Article

# The Cyclic Helix and Cyclic Coil Forms of Polyoma Viral DNA

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## Abstract

The DNA extracted from polyoma virus exhibits certain properties which have not been reported for other viral base-paired DNA's. (1) The DNA renatures monomolecularly. The loss of helical configuration does not impair biological activity. Heating at 100° for 10-20 min followed by rapid cooling does not reduce the infective titer. Dulbecco has given evidence suggesting that a fraction of the polyoma DNA molecules are cyclic. (2) This form would in part account for the above properties.

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... The term "denaturation", in that setting, meant irreversible disruption of base-pairing (as verified by changes in A 260 ), in a setting in which the two strands of the plasmid remained unequivocally linked. The resulting duplex non-base-paired structure was referred to by various names, of which I shall adhere to the Roman numeral system introduced by Vinograd [2] and extended by Strider and Warner [4] [5]: ...
... Dozens of papers on Form IV were published between 1963 [2] and 1981 [6], after which the molecular biological community lost all interest in it. Conspicuously absent from all those papers was any proposal for a Form IV structure, or any explanation for its extraordinary compactness. ...
... This gap in our knowledge may have been closed by the recent publication of a detailed molecular model for Form IV, which accounts for all of its properties, including its high sedimentation coefficient (S) in velocity ultracentrifugation studies [7] [8]. Weak organic solvents 3 Strand separation Nothing -no strand separation Strong organic solvents 4 Strand separation Denaturation to Form IV 2 1 As long as the two strands of a circular chromosome are intact, boiling has no effect [2]. If one or both strands are nicked, however, the strands will then usually behave like the strands of linear DNA, and separate when boiled; 2 Form IV, described below, is a tremendously-compact duplex form of DNA which appears to be stabilized by salt bridges between phosphate groups. ...
Article
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Although it is not widely-known, the strands of circular duplex plasmid and viral chromosomes have been non-destructively separated, and the separated strands have been reconstituted to yield a new duplex structure with all the properties of the native chromosome restored. This suggests a paranemic structure for the DNA, that is, a structure whose strands are not topologically linked by plectonemic (i.e., Watson-Crick) twists. The reason that these phenomena are largely unknown to the general scientific public is that they were either published in obscure journals, or not published at all. Moreover, the methods employed to obtain these results were very difficult, time-consuming and expensive, wherefore they are not likely to be repeated anytime soon. Since these phenomena would be of great interest to the general scientific public, the experiments therefore need to be repeated, but in a way that is easy, fast and inexpensive to perform, so that the results may be readily reproduced in other laboratories. Two such experiments are described herein.
... CPM in fact appears in many biological contexts. This type of circular pattern occurs in the DNA of viruses [9,10], bacteria [11], eukaryotic cells [12], and archaea [13]. As a result, as has been noted in [14], algorithms on circular strings seem to be important in the analysis of organisms with such structures. ...
... Furthermore, as has been mentioned in [5], this problem seems to be related to the much studied swap matching problem (in CPM, the patterns can be thought of as having a swap of two parts of it) [18] and also to the problem of pattern matching with address error (the circular pattern can be thought of as having a special type of address error) [19,20]. For further details on the motivation and applications of this problem in computational biology and other areas the readers are kindly referred to [9][10][11][12][13][14][15][16][17] and references therein. ...
... initialize all defined variables to zero (7) initialize fixed array to {1, 2, 3, 4} (8) for ← 1 to | | do (9) if ̸ = | | then (10) calculate different filtering values via Observations 1 and 4 and make a running sum (11) end if (12) calculate different filtering values via Observations 2, 3, 5, and 6 and make a running sum (13) end for (14) return all observations values (15) end procedure Algorithm 1: Exact circular pattern signature using Observations 1-6 in a single pass. Now consider another string T = of the same length, which is different from T. It can easily be checked that C(P) does not match T . ...
Article
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This paper deals with the circular pattern matching (CPM) problem, which appears as an interesting problem in many biological contexts. CPM consists in finding all occurrences of the rotations of a pattern 𝒫 of length m in a text 𝒯 of length n. In this paper, we present SimpLiFiCPM (pronounced “Simplify CPM”), a simple and lightweight filter-based algorithm to solve the problem. We compare our algorithm with the state-of-the-art algorithms and the results are found to be excellent. Much of the speed of our algorithm comes from the fact that our filters are effective but extremely simple and lightweight.
... Circular patterns are known to occur in the DNA of viruses [3,4], bacteria [5], eukaryotic cells [6], and archaea [7]. Gusfield [8] rightfully identified the algorithms on circular strings to be important in the analysis of organisms with such structures. ...
... Lee et al. [12] have considered Hamming distance and have presented efficient algorithms for finding the optimal alignment and consensus sequence of circular sequences on this distance metric. Interested readers are referred to [3][4][5][6][7][8][10][11][12] and references therein for further discussion on applications of circular pattern matching in computational molecular biology and other areas. ...
... Like the classic version, CPM is a nice and harder combi- natorial problem. However, apart from being interesting from the pure combinatorial point view, CPM has applications in areas like, geometry, astronomy, computational biology etc. Circular patterns are known to occur in the DNA of viruses [9], [20], bacteria [19], eukaryotic cells [16], and archaea [3]. Gusfield [12] rightfully identified the algorithms on circular strings to be important in the analysis of organisms with such structures. ...
... Lee et al. [14] have considered Hamming distance and have presented efficient algorithms for finding the optimal alignment and consensus se- quence of circular sequences on this distance metric. Interested readers are referred to [3], [9], [10], [12], [14], [16], [18]- [20] and references therein for further discussion on applications of circular pattern matching in computational molecular biology and other areas. ...
Article
This paper deals with the approximate version of the circular pattern matching (ACPM) problem, which appears as an interesting problem in many biological contexts. The circular pattern matching problem consists in finding all occurrences of the rotations of a pattern P of length m in a text T of length n. In ACPM, we consider occurrences with k-mismatches under the Hamming distance model. In this paper, we present a simple and fast filter-based algorithm to solve the ACPM problem. We compare our algorithm with the state of the art algorithms and the results are found to be excellent. In particular, our algorithm runs almost twice as fast than the state of the art. Much of the efficiency of our algorithm can be attributed to its filters that are effective but extremely simple and lightweight.
... Small DNA tumour viruses like SV40 and polyoma were key models for the study of gene expression in eukaryotes (reviewed in [311]). Their DNA forms a cyclic helix or cyclic coil [312] (Fig. 8A). Their genome organisation and modes of expression by differential splicing [313] led to ideas about the mechanisms of transcription and RNA processing in animal cells in general. ...
Article
The main purpose of this review is to recall for investigators - and in particular students -, some of the early data and concepts in molecular genetics and biology that are rarely cited in the current literature and are thus invariably overlooked. There is a growing tendency among editors and reviewers to consider that only data produced in the last 10-20 years or so are pertinent. However this is not the case. In exact science, sound data and lucid interpretation never become obsolete, and even if forgotten, will resurface sooner or later. In the field of gene expression, covered in the present review, recent post-genomic data have indeed confirmed many of the earlier results and concepts developed in the mid-seventies, well before the start of the recombinant DNA revolution. Human brains and even the most powerful computers, have difficulty in handling and making sense of the overwhelming flow of data generated by recent high-throughput technologies. This was easier when low throughput, more integrative methods based on biochemistry and microscopy dominated biological research. Nowadays, the need for organising concepts is ever more important, otherwise the mass of available data can generate only "building ruins" - the bricks without an architect. Concepts such as pervasive transcription of genomes, large genomic domains, full domain transcripts (FDTs) up to 100 kb long, the prevalence of post-transcriptional events in regulating eukaryotic gene expression, and the 3D-genome architecture, were all developed and discussed before 1990, and are only now coming back into vogue. Thus, to review the impact of earlier concepts on later developments in the field, I will confront former and current data and ideas, including a discussion of old and new methods. Whenever useful, I shall first briefly report post-genomic developments before addressing former results and interpretations. Equally important, some of the terms often used sloppily in scientific discussions will be clearly defined. As a basis for the ensuing discussion, some of the issues and facts related to eukaryotic gene expression will first be introduced. In chapter 2 the evolution in perception of biology over the last 60 years and the impact of the recombinant DNA revolution will be considered. Then, in chapter 3 data and theory concerning the genome, gene expression and genetics will be reviewed. The experimental and theoretical definition of the gene will be discussed before considering the 3 different types of genetic information - the "Triad" - and the importance of post-transcriptional regulation of gene expression in the light of the recent finding that 90% of genomic DNA seems to be transcribed. Some previous attempts to provide a conceptual framework for these observations will be recalled, in particular the "Cascade Regulation Hypothesis" (CRH) developed in 1967-85, and the "Gene and Genon" concept proposed in 2007. A knowledge of the size of primary transcripts is of prime importance, both for experimental and theoretical reasons, since these molecules represent the primary units of the "RNA genome" on which most of the post-transcriptional regulation of gene expression occurs. In chapter 4, I will first discuss some current post-genomic topics before summarising the discovery of the high Mr-RNA transcripts, and the investigation of their processing spanning the last 50 years. Since even today, a consensus concerning the real form of primary transcripts in eukaryotic cells has not yet been reached, I will refer to the viral and specialized cellular models which helped early on to understand the mechanisms of RNA processing and differential splicing which operate in cells and tissues. As a well-studied example of expression and regulation of a specific cellular gene in relation to differentiation and pathology, I will discuss the early and recent work on expression of the globin genes in nucleated avian erythroblasts. An important concept is that the primary transcript not only embodies protein-coding information and regulation of its expression, but also the 3D-structure of the genomic DNA from which it was derived. The wealth of recent post-genomic data published in this field emphasises the importance of a fundamental principle of genome organisation and expression that has been overlooked for years even though it was already discussed in the 1970-80ties. These issues are addressed in chapter 5 which focuses on the involvement of the nuclear matrix and nuclear architecture in DNA and RNA biology. This section will make reference to the Unified Matrix Hypothesis (UMH), which was the first molecular model of the 3D organisation of DNA and RNA. The chapter on the "RNA-genome and peripheral memories" discusses experimental data on the ribonucleoprotein complexes containing pre-mRNA (pre-mRNPs) and mRNA (mRNPs) which are organised in nuclear and cytoplasmic spaces respectively. Finally, "Outlook " will enumerate currently unresolved questions in the field, and will propose some ideas that may encourage further investigation, and comprehension of available experimental data still in need of interpretation. In chapter 8, some propositions and paradigms basic to the authors own analysis are discussed. "In conclusion" the raison d'être of this review is recalled and positioned within the overall framework of scientific endeavour.
... When Form IV was first discovered in 1963 [4], it generated a wave of intense interest, mainly because of its extreme compactness. Because separation of viral and plasmid DNA from cellular chromosomal DNA was a major problem in those days, it was fondly hoped that the compactness of Form IV would provide researchers with a simple and inexpensive way to purify these small circular DNA molecules, by massively increasing their buoyant density relative to that of the host cell DNA. ...
Article
Full-text available
A detailed molecular model for alkali-denatured duplex circular DNA (“Form IV”) is proposed. The illustrative biological example used is the replicative form of fx174, a 5 kb duplex circular chromosome. The model explains all of Form IV’s known and peculiar features. In a sedimentation coefficient vs. pH titration, Form IV begins to appear at pH 12.3, at which point it can be persuasively argued that no further supertwists can be added to the already-highly-supertwisted chromosome. Therefore a new structure must appear. The sedimentation coefficient s then undergoes a massive, but initially reversible increase as the pH is raised further, culminating at pH 12.8 with a 250% increase. This degree of compactness can only be explained by a 4-stranded tetraplex structure, consisting of a pair of duplexes whose base pairs are mutually intercalated. Above pH 12.8, the structural changes become irreversible, suggesting a further conformational change. It is proposed that this involves an axial rotation of the component duplex strands, so that the bases now stack on the outside, and the phosphate groups lie in the core, where they bond ionically by means of salt bridges. When the irreversibly denatured compact structure is neutralized at moderate-to-high salt concentrations, a third novel structure appears, which has a sedimentation coefficient midway between the native 21 s and the denatured 50 s. It is proposed that this is a hybrid structure; part tetraplex, part duplex. To return to a fully-duplex form, it is necessary to both neutralize the solution, and also to greatly reduce the ionic strength, i.e., to the range 0.001-0.01 M. Since the DNA, under those conditions, cannot possibly have normal complementary base-pairing, the duplex structure must either be tautomerically base-paired, or else stabilized solely by base-stacking, with no base-pairing at all.
... This process is repeated as the evolution continues. The 'Ring' in RMM denotes that chromosomes of individuals are considered in a ring form [18,39,40] and a random section of the chromosomes are selected, which is not limited to the length of the chromosome. All individuals are evaluated using a fitness function before the next generation is produced. ...
Article
One of the key aspects of Tidal Range Schemes globally is identifying the most appropriate site and the optimised design and operation of the scheme, to maximise societal needs and the benefits from electricity generation. Variations in the design parameters of Tidal Range Schemes for electricity generation could therefore lead to a very large number of design and operation scenarios. In this study, a novel Genetic Algorithm model was developed to deliver the complete design of the most optimised Tidal Range Schemes for electricity generation, including the number of turbines, sluicing areas and the maximum amount of electricity that could be generated, through identifying the most optimised operation scheme for a particular site. The Genetic Algorithm model has been used to design a new Tidal Range Scheme proposed for development in the Bristol Channel, UK, with a potential to generate about 7.16 TWh/yr. The design of the scheme was also investigated using a traditional grid search approach for a range of scenarios, together with the model being used to investigate the performance of the complete design of the scheme, evaluated through a comparison of the most optimised design in terms of electricity generation. This comparison has shown that the Genetic Algorithm model was capable of achieving largely the same outcomes and reducing the computational time by approximately 95% to that based on using traditional Grid Search methods.
... Early studies of DNA plasmids using ultracentrifugation approaches showed that different structures were present in a sample containing only plasmids of equal molecular weight [24][25][26][27]. The nature of this structural difference was determined by Vinograd et al. [28], who showed that a single-strand nick triggered the sedimentation of a single species, indicating that DNA normally had a constrained 'twisted circular structure'. ...
Article
Full-text available
Supercoiling is a fundamental property of DNA, generated by polymerases and other DNA-binding proteins as a consequence of separating/bending the DNA double helix. DNA supercoiling plays a key role in gene expression and genome organization, but has proved difficult to study in eukaryotes because of the large, complex and chromatinized genomes. Key approaches to study DNA supercoiling in eukaryotes are (1) centrifugation-based or electrophoresis-based techniques in which supercoiled plasmids extracted from eukaryotic cells form a compacted writhed structure that migrates at a rate proportional to the level of DNA supercoiling; (2) in vivo approaches based on the preferential intercalation of psoralen molecules into under-wound DNA. Here, we outline the principles behind these techniques and discuss key discoveries, which have confirmed the presence and functional potential of unconstrained DNA supercoiling in eukaryotic genomes.
... In 1962, the first circular DNA was discovered from polyoma virus by Weil and Vinograd [11]. Afterwards, lots of extra-chromosomal circular DNA was found from various sources, including bacteria, mitochondria, chloroplasts, etc. ...
... It should be noted that the selected position of the start point is limited to be prior to the end point and its length should be smaller than the total length of the chromosome in LRM. However, a RRM was carried out by a discovery that some polyoma DNA molecules in a form of circle structure in 1963 [29,30]. In the proposed RRM, the two cross-over points were released from these limitation because of the loop structure of chromosomes, as shown in the Figure 2 [15,17]. ...
Conference Paper
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—This paper focused on facilitating the development of Tidal Range Structures (TRSs) including tidal lagoons by using an improved Genetic Algorithm (GA) model instead of common Grid Search (GS) method which has traditionally been used for the optimisation of operation schemes. The GA model splits the operation into single tidal cycle and optimise the operation of TRSs through the process of mutation, recombination and selection, which create the new schemes. The GA model which takes the 0-D approach as the fitness function was established and developed with different recombination methods, to reveal an enhanced efficiency of the GA with a ring structure recombination method. With a proposed case study of tidal lagoons, the optimised operational scheme using the GA was in consist with the GS method, with an approximately 10% increase of the electricity generation, comparing to the fixed head schedule. However, better convergence can be obtained with the application of the GA than the GS method, which proved the feasibility of utilising the GA model to solve the operational characteristics optimisation in TRSs.
... The finding of circular chromosomal DNA and many plasmids in E. coli definitely frustrated many molecular biologists, since if the two complementary circular rings are always tightly tangled with each other, for topological reasons, their separation would be very difficult [7][8][9]. ...
Article
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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.
... The former considers a linear representation of each individual and sections of two individual, also called parents, are recombined to generate the individuals in the next generation as shown in Fig. 4 [34]. The RRM is based on the fact that polyoma DNA molecules exist in cyclic forms of equal molecular weight as well as linear form [35,36] and such cyclic DNA forms display more diversity in the offspring. It has been found that using RRM with SMM could enhance the convergence of GAs in comparison with using LRM by reducing the number of times that the fitness assessment has to be called [30]. ...
Article
Tidal energy has a significant advantage over many other forms of renewable energy because of the predictability of tides. Tidal Range Structures (TRSs) are one of the main forms of tidal renewable energy. Designing the operation of TRSs is one of the challenging aspects in early stages due to the large variety of scenarios. Traditionally this has been done using a grid search. However, grid search can be very elaborate and time consuming during the design of TRSs. This paper proposes a novel and more efficient method to optimise the design of the operation of TRSs by maximising their electricity generation using a Genetic Algorithm. This GA model is coupled with a 0-D model which breaks the tides into small units and considers flexible operation. This approach delivered more than a 10% increase in electricity generation when compared to non-flexible operation, i.e. using fixed heads for all tides, just by optimising the operation. The GA model was able to achieve the same amount of electricity compared to the best grid search method with flexible operation more efficiently, i.e. with about a 50% reduction in simulation time. The feasibility of the elite operational scheme is validated through a developed 2-D model.
... They had sedimentation values of 5 X 106 for Shope papilloma virus DNA coefficients of 28S, 20S, and 18S, respectively. (77) and 3.0 x 106 for polyoma virus DNA (153). Crawford (34) Inclusion Bodies Intranuclear inclusion bodies have been observed in warts for many years (14,85,90,115,122,136). ...
... Twenty years ago hydrodynamic studies by Vinograd and co-workers (160) showed that closed, circular DNA molecules are more compact than their nicked or linear counterparts. When examined by electron microscopy, the closed, circular DNA molecules appeared to be twisted (166). The term supercoiling was coined to signify this compaction and twisting, and subsequent studies showed that supercoiling is a ubiquitous property of DNA extracted from natural sources whenever DNA molecules lack ends capable of rotation. ...
Chapter
The study of cyclic or ring macromolecules may appear at first sight to be a subject of pure mathematics and of little practical interest, though of great beauty. Often the value of this research and its relation to applied polymer science has not been recognized. It is therefore not surprising that the theory of ring macromolecules is incomplete and fragmentary. Several gaps will become evident in this chapter, and only a few of them could be filled when writing it. In other cases, the unsolved problems will be mentioned and it is hoped that they may be considered by theoreticians as a challenge and a spur.
Chapter
It is well known that open complex formation between promoters and RNA polymerase is thermodynamically favored by negative su-percoiling of the DNA template. The effects of template supercoiling on the kinetics of transcription are, however, much more complex even in simple cases involving no regulatory factors; a priori predictions of such effects are at best tenuous. In this chapter, we focus on insights gained from experimental data accumulated in the past two decades on how template supercoiling and transcription affect each other. We begin with a review of the historical link between DNA supercoiling and transcription. This introduction is followed by a brief account of how gene expression is affected upon decreasing the cellular level of gyrase, a DNA topoisomerase that negatively supercoils DNA, or DNA topoisomerase I, an enzyme that specifically relaxes negatively super-coiled DNA. Mechanistic considerations are then presented for several cases of increasing complexity: from the simplest case in which the rate of transcription is determined by that of open complex formation between RNA polymerase and promoter, to cases involving regulatory and auxiliary DNA binding proteins, and finally to cases in which the rate of transcription is determined by a step that occurs after open complex formation.
Chapter
DNA is unique among polymers in its being the genetic material of living organisms. The first hint of the existence of circular DNA came not from physical measurements but from genetic analysis. When the relative positions of a larger number of genes of the bacterium Escherichia coli were determined by genetic crosses, the genes were found to form a single circular linkage map.1
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Chapter
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Mouse polyomavirus (MPyV) lytically infects mouse cells, transforms rat cells in culture, and is highly oncogenic in rodents. We have used deep sequencing to follow MPyV infection of mouse NIH3T6 cells at various times after infection and analyzed both the viral and cellular transcriptomes. Alignment of sequencing reads to the viral genome illustrated the transcriptional profile of the early-to-late switch with both early-strand and late-strand RNAs being transcribed at all time points. A number of novel insights into viral gene expression emerged from these studies, including the demonstration of widespread RNA editing of viral transcripts at late times in infection. By late times in infection, 359 host genes were seen to be significantly upregulated and 857 were downregulated. Gene ontology analysis indicated transcripts involved in translation, metabolism, RNA processing, DNA methylation, and protein turnover were upregulated while transcripts involved in extracellular adhesion, cytoskeleton, zinc finger binding, SH3 domain, and GTPase activation were downregulated. The levels of a number of long noncoding RNAs were also altered. The long noncoding RNA MALAT1, which is involved in splicing speckles and used as a marker in many late-stage cancers, was noticeably downregulated, while several other abundant noncoding RNAs were strongly upregulated. We discuss these results in light of what is currently known about the MPyV life cycle and its effects on host cell growth and metabolism.
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The discoveries of DNA supercoiling and DNA topoisomerases have been two of the most important breakthroughs in biology in the last century. Negative supercoiling is a critical feature of bacterial genomes and transient supercoiling is produced in all organisms by DNA binding proteins and/or various DNA tracking processes. DNA topoisomerases are major elements in cellular life and the plethora of natural antibiotics and antitumor drugs that target these enzymes testify for their importance. DNA topoisomerases I and II, catalyzing DNA strand transfer via single or double-strand breaks in DNA molecules respectively, originated and evolved to solve topological problems raised by the plectonemic coiling of two DNA strands in the double helix, and specialized topoisomerases acquired the ability to produce supercoiling. The first DNA topoisomerases were discovered in Escherichia coli (protein ω, DNA gyrase, Topo III, and Topo IV) and eukaryotic cells (Topo IB, Topo II, Topo III). Later on, new families and subfamilies of DNA topoisomerases were discovered in Archaea, the third domain of life (reverse gyrase, Topo V, Topo VI), challenging the prokaryote/eukaryote dichotomy. DNA topoisomerases are now classified into five families of homologous proteins (Topo IA, IB, IC, Topo IIA, IIB) based on structural similarities. These families have been divided into subfamilies, some of them characterized by unique enzymatic properties (gyrase, reverse gyrase). The distribution of these families and subfamilies do not overlap with the universal tree of life, and some subfamilies are specific for viruses. This suggests that viruses played an important role in the origin and distribution of DNA topoisomerases among cellular organisms.
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The thermodynamical stability of a set of circular double helical molecules is analyzed by path integral techniques. The minicircles differ only in \textit{i)} the radius and \textit{ii)} the number of base pairs ($N$) arranged along the molecule axis. Instead, the rise distance is kept constant. For any molecule size, the computational method simulates a broad ensemble of possible helicoidal configurations while the partition function is a sum over the path trajectories describing the base pair fluctuational states. The stablest helical repeat of every minicircle is determined by free energy minimization. We find that, for molecules with $N$ larger than $100$, the helical repeat grows linearly with the size and the twist number is constant. On the other hand, by reducing the size below $100$ base pairs, the double helices sharply unwind and the twist number drops to one for $N=\,20$. This is predicted as the minimum size for the existence of helicoidal molecules in the closed form. The helix unwinding appears as a strategy to release the bending stress associated to the circularization of the molecules.
Chapter
Quinacrine, also known as atebrin, atabrine, mepacrine and acrichin, is a 9-alkylaminoacridine (Fig. 1), and was developed as one of a group of potential antimalarial drugs (Mietzsch and Mauss, 1930), apparently patterned after successful antimalarials possessing alkyl side chains as, for example, pamaquine (Goodman and Gilman, 1960; The Acridines, A. Albert, 1966). Quinacrine was introduced clinically in April, 1932 (Mauss and Mietzsch, 1936), but despite rapid professional acceptance, its structure remained masked by inadequate patent disclosure until its degradation and synthesis by Russian scientists (Chelintsev et al., 1934). Previously, acridines, particularly proflavine (Browning and Gilmour, 1913) and its 10-methyl acridinium derivative, in conjunction known as acriflavine, had been used as antibacterial agents, but only with the advent of quinacrine and additional 9-alkylaminoacridine derivatives, were acridines developed into highly effective antimalarial drugs. During the Second World War, the Allies, separated from their sources of quinine, turned to the synthetic compound, quinacrine, for both prophylaxis and overt therapy of malaria. As a result of the War, of the prevalence of malaria, and of the many cellular and molecular effects of quinacrine, a vast literature has developed, and for detailed knowledge, the reader should consult the very excellent and comprehensive monographs, The Acridines by A. Albert (2nd edition, St Martin’s Press, New York, 1966), Malaria Parasites and Other Haemosporidia, by P.C.C. Garnham (Black-well Scientific Publications, Oxford, 1966), and Chemotherapy and Drug Resistance in Malaria, by W. Peters (Academic Press, London and New York, 1970).
Chapter
DNA, der universelle Träger genetischer Information, konnte durch Erkenntnisse der letzten Jahre als ein Molekül charakterisiert werden, das strukturell in verschiedenen polymorphen Formen existiert. Die Aufgabe dieses Artikels soll deshalb sein, eine Beschreibung des DNA Moleküles unter Berücksichtigung dessen struktureller Flexibilität zu geben.
Article
Circular nucleic acids (CNAs) refer to nucleic acid molecules with a closed‐loop structure. This feature comes with a number of advantages, including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology controlled or enabled molecular devices. This article will begin with summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts on coupling functional nucleic acids with rolling circle amplification for ultra‐sensitive biosensing, and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery, will be recapitulated.
Chapter
The principal members of the papova group are polyoma virus (Stewart et al., 1957), simian virus 40 (SV40), which is a vacuolating virus of monkeys (Sweet and Hilleman, 1960), and the papilloma viruses (Melnick, 1962). The name for this group of viruses is derived from the first two letters of the names of each of the viruses that were first included in the group, papilloma, polyoma, vacuolating virus (Melnick, 1962). The viruses are 40–57 nm in diameter and, as determined by negative staining, the outer shell has symmetry of the T = 7 icosahedral surface lattice and is composed of 72 morphological subunits (Finch and Klug, 1965; Anderer et al., 1967). The viruses contain no lipids and therefore are resistant to ether. Polyoma and SV40 do not share common antigens, nor is there evidence for the existence of any homology between their DNAs. The papovaviruses are capable of initiating a lytic cycle of replication or a latent infection. For the papilloma viruses it is difficult to obtain a suitable cell line in which the lytic cycle can be studied and for this reason studies that we will discuss concerning viral replication will deal exclusively with SV40 and polyoma.
Conference Paper
This paper deals with the Approximate Circular Pattern Matching (ACPM) problem, which appears as an interesting problem in many biological contexts. Here the goal is to find all approximate occurrences of the rotations of a pattern $$\mathcal{P}$$ of length m in a text $$\mathcal{T}$$ of length n. In this article, we present a filter-based approach to solve the problem. We experimentally compare our approach with the state of the art algorithms in the literature and the results are found to be excellent.
Chapter
Vor etwas mehr als 20 Jahren machten Avery, McLeod und McCarty, 1944, die unerwartete Entdeckung, daß die Desoxyribonucleinsäure (DNS) Träger der genetischen Information ist. Etwa 10 Jahre später stellten Watson und Crick, 1953, ein Strukturmodell für die DNS auf. Danach besteht die DNS aus zwei umeinandergewundenen und einander komplementären Strängen. Die Komplementarität der Stränge ließ Watson und Crick vermuten, daß sich bei Vermehrung der DNS die beiden Stränge voneinander trennen und an ihnen neue, komplementäre DNS-Stränge gebildet werden. Einen solchen Vermehrungsmechanismus hat man semikonservativ genannt, weil die beiden Hälften der elterlichen DNS auch bei mehrfacher Replikation als Einheiten erhalten bleiben. Die Richtigkeit dieses von Watson und Crick postulierten Mechanismus wurde durch Meselson und Stahl, 1958 a, b, bewiesen.
Chapter
The term “pseudovirus” was used first by Michel et al. (1967) to describe a particle which is produced during the infection of cultured mouse cells by polyoma virus. This polyoma-related particle was found to contain fragments of mouse DNA encapsidated within the protein coat of polyoma virus. Since the discovery of polyoma pseudovirions by Michel et al. (1967) and independently by Winocour (1967a,b), pseudovirions have been discovered in preparations of simian virus 40 (SV40) and tobacco mosaic virus (TMV). Although pseudovirions have been found only recently in animal cells and plant cells, they appear to be analogous in many ways to particles containing fragments of host-cell DNA, but no detectable virus-specific DNA, that are produced during the infection of bacterial cells by some bacterial viruses. Although these phagelike particles have not been called pseudovirions in the past, they fit the definition of pseudovirions and will be referred to as such in this chapter. Many of these bacterial pseudovirions have been shown to be capable of generalized transduction. However, generalized transduction has not been demonstrated, as yet, with any pseudovirions of animal- or plant-cell origin.
Chapter
Unlike other organic molecules catenanes and rotaxanes are not only defined and held together by common chemical bonds, they also bear mechanical bonds in their structure. Catenanes (lat. catena = chain) consist of two or more macrocycles that are intertwined as the links of a chain [1]. The term rotaxane is a combination of the two Latin words rota(= wheel) and axis(= axle). Indeed, these compounds possess (at least) one wheel and one axle running through it. The latter is equipped with large stopper units that prevent the wheel from slipping off [1] (fig. 1).
Chapter
Bacterial DNA replication is, at least in part, discontinuous. An important fraction of the newly synthesized DNA can be isolated in the form of short molecules (Okazaki fragments). In the process of chain elongation these fragments are subsequently joined to long molecules (Sakabe and Okazaki, 1966; Okazaki et al., 1973). In Escherichia coli Okazaki fragments are preferentially synthesized in the 3′ → 5′ direction of replication (Louarn and Bird, 1974).
Chapter
The function of DNA is to carry the genetic message from generation to generation, and to allow the expression of that message under appropriate conditions. DNA molecules are very large and carry the information for the synthesis of many proteins, not all of which are required at the same time. Problems will obviously arise when it comes to packaging such long lengths of DNA into a cell in such a way as to allow programmed access to the encoded information. These problems are compounded by the fact that the DNA duplex must replicate and the two daughter DNA molecules must segregate to the two daughter cells. In this chapter we shall look at the structures involved in these processes. These structures are called chromosomes and consist not only of the DNA but of a variety of associated proteins.
Chapter
The principal members of the papova group are polyoma virus (Stewart et al., 1957), simian virus 40 (SV40), which is a vacuolating virus of monkeys (Sweet and Hilleman, 1960), and the papilloma viruses (Melnick, 1962). The name for this group of viruses is derived from the first two letters of the names of each of the viruses that were first included in the group, papilloma, polyoma, vacuolating virus (Melnick, 1962). The viruses are 40–57 nm in diameter and, as determined by negative staining, the outer shell has symmetry of the T = 7 icosahedral surface lattice and is composed of 72 morphological subunits (Finch and Klug, 1965; Anderer et al., 1967). The viruses contain no lipids and therefore are resistant to ether. Polyoma and SV40 do not share common antigens, and presently there is no evidence for the existence of homology betweeen their DNAs. The papovaviruses are capable of initiating a lytic cycle of replication or a latent infection. For the papilloma viruses it is difficult to obtain a suitable cell line in which the lytic cycle can be studied; therefore, studies that we will discuss concerning viral replication will deal exclusively with SV40 and polyoma.
Chapter
Eine der grundlegenden Fragen, die sich seit jeher der Forschung stellt, ist: Wodurch unterscheiden sich lebende Organismen von der unbelebten Materie, obwohl beide aus denselben Strukturelementen (Atome, Moleküle) aufgebaut sind?
Chapter
Die Analyse physikalischer und chemischer Eigenschaften der Nucleinsäuren von Viren ist von besonderer Bedeutung a) für die Kenntnis der Struktur hochmolekularer Nucleinsäuren allgemein; b) für die Virusarchitektur und damit die systematische Einordnung der Viren; c) für den Mechanismus der Virusreplikation und Viruswirkung.
Chapter
The function of DNA is to carry the genetic message from generation to generation, and to allow the expression of that message under appropriate conditions. DNA molecules are very large and carry the information for the synthesis of many proteins, not all of which are required at the same time. Problems will obviously arise when it comes to packaging such long lengths of DNA into a cell in such a way as to allow programmed access to the encoded information. These problems are compounded by the fact that the DNA duplex must replicate and the two daughter DNA molecules must segregate to the two daughter cells. In this chapter we shall look at the structures involved in these processes. These structures are called chromosomes and consist not only of the DNA but of a variety of associated proteins.
Chapter
Die kanzerogene Wirkung von Viren läßt sich an den zahlreichen onkogenen Virusarten erkennen, die in verschiedenen Säugetier- und Vogelarten Tumoren oder Leukämien hervorrufen. Für eine Virusätiologie bestimmter Tumor- und Leukämieformen auch des Menschen bestehen sehr starke Hinweise. Der Beweis steht allerdings noch aus. Klinische Beobachtungen und epidemiologische Studien konnten bisher eine endgültige Beweisführung deshalb nicht erbringen, weil die onkogenen Funktionen dieser Viren nicht nach den Bedingungen der klassischen Infektionslehre ablaufen. Das betrifft vor allem die Tatsache, daß aus Tumoren oder dem tumortragenden Organismus das onkogene Virus nicht direkt, sondern nur durch indirekte, wenn auch spezifische Funktionszeichen und -merkmal nachgewiesen werden kann. Um sie exakter zu erkennen und damit möglicherweise die Aufklärung und Diagnose virusinduzierter Tumoren verbessern zu können, müssen zur Zeit vorwiegend experimentelle Arbeiten mit onkogenen Virusarten vorgenommen werden. Der Virusforschung stehen hier günstige experimentelle Modellsysteme zur Verfügung, mit denen die Mechanismen der Krebszellentstehung und Tumorbildung durch Viren bis in molekularbiologische Dimensionen hinein verfolgt werden können.
Chapter
The plasmid concept is rooted in the notion of particulate determinants of inheritance and the chromosome theory of heredity, but some biologists saw genes as determinants of the way an organism developed from a fertilized ovum into a mature adult; some of these determinants seem to be passed on through cytoplasmic transfer. In a 1952 review, J. Lederberg proposed that all “extrachromosomal hereditary determinants” be designated “plasmids.” In 1958, Jacob and Wollman suggested that genetic elements which were optionally associated with the chromosomes, such as the F-factor, the colicinogenic factor, and bacteriophage lambda, be termed “episomes.” Allan Campbell (Adv Genetics 11:101–145, 1962) proposed a beautifully simple solution to the problem of how episomes could be associated with the chromosome when he suggested the recombinational interaction of one circular molecule with another. The key to the modern concept of the plasmid was the confirmation that DNA molecules can, and often do, exist as circular structures. Many observations (mainly on yeast and protozoans) suggested that nonchromosomal heredity exists in eucaryotes as well, and eventually, cytochemical, electron microscopic, and biochemical evidence established the existence of cytoplasmic genes in eucaryotes. By the end of the 1960s, both the genetic and physical understanding of plasmids and cytoplasmic heredity had reached a level of detail to allow exploitation of these genetic elements as tools to manipulate and study cell genetics by various techniques of lateral gene transfer.
Article
An X-ray diffraction study of the basic proteins histone and protamine and of their complexes with DNA has been made with a view to elucidating the molecular structure of the proteins and of nucleohistone and nucleoprotamine. Isolated histone, when undenatured, gives diffuse diffraction rings in the regions of 4·5 and 10 Å. In some patterns a sharp 4·7 Å reflection is visible. In sheet specimens the direction of the 4·7 Å spacing is parallel to the plane of the sheet and the 10 Å spacing is perpendicular to the plane. The appearance of the diffuse diffraction patterns is compatible with the presence of α-helices; the sharp 4·7 Å reflection probably arises from a β-type structure produced by denaturation. Protamine sulphate gives a strong diffuse ring at about 4·2 Å and a weak ring at 7·5 Å. Dry nucleohistone and nucleoprotamine give patterns similar to those of the isolated proteins.
Article
Protein monolayers, or true H-films, can be spread quickly and without loss on distilled water or dilute buffer solutions, if the protein solution before reaching the water surface of the film trough is spread out into a very thin layer around a glass rod. During the flow time along the glass rod the vast majority of all protein molecules diffuse to the water/air interface and spread, if flow rate, protein concentration, glass rod length, and diameter are chosen correctly. The influence of these parameters is investigated theoretically, and the theoretical predictions are compared with results from spreading experiments.
Article
Brief high-speed mixing of DNA solutions results in a decrease of the ; sedimentation coefficient of the sample as well as a narrowing of the ; distribution of sedimentation coefficients. This is interpreted as being due to ; scission of those DNA macromolecules above a certain size (S > 26). This ; behavior is not accompanied by significant denaturation. (auth);
Article
A comprehensive study of the buoyant density of DNA as a function of composition has been made. The linear relation previously reported has been confirmed. Based on a value of 1·710 g cm−3 for DNA from Escherichia coli the following relation was obtained from the best fit of measurements on 51 different DNA samples: ρ=1⋅660+0⋅098(GC) where ρ refers to buoyant density and (GC) to the mole fraction of guanine plus cytosine. On this basis the composition of DNA from 36 other sources, not previously reported, has been estimated. Several specific observations were made. Bimodal distributions in the density-gradient band patterns were found in DNA from calf thymus and salmon sperm. The DNA of the commonly studied T-even bacteriophages exhibits altered densities due to the presence of gluco-sylated hydroxymethylcytosine. The DNA of φX174 phage is abnormally heavier suggesting less base-pairing than normal denatured, single-stranded DNA.
Article
High-titer polyma virus lysates were routinely obtained through the use of tissue cultures made from the kidneys of suckling mice that were inoculated with virus a few days after birth. The virus was then concentrated by sedimentation and purified by equilibrium centrifugation in a cesium chloride density gradient. By this procedure 316-fold and 375-fold increases of the ratio infectivity to protein content were obtained.Evidence in support of homogeneity of the purified virus preparations was obtained from analytical ultracentrifuge studies. Sedimentation velocity experiments revealed a single sedimenting component with a sedimentation constant, S20 w, of 242 ± 1 Svedbergs; equilibrium centrifugation in a cesium chloride density gradient showed the presence of a single symmetrical concentration distribution. Additional support for homogeneity was obtained from electron microscope observations and the ultraviolet absorption spectrum.After equilibrium centrifugation in a cesium chloride density gradient, crude polyoma virus fractionates into two main bands at levels corresponding to densities 1.339 g/ml and 1.297 g/ml. At density 1.339, virus displayed infectivity comparable to its hemagglutinating activity, showed an ultraviolet absorption spectrum typical of a nucleoprotein, and appeared to consist mainly of “full” particles in the electron microscope. At density 1.297, virus was characterized by hemagglutinating activity without corresponding infectivity, a typical protein-like ultraviolet absorption spectrum, and the appearance of “empty” particles in the electron microscope. Using the difference in buoyant densities between the two types of polyoma particles, the amount of deoxyribonucleic acid in the “full” particles was estimated as 13.4%.
Article
Depurination by heat of DNA and DNA constituents, in solution and in the dry state, has been further investigated. The extent of depurination in solution varies inversely with the ionic strength and pH. Depurination at elevated temperatures in solution appears to be mainly an acid-catalysed hydrolysis. Studies of depurination in the dry state, in the same conditions of heating used to induce mutations in dry cells and spores, indicated that approximately 30 molecules of purine are liberated per molecule of DNA, probably by the pyrolytic breakage of the N-glycosidic bond and/or destruction of the sugar. In solution and in the dry state, the nature and the extent of depurination of DNA by heat differs from that of the constituent deoxymononucleotides. Depurination, which appears to occur throughout the entire molecule of DNA, results in most conditions in a slightly greater liberation of guanine compared with adenine. The energies of activation of depurination of DNA in solution and in the dry state were calculated. The extent of depurination was unaffected by incorporation of 5-bromouracil into the DNA. Correlations between depurination and changes in the viscosity and transforming activity of DNA and the nature and extent of heat-induced mutational sites are discussed.
Single DNA molecules can be rendered visible in the electron microscope by "staining" with water-soluble salts of heavy metals. The best results were obtained with lanthanum nitrate, uranyl acetate, and lead perchlorate. The molecules appear as filaments approximately 20 A wide. Their length was not determined, but it could be shown that it varied with the molecular weight of the DNA used. The same heavy metal salts will preferentially "stain" the nucleic acid in a protein-DNA complex. Evidence is provided for the possibility of a partial separation of a double-stranded molecule into single strands on adsorption to the supporting film.
Article
The rate, temperature, and pH dependence of thermal inactivation of φX174 DNA suggest that this inactivation may be a consequence of depurination. This depurination is not immediately followed by chain scission.
Article
By velocity sedimentation, in appropriate solvents, the presence of two discrete components can be demonstrated in preparations of the DNA of bacteriophage φX174. The major, faster-moving S_1 and the slower S_2 are present under conditions which exclude the possibility of hydrogen-bond formation. It can be shown, either by treatment with pancreatic deoxyribonuclease or by thermal inactivation, that S_2 is the first degradation product of S_1, formed by scission of S_1, without significant decrease in molecular weight. A subsequent chain scission in S_2, which occurs with equal likelihood, results in random fragmentation. These results are interpreted to mean that the S_1 component is a covalently linked ring structure and the S_2 component is the corresponding open-chain degradation product. Under certain conditions the S_2 component can be selectively degraded by E. coli phosphodiesterase. The digestion is not complete and there appears to be a single discontinuity, resistant to phosphodiesterase, present in the φX-DNA ring.
Article
The reaction between formaldehyde and phage T7 DNA has been studied by optical absorbance and sedimentation measurements. Through the course of denaturation, OD(200) and s(20, w) rise; after the attainment of full hyperchromicity the s(20, w) falls sharply, suggesting a decrease in molecular weight. Conditions in which formaldehyde causes cross-linking are defined. Some experimental applications of the denaturation technique are given. Evidence which suggests that preformed single-strand interruptions may exist in phage DNA is briefly discussed.
Article
This communication presents a new method of carrying out sedimentation velocity experiments. A thin lamella of a solution of macromolecules is layered onto a denser miscible liquid in a rotating ultracentrifuge cell. The macromolecules then sediment through the liquid in a narrow concentration distribution, or band, which is observed photographically as a function of time. The density gradients necessary to stabilize the system against convection are generated during the experiment by the diffusion of small molecules between the lamella and the bulk solution, and in some cases by the sedimentation of the small molecules in the bulk solution. The inhomogeneities in the solvent are usually small enough to have no observable effect on the motion of the macromolecules. Sedimentation coefficients of macromolecules may be evaluated from the motion of bands. Diffusion, hydrodynamic interactions, and chemical reactions affect the shapes of bands.
Article
The isolation and the physical characterization of the DNA from T7 bacteriophage are described. The DNA is shown to be homogeneous by ultracentrifugation and chromatography. It is probable that this DNA preparation yields a mono-disperse solution of molecules of molecular weight 19 × 106.
Article
The DNA of polyoma (PY) virus has two interesting features: it is unusually resistant to heat or formamide denaturation,(1) and it has two distinct components, of sedimentation coefficient 14 and 21, respectively.(2) A two-component sedimentation was formerly shown to be a characteristic of the DNA of papilloma virus,(3) which is considered a member of the same group of viruses.
10 This value was obtained from the relative values of sedimentation coefficients of I and III in CsCl, p = 1.35, and the value for s'.° for I in 1.0 M NaCl
10 This value was obtained from the relative values of sedimentation coefficients of I and III in CsCl, p = 1.35, and the value for s'.° for I in 1.0 M NaCl. L. \r. Crawford in Virology, 19, 279 (1963), obtained 21 S and 14 S for two components in polyoma DNA. 11 Similar results were obtained independently by Dulbecco and Vogt.3
• J Vinograd
• R Bruner
• R Kent
• J Weigle
5 Vinograd, J., R. Bruner, R. Kent, and J. Weigle, these PROCEEDINGS, 49, 902 (1963). 6Vinograd, J., and J. Hearst, Prog. in Chem. Org. Nat. Prods., 20, 372 (1962).
• M H F Wilkins
• G Zubay
• H R Wilson
19 Wilkins, M. H. F., G. Zubay, and H. R. Wilson, J. Mol. Biol. 1, 179 (1959).
• A K Kleinschmidt
• R K Zahn
22 Kleinschmidt, A. K., and R. K. Zahn, Z. Naturforsch., 14b, 770 (1959).
Baltimore: Williams and Wilkins), in press
• M D Anderson Hospital
• M Vogt
M. D. Anderson Hospital, Houston, Texas, Feb. 20, 1963 (Baltimore: Williams and Wilkins), in press. 3 Dulbecco, R., and M. Vogt, these PROCEEDINGS, 50, 236 (1963). 4Winocour, E., Virology, 19, 158 (1963).
• R L Sinsheimer
12 Sinsheimer, R. L., J. Mol. Biol., 1, 43 (1959).
7a These solutions were not free of carbon dioxide
• J Vinograd
• J Morris
• N Davidson
• W F Dove
Vinograd, J., J. Morris, N. Davidson, and W. F. Dove, Jr., these PROCEEDINGS, 49, 12 (1963). 7a These solutions were not free of carbon dioxide. 8 Freifelder, D., and P. F. Davison, Biophys. J., 3, 49 (1963).