assayed on a purified AP endonuclease from Microccoccus luteus using apurinic supercoiled PM2 DNA as a substrate. Binding on apurinic sites was estimated through the competition with the intercalating compound, 9-NH2-ellipticine, which displays great specificity for apurinic sites. An acridine dimer with a spermine linker is at 0.1 microM the best inhibitor of cleavage at the apurinic site induced either by the AP endonuclease or by 9-NH2-ellipticine. Bisintercalating agents are more effective inhibitors of AP endonuclease than monointercalating ones. Most effective inhibitors among dimers have acridine residues.

Integration of staphylococcal phage L54a occurs by site-specific recombination: structural analysis of the attachment sites

Lysogenization by staphylococcal phage L54a induces the loss of lipase (glycerol ester hydrolase) activity in its host Staphylococcus aureus. The attachment site of the bacterial chromosome (attB) for the phage is at the 3' end of the lipase gene, geh. The DNA fragment containing the attB (base pairs 2620-2637 inclusive) site has been sequenced. We have also cloned and determined the nucleotide sequence of the DNA fragments containing the other three attachment sites--i.e., the attP locus on the circularly permuted phage genome and the attL and attR loci at the left and right ends of the prophage in the lysogenized strain. These results reveal that an 18-base-pair core sequence is common to all four att sites. These data indicate that the crossover point must exist within the core sequence and, further, that integration is site- and orientation-specific. We also localized the viral recombinase gene to a 2.1-kilobase DNA segment extending rightward to the attP site. This region was found to be essential for integration of plasmids containing the attP site.

Changes in site specificity of single-strand-specific endonucleases on supercoiled PM2 DNA with temperature and ionic environment

Mung bean nuclease sites in supercoiled PM2 DNA at neutral pH were located by linearizing the singly-nicked circular DNA product with venom phosphodiesterase followed by restriction endonuclease mapping. The locations of the sites varied with small changes in temperature and in concentration of NaC1 or magnesium ion. Different environmental changes which affect duplex stability in the same direction showed similar effects on the number of sites and in some cases resulted in identical cleavage patterns. Venom phosphodiesterase and P1 nuclease showed cleavage patterns similar to mung bean nuclease under the same environmental conditions and showed similar variations in cleavage patterns when environmental conditions were changed. Relaxed, closed-circular DNA was slowly cleaved at numerous sites whose locations did not vary with environment. Changes in site specificity are likely the result of environmental effects on the conformation of supercoiled DNA as opposed to effects on the single-strand-specific endonucleases themselves.

Mung bean nuclease cleavage of a dA + dT-rich sequence or an inverted repeat sequence in supercoiled PM2 DNA depends on ionic environment

We have determined the nucleotide sequences around two alternative sites cleaved in supercoiled PM2 DNA by single-strand-specific mung bean nuclease in different ionic environments. In 10 mM Tris-HC1 (pH 7.0, 37 degrees C), the major site is a dA+dT-rich sequence which maps with a known early denaturation region at 0.75 map units. About 30 cleavages occurred in a 135 bp region. Cleavages were largely excluded at (dA)n . (dT)n (n = 3-7) sequences. Cleavage patterns of this type have not been previously observed in dA+dT-rich sequences. With the addition of 0.1 M NaC1 the major alternative site occurred in a hyphenated inverted repeat sequence 500 bp away (0.70 map units) and did not map to an early denaturation region. One major and 4 minor cleavages occurred in the region between the repeats, suggesting that a hairpin containing at most a 12 bp stem and 10 base loop is recognized. The basis for nuclease recognition of the dA+dT-rich sequence is not clear. The differences in the sequences and cleavage patterns at the alternative sites indicate that their secondary structures differ.

A monoclonal antibody recognizes an epitope common to an avian-specific nuclear antigen and to cytokeratins

X3, a monoclonal antibody of unusual specificity, is described. This antibody reacts with one or more cytokeratin polypeptides and also reacts with an avian (chicken, quail) nuclear antigen that appears to be present in all cell types (chicken) tested, although with variable staining pattern and intensity. This antigen is distinct from the cytokeratins but does have an epitope in common with this class of proteins. It disappears from the nucleus during the early stages of cell division and reappears during anaphase as a granular cytoplasmic structure. In late telophase the antigen is relocated in the nucleus. This antigen, which we have designated as avian-specific nuclear antigen ( AVNA ), is not associated with chromatin or ribonucleoproteins. From immunoblotting experiments on chicken fibroblast nuclei, AVNA is probably a complex composed of one or several polypeptides, one of which has a molecular weight of approximately 60 kD. The proteins were identified as nuclear matrix proteins rather than pore complex-lamina proteins by immunoblotting experiments on the purified nuclear matrix of chicken erythrocytes. The major polypeptide had a molecular weight of 60 kD and the minor polypeptide a molecular weight of 69 kD.

DNA of the Streptomyces phage SH10: binding sites for Escherichia coli RNA polymerase and denaturation map

Escherichia coli RNA polymerase bound to Streptomyces phage SH10 DNA was visualized by electron microscopy. Six specific binding sites were observed at map units 53, 85, 93, 97, 98, and 99 on the physical map of the 48 kb long genome. Electron microscopy of partially denatured SH10 DNA revealed a characteristic melting pattern of A + T-rich regions around map units 1, 3, 48, 52, and 99. A comparison of the denaturation map with the RNA polymerase binding sites indicates that three binding sites are located in the most A + T-rich regions, two in other early melting regions and one in a segment of higher DNA helix stability.

Monoclonal antibody which recognizes a common antigenic determinant on intermediate filament proteins, actin, and myosin

A monoclonal antibody is described which reacts with the intermediate filament proteins vimentin, desmin, keratins, actin, and myosin. This is the first report of an epitope common to intermediate filament proteins and myosin. X1, the wide-spectrum monoclonal antibody in question, was isolated in the course of screening monoclonal antibodies to chicken thymocytes. Cross-reactivities were investigated by immunofluorescence on various types of cultured cells and sectioned tissues, ELISA with a panel of purified antigens, immunoprecipitation, immunodot tests, and immunoblotting.

Analysis of chromatin structure and DNA sequence organization: use of the 1,10-phenanthroline-cuprous complex

Limited treatment of Drosophila nuclei with the 1,10-phenanthroline-cuprous complex leads to rapid production of nucleosomal ladders indistinguishable from those obtained by micrococcal nuclease digestion. An investigation of the preferential sites of cleavage of protein-free DNA at locus 67B1 surprisingly indicated that both reagents recognized very similar features. Thus, a virtually identical pattern of preferential cleavages was generated over a 12 kb fragment encoding four transcripts at this locus. The distribution of cleavage sites was highly non-random, with major sites falling in the spacers between the genes. Both reagents cleaved certain chromatin-specific sites near the 5' ends of the genes. However, an analysis of preferential cleavages at the sequence level did not reveal the same close correspondence. We suggest that both reagents can recognize some localized secondary structural features of the DNA and that the particular distribution of sequences present at this locus results in a distinctive pattern of cleavage sites that delineates gene and spacer segments.

A comparison of the phage T4 gene 32 protein and Escherichia coli RNA polymerase binding sites on hamster papovavirus DNA

Phage T4 gene 32 protein and Escherichia coli RNA polymerase were bound to hamster papovavirus DNA. The binding regions were identified by electron microscopy employing a protein-free spreading technique. After gene 32 protein treatment four denaturation regions could be mapped, at 0.04-0.12, 0.30-0.36, 0.50-0.60 and 0.75-0.90 DNA map units, respectively, using the unique BamHI cleavage site as zero point. Eight RNA polymerase binding sites can be found which are localized at positions 0.05; 0.11; 0.18; 0.31; 0.57; 0.66; 0.76 and 0.82. A comparison of the RNA polymerase binding sites with the gene 32 protein denaturation pattern reveals a correspondence of six of eight polymerase binding sites with (A+T)-rich regions within the hamster papovavirus genome.

Pisum sativum endonuclease. Studies on substrate specificity and possible use as a biochemical tool

An endonuclease purified from germinating pea (Pisum sativum) seeds has been shown to catalyze the hydrolysis of heat-denatured single-stranded DNA. Since P. sativum endonuclease shows appreciable activity in the presence of DNA destabilizing agents and, unlike many similar endonucleases, significant activity at neutral pH, it is a potentially valuable tool for studies of the secondary structure of nucleic acids. The residual hydrolysis of duplex DNA is directed towards partially denatured, A,T-rich areas in native DNA. The rate of hydrolysis of deoxypolynucleotides was in the order poly(dT) greater than denatured DNA greater than poly(dA) greater than poly(dA-dT) = native DNA. Neither poly(dC), poly(dG) nor poly(dC).poly(dG) were attacked by the enzyme. Supercoiled, covalently closed circular phage PM2 form I DNA is converted to singly hit nicked circular form II and doubly hit linear from III duplexes. Prolonged treatment with enzyme does not further cleave the linear form III DNA. Addition of increasing concentrations of NaCl in the incubation mixture suppresses the conversion of form I to form II, but not the conversion of form II to form III, which is enhanced with the increasing ionic strength. The enzymatically relaxed circular form, I degree, obtained by unwinding of supercoiled DNA with a DNA-relaxing protein, is resistant to the action of the enzyme. Molecules with intermediate superhelix densities do not serve as substrates. The sites of cleavage of P. sativum endonuclease in PM2 DNA occur within regions that are readily denaturable in a topologically constrained superhelical molecule.

DNA electron microscopy

In recent years DNA electron microscopy has become a tool of increasing interest in the fields of molecular genetics and molecular and cell biology. Together with the development of in vitro recombination and DNA cloning, new electron microscope techniques have been developed with the aim of studying the structural and functional organization of genetic material. The most important methods are based on nucleic acid hybridizations: DNA-DNA hybridization (heteroduplex, D-loop), RNA-DNA hybridization (R-loop), or combinations of both (R-hybrid). They allow both qualitative and quantitative analysis of gene organization, position and extension of homology regions, and characterization of transcription. The reproducibility and resolution of these methods make it possible to map a specific DNA region within 50 to 100 nucleotides. Therefore they have become a prerequisite for determining regions of interest for subsequent nucleotide sequencing. Special methods have been developed also for the analysis of protein-DNA interaction: e.g., direct visualization of specific protein-DNA complexes (enzymes, regulatory proteins), and analysis of structures with higher complexity (chromatin, transcription complexes).

Deoxyribonuclease I generates single-stranded gaps in chromatin deoxyribonucleic acid

Production of 10-base multiple DNA ladder fragments during DNase I digestion of chromatin is explained by a model which does not involve site-specific nicking by the DNase I. This model was tested because it explains why 10-base (actually 10.4 base) multiple-related fragments are paradoxically generated by both endonucleolytic (DNase I) and exonucleolytic (exonuclease III) mechanisms. This new model also explains the phenomenon of substantial single-stranded DNA production during DNase I digestion of chromatin. The latter phenomenon has been widely observed but is not explained by previous models. The single-stranded gap model to be presented makes testable predictions. Primarily, these are that DNase I produces single-stranded gaps in chromatin DNA and that the termini of 10-base multiple ladder fragments are separated by single-stranded gaps. Single-stranded gap production by DNase I was confirmed by a number of methods. Sensitivity of ladder band components (from DNase I but not staphylococcal nuclease digests) to S1 nuclease suggested that the ladder fragments themselves may compose a significant portion of these gaps. Separation of ladder fragment termini by single-stranded gaps was verified by demonstrating both resistance to the nick-specific NAD+-dependent ligase and sensitivity to T4 ligase which can ligate across gaps. Many single-stranded gaps, occurring both individually and clusters, were observed by electron microscopy using either cytochrome c labeling (where the gaps) are thinner than duplex) or gene 32 protein labeling (gaps thicker than duplex). Gap sizes were estimated by protecting them with gene 32 protein and digesting away unprotected duplexes. By this method, gap sizes fall into a ladder distribution (from 10 or 20 bases up to 120 bases), which, at least in the region of the shorter sizes, clearly indicates the sizes of single-stranded gaps formed in chromatin by DNase I.

X-ray scattering from randomly oriented superhelices. Circular superhelical DNA

The scattering functions of randomly oriented filaments of finite length exhibiting two orders of helicity have been calculated. It is shown to a good approximation that each order scatters as if present alone as a first order helix of the same contour length and pitch angle. These results show that the measured scattering pattern from dissolved superhelical DNA molecules is consistent with the scattering pattern calculated for a coiled coil geometry.

Cloning of bacteriophage PM2 DNA in Escherichia coli K12

DNA fragments of phage PM2 restricted with Hin dIII endonuclease was cloned in the vector pBR 322 in an Escherichia coli K12 host. The attempt to clone full length PM2 DNA restricted with PstI endonuclease has been unsuccesful. From six randomly chosen recombinant clones DNA was purified and analysed with EcoRI, PstI and Hin dIII endonucleases. The physical map of three chimeric plasmids was unequivocally established. It was shown, that the whole PM2 genome was cloned, although in separate fragments. However, most of the recombinant clones were instable in the absence of selective pressure.

The recognition of mismatched base pairs in DNA by DNase I from Ustilago maydis

The activity of Ustilago maydis DNase I, an enzyme implicated in genetic recombination, on DNA substrates containing unpaired or mismatched bases, was examined. The enzyme nicked supercoiled PM-2 molecules, converting these to relaxed circular and linear molecules. Discrete double stranded linear fragments smaller than unit length were also observed after digestion at high enzyme concentration. Heteroduplex molecules were constructed using phi80 bacteriophage derivatives which contained single base substitutions within the E. coli tRNA1tyr gene. Single and double stranded nicking at or near the single mismatched site was observed with three out of the five pairs of heteroduplexes.

Stable denaturation of chromosomal DNA from Saccharomyces cerevisiae during meiosis

Partial denaturation of Saccharomyces cerevisiae chromosomal DNA was found to occur spontaneously during meiosis. Short regions of strand separation (300 base pairs long) were seen in DNA molecules prepared for electron microscopy by the aqueous spreading technique. These regions were clustered along the DNA. The time course of their appearance indicated that the denatured regions were present during the periods of premeiotic DNA replication and recombination. A similar pattern of denaturation was also detected in the DNA from vegetatively grown cells of a conditional cdc8 mutant, which is defective in DNA replication.

Conformational variation in superhelical deoxyribonucleic acid

Sedimentation experiments have shown that superhelical DNA undergoes a sharp structural transition at low ionic strength. Light-scattering experiments show that this is due to a change in conformation of the DNA rather than to a change in interactions among DNA molecules. The results show that two possible conformations can occur for superhelical DNA under routine experimental conditions and may explain the discrepancies in the number of early unwinding sites exposed by different techniques.