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Li J, Mohammed-Elsabagh M, Paczkowski F, Li Y. Circular Nucleic Acids: Discovery, Functions and Applications. Chembiochem 2020; 21:1547-1566. [PMID: 32176816 DOI: 10.1002/cbic.202000003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Circular nucleic acids (CNAs) are 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 by 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 to couple 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.
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Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Freeman Paczkowski
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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Onaga LA. Ray Wu as Fifth Business: Deconstructing collective memory in the history of DNA sequencing. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2014; 46:1-14. [PMID: 24565976 DOI: 10.1016/j.shpsc.2013.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Revised: 12/31/2013] [Accepted: 12/31/2013] [Indexed: 05/22/2023]
Abstract
The concept of 'Fifth Business' is used to analyze a minority standpoint and bring serious attention to the role of scientists who play a galvanizing role in a science but for multiple reasons appear less prominently in more common recounts of any particular development. Biochemist Ray Wu (1928-2008) published a DNA sequencing experiment in March 1970 using DNA polymerase catalysis and specific nucleotide labeling, both of which are foundational to general sequencing methods today. The scant mention of Wu's work from textbooks, research articles, and other accounts of DNA sequencing calls into question how scientific collective memory forms. This alternative history seeks to understand why a key figure in nucleic acid sequence analysis has remained less visibly connected or peripheral to solidifying narratives about the history of DNA sequencing. The study resists predictable dismissals of Wu's work in order to seriously examine the formation of his nucleic acid sequence analysis research program and how he shared his knowledge of sequencing during a period of rapid advancement in the field. An analysis of Wu's work on sequencing the cohesive ends of lambda bacteriophage in the 1960s and 1970s exemplifies how a variety of individuals and groups attempted to develop protocol for sequencing the order of nucleotide base pairs comprising DNA. This historical examination of the sociality of scientific research suggests a way to understand how Wu and others contributed to the very collective memory of DNA sequencing that Wu eventually tried to repair. The study of Wu, who was a Chinese immigrant to the United States, provides a foundation for further critical scholarship on the heterogeneous histories of Asian American bioscientists, the sociality of their scientific works, and how the resulting knowledge produced is preserved, if not evenly, in a scientific field's collective memory.
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Affiliation(s)
- Lisa A Onaga
- History Programme, School of Humanities and Social Sciences, Nanyang Technological University, 14 Nanyang Dr., Singapore 637332, Singapore.
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Gabor M, Hotchkiss RD. Manifestation of linear organization in molecules of pneumococcal transforming DNA. Proc Natl Acad Sci U S A 2010; 56:1441-8. [PMID: 16591391 PMCID: PMC219994 DOI: 10.1073/pnas.56.5.1441] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Abstract
I was born in China and would have remained there but for the tumultuous events that led many of my generation to the United States for graduate studies. Norman Davidson introduced me to DNA when I became a postdoctoral fellow in his group at the California Institute of Technology in 1964, and a fortuitous conversation there ignited my interest in DNA ring formation, which later led me to study different topological forms of DNA rings-catenanes, knots, and supercoils. In 1968, a chance observation led me to identify a new enzyme capable of converting one DNA ring form to another, an enzyme now known as a DNA topoisomerase. My interest in DNA rings and DNA topoisomerases continued throughout my years at the University of California, Berkeley, and Harvard. The fascinating ability of the topoisomerases in passing DNA strands or double helices through one another and their importance in cellular processes have kept me and many others excited in their studies.
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Affiliation(s)
- James C Wang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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Baldwin RL. Recollections of Arthur Kornberg (1918-2007) and the beginning of the Stanford Biochemistry Department. Protein Sci 2008; 17:385-8. [PMID: 18350670 PMCID: PMC2248304 DOI: 10.1002/pro.170385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Robert L Baldwin
- Biochemistry Department, Beckman Center, Stanford Medical Center, Stanford, California 94305, USA
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Yi D. Cancer, viruses, and mass migration: Paul Berg's venture into eukaryotic biology and the advent of recombinant DNA research and technology, 1967-1980. JOURNAL OF THE HISTORY OF BIOLOGY 2008; 41:589-636. [PMID: 19244843 DOI: 10.1007/s10739-008-9149-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The existing literature on the development of recombinant DNA technology and genetic engineering tends to focus on Stanley Cohen and Herbert Boyer's recombinant DNA cloning technology and its commercialization starting in the mid-1970s. Historians of science, however, have pointedly noted that experimental procedures for making recombinant DNA molecules were initially developed by Stanford biochemist Paul Berg and his colleagues, Peter Lobban and A. Dale Kaiser in the early 1970s. This paper, recognizing the uneasy disjuncture between scientific authorship and legal invention in the history of recombinant DNA technology, investigates the development of recombinant DNA technology in its full scientific context. I do so by focusing on Stanford biochemist Berg's research on the genetic regulation of higher organisms. As I hope to demonstrate, Berg's new venture reflected a mass migration of biomedical researchers as they shifted from studying prokaryotic organisms like bacteria to studying eukaryotic organisms like mammalian and human cells. It was out of this boundary crossing from prokaryotic to eukaryotic systems through virus model systems that recombinant DNA technology and other significant new research techniques and agendas emerged. Indeed, in their attempt to reconstitute 'life' as a research technology, Stanford biochemists' recombinant DNA research recast genes as a sequence that could be rewritten thorough biochemical operations. The last part of this paper shifts focus from recombinant DNA technology's academic origins to its transformation into a genetic engineering technology by examining the wide range of experimental hybridizations which occurred as techniques and knowledge circulated between Stanford biochemists and the Bay Area's experimentalists. Situating their interchange in a dense research network based at Stanford's biochemistry department, this paper helps to revise the canonized history of genetic engineering's origins that emerged during the patenting of Cohen-Boyer's recombinant DNA cloning procedures.
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Affiliation(s)
- Doogab Yi
- Program in History of Science, Princeton University, 129 Dickinson Hall, Princeton, NJ 08544-1017, USA.
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Abstract
Fortunately, I began research in 1950 when the basic concepts of microbial genetics could be explored experimentally. I began with bacteriophage lambda and tried to establish the colinearity of its linkage map with its DNA molecule. My students and I worked out the regulation of lambda repressor synthesis for the establishment and maintenance of lysogeny. We also investigated the proteins responsible for assembly of the phage head. Using cell extracts, we discovered how to package DNA inside the head in vitro. Around 1972, I began to use molecular genetics to understand the developmental biology of Myxococcus xanthus. In particular, I wanted to learn how myxococcus builds its multicellular fruiting body within which it differentiates spores. We identified two cell-to-cell signals used to coordinate development. We have elucidated, in part, the signal transduction pathway for C-signal that directs the morphogenesis of a fruiting body.
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Affiliation(s)
- Dale Kaiser
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA.
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Wu R. Development of enzyme-based methods for DNA sequence analysis and their applications in the genome projects. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 67:431-68. [PMID: 8322619 DOI: 10.1002/9780470123133.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- R Wu
- Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY
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MANDEL M, HIGA A. Calcium-dependent Bacteriophage DNA Infection. Mol Biol 1989. [DOI: 10.1016/b978-0-12-131200-8.50033-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Abstract
The fungicide Bavistin was assessed for mutagenic potential by various assays. Bavistin was found to be unable to induce gene mutation in Salmonella typhimurium, but it was able to induce transfection inhibition in Mycobacterium smegmatis. Bavistin was able to induce immediate genotoxic effects in plants but these were not carried through in development as in the long term no genotoxic effects were observed by the progeny test. Bavistin did induce micronuclei formation and did cause an increase in the ratio of normochromatic to polychromatic erythrocytes in mice. It was able to induce a very low frequency of sister-chromatid exchange in human lymphocytes and in addition, it was observed that the chemical affected the mitotic index but did not affect the cell cycle duration. Present studies indicate that the pesticide shows a positive response in 4 out of 5 different test systems (Table 8) and most of the observations support that Bavistin is genotoxic.
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Affiliation(s)
- T K Pandita
- Microbiology and Cell Biology Laboratory, Indian Institute of Science, Bangalore
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Abstract
The insecticide Thimet 10-G was tested for mutagenic activity by 4 different genetic systems. It was unable to induce gene mutation in Salmonella, transfection inhibition in Mycobacterium, micronuclei formation in mice, and sister-chromatid exchange (SCE) in human lymphocytes were evaluated. It caused in mice an increase in the ratio of normochromatic to polychromatic erythrocytes and in human lymphocytes a decrease in mitotic index and delay in cell cycle. The results indicate that the insecticide is not mutagenic in the 4 test systems used at present.
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Goorha R, Murti KG. The genome of frog virus 3, an animal DNA virus, is circularly permuted and terminally redundant. Proc Natl Acad Sci U S A 1982; 79:248-52. [PMID: 6952182 PMCID: PMC345703 DOI: 10.1073/pnas.79.2.248] [Citation(s) in RCA: 97] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We examined the structure of the frog virus 3 (FV 3) genome by using electron microscopic and biochemical techniques. The linear FV 3 DNA molecules (Mr approximately 100 x 10(6) formed circles when partially degraded with bacteriophage lambda 5'-exonuclease and annealed, but not when the annealing was done without prior exonuclease digestion. The results suggest that the DNA molecules contain direct terminal repeats. The repeated region composed about 4% of the genome. Complete denaturation of native FV 3 DNA molecules followed by renaturation produced duplex circles each bearing two single-stranded tails at different points along the circumference. The tails presumably represent the terminal repeats. The formation of duplex circles suggests that the FV 3 genome is circularly permuted. This is further borne out by (i) failure to identify a specific restriction endonuclease fragment containing the label when the molecular ends were radiolabeled by using the polynucleotide kinase procedure, and (ii) similarity in the restriction patterns of virion DNA and large concatemeric replicating viral DNA as revealed by endonucleolytic cleavage of both DNAs with HindIII. From the above data, we conclude that the FV3 genome is both circularly permuted and terminally redundant--unique features for an animal virus.
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Thompson NE, Pattee PA. Genetic transformation in Staphylococcus aureus: demonstration of a competence-conferring factor of bacteriophage origin in bacteriophage 80 alpha lysates. J Bacteriol 1981; 148:294-300. [PMID: 6457025 PMCID: PMC216192 DOI: 10.1128/jb.148.1.294-300.1981] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A virion component that is responsible for conferring competence to Staphylococcus aureus was demonstrated in lysates of bacteriophage 80 alpha, a serological group B phage. Isolated particles of 80 alpha could not be shown to confer significant levels of competence. The phage component had a density of about 1.3 g/cm3, was inactivated by pronase, and was inhibited by antiserum prepared against isolated infectious particles of a serological group B phage. Centrifugation through a Ficoll gradient resulted in separation of competence-conferring activity and plaque-forming units. It is concluded that this proteinaceous subvirion component constitutes a bona fide competence factor of bacteriophage origin.
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Elseth GD, Juetersonke G, Bierman MA, Karcher LP. A kinetic model for bacterial transfection: the lambda DNA system. J Theor Biol 1978; 72:429-41. [PMID: 353389 DOI: 10.1016/0022-5193(78)90310-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Blackburn EH, Gall JG. A tandemly repeated sequence at the termini of the extrachromosomal ribosomal RNA genes in Tetrahymena. J Mol Biol 1978; 120:33-53. [PMID: 642006 DOI: 10.1016/0022-2836(78)90294-2] [Citation(s) in RCA: 638] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Thompson NE, Pattee PA. Transformation in Staphylococcus aureus: role of bacteriophage and incidence of competence among strains. J Bacteriol 1977; 129:778-88. [PMID: 138674 PMCID: PMC235011 DOI: 10.1128/jb.129.2.778-788.1977] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
When used in a helper phage capacity, phages 29, 52, 52A, 79, 80, 55, 71, 53, 83A, 85, 95, 96, phi11, and 80 alpha, all serological group B Staphylococcus phages, conferred competence for transformation to S. aureus 8325-4, a strain that does not normally become competent. Of the serological group A phages tested, only phage 3A showed significant competence-conferring activity. Phages 29, 55, 53, 83A, .85, 95, phi11, and 80 alpha showed an enhancement of competence-conferring activity if exposure to the cells occurred in the presence of nromal rabbit serum. All of the propagating strains for the Staphylococcus reference typing phages were rendered competent for transformation by exposure to at least one of these helper phages. The use of a helper phage to confer competence to S. aureus did not result in distortion of the genetic linkages observed in an inherently competent strain. Lysogenization by phages phi11 or 83A is shown not to be required for the expression of competence, and evidence is presented which indicates that competence in the inherently competent 8325 strain is due to a helper phage effect initiated by the adsorption to cells of phi11 virion parts [or phi11 particles in the case of the single lysogen 8325-4(phi11)] that have been liberated by prophage induction.
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Flint SJ, Berget SM, Sharp PA. Characterization of single-stranded viral DNA sequences present during replication of adenovirus types 2 and 5. Cell 1976; 9:559-71. [PMID: 1009576 DOI: 10.1016/0092-8674(76)90038-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Replication intermediates of adenovirus DNA apparently contain extensive stretches of single-stranded DNA. Such single-stranded viral DNA sequences homologous to different regions of the viral genome present in adenovirus-infected cells during viral DNA replication have therefore been characterized by hybridization to the separated strands of restriction endonuclease fragments of 32P-labeled adenovirus types 2 and 5 DNA. Saturation hybridization experiments with infected cell DNA extracted at late times suggest that all regions of the adenovirus genome are represented in the single-stranded fraction, but at unequal frequencies. This nonuniform representation has been characterized in more detail with self-annealed, total cell DNA extracted 18 hr after adenovirus type 2 infection: the concentration of single-stranded sequences homologous to different regions of the viral genome was determined by comparing the rates of hybridization of 32P-labeled, single-stranded DNA probes with such self-annealed 18 hr DNA to the rates of hybridization of the same probes with equal concentrations of their complements. This approach allows the concentration of single-stranded viral DNA sequences in excess of their complements to be determined. Such sequences can be represented by two concentration gradients across the viral genome: those homologous to the r strand increase in concentration from 27.8-40.9 units toward the right end, whereas sequences homologous to the 1 strand increase from an area 27.8-40.9 units toward the left end. The time course of synthesis of single-stranded viral DNA sequences relative to accumulation of total viral DNA during the productive cycle and their behavior following a shift of H5ts125-infected cells in which viral DNA replication has begun from a permissive to a nonpermissive temperature support the contention that these sequences are indeed generated as adenovirus DNA is replicated. These results are therefore discussed in terms of current models of adenovirus DNA replication.
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Freifelder D, Brimlow N, Plotkin S. Formation of covalently closed cyclic dimers and catenanes of Escherichia coli phage lambda in the absence of known recombination systems. Virology 1976; 74:169-73. [PMID: 982813 DOI: 10.1016/0042-6822(76)90138-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Ehrlich S, Sgaramella V, Lederberg J. Transfection of restrictionless Escherichia coli by bacteriophage T7 dna: effect of in vitro erosion of DNA by gamma exonuclease. J Mol Biol 1976; 105:603-9. [PMID: 787542 DOI: 10.1016/0022-2836(76)90238-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Freifelder D. Preparation of covalently closed and open circular DNA molecules of phage lambda. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 432:113-7. [PMID: 4146 DOI: 10.1016/0005-2787(76)90047-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Grafstrom RH, Alwine JC, Steinhart WL, Hill CW, Hyman RW. The terminal repetition of herpes simplex virus DNA. Virology 1975; 67:144-57. [PMID: 169623 DOI: 10.1016/0042-6822(75)90412-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Murray K, Murray NE, Bertani G. Base changes in the recognition site for ter functions in lambdoid phage DNA. Nature 1975; 254:262-5. [PMID: 1113894 DOI: 10.1038/254262a0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Specific Hydrolysis of the Cohesive Ends of Bacteriophage λ-Deoxyribonucleic Acid by Micrococcus luteus Ultraviolet Exonuclease. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)81273-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Murray NE, Murray K. Manipulation of restriction targets in phage lambda to form receptor chromosomes for DNA fragments. Nature 1974; 251:476-81. [PMID: 4608939 DOI: 10.1038/251476a0] [Citation(s) in RCA: 216] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Mangel WF. Initial steps in the large-scale purification of Escherichia coli deoxyribonucleic acid-dependent ribonucleic acid polymerase. Arch Biochem Biophys 1974; 163:172-7. [PMID: 4604619 DOI: 10.1016/0003-9861(74)90466-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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29
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Paoletti E, Moss B. Two Nucleic Acid-dependent Nucleoside Triphosphate Phosphohydrolases from Vaccinia Virus. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42669-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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Murray K, Old RW. The primary structure of DNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1974; 14:117-85. [PMID: 4367574 DOI: 10.1016/s0079-6603(08)60207-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Lawhorne L, Kleber I, Mitchell C, Benzinger R. Transfection of Escherichia coli spheroplasts. II. Relative infectivity of native, denatured, and renatured lambda, T7, T5, T4, and P22 bacteriophage DNAs. J Virol 1973; 12:733-40. [PMID: 4591046 PMCID: PMC356691 DOI: 10.1128/jvi.12.4.733-740.1973] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The change of infectivity of phage DNAs after heat and alkali denaturation (and renaturation) was measured. T7 phage DNA infectivity increased 4- to 20-fold after denaturation and decreased to the native level after renaturation. Both the heavy and the light single strand of T7 phage DNA were about five times as infective as native T7 DNA. T4 and P22 phage DNA infectivity increased 4- to 20-fold after denaturation and increased another 10- to 20-fold after renaturation. These data, combined with other authors' results on the relative infectivity of various forms of phiX174 and lambda DNAs give the following consistent pattern of relative infectivity. Covalently closed circular double-stranded DNA, nicked circular double-stranded DNA, and double-stranded DNA with cohesive ends are all equally infective and also most highly infectious for Escherichia coli lysozyme-EDTA spheroplasts; linear or circular single-stranded DNAs are about 1/5 to 1/20 as infective; double-stranded DNAs are only 1/100 as infective. Two exceptions to this pattern were noted: lambda phage DNA lost more than 99% of its infectivity after alkaline denaturation; this infectivity could be fully recovered after renaturation. This behavior can be explained by the special role of the cohesive ends of the phage DNA. T5 phage DNA sometimes showed a transient increase in infectivity at temperatures below the completion of the hyperchròmic shift; at higher temperatures, the infectivity was completely destroyed. T5 DNA denatured in alkali lost more than 99.9% of its infectivity; upon renaturation, infectivity was sometimes recovered. This behavior is interpreted in terms of the model of T5 phage DNA structure proposed by Bujard (1969). The results of the denaturation and renaturation experiments show higher efficiencies of transfection for the following phage DNAs (free of single-strand breaks): T4 renatured DNA at 10(-3) instead of 10(-5) for native DNA; renatured P22 DNA at 3 x 10(-7) instead of 3 x 10(-9) for native DNA; and denatured T7 DNA at 3 x 10(-6) instead of 3 x 10(-7) for native DNA.
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Murray K, Murray NE. Terminal nucleotide sequences of DNA from temperate coliphages. NATURE: NEW BIOLOGY 1973; 243:134-9. [PMID: 4515740 DOI: 10.1038/newbio243134a0] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Georgopoulos CP, Hendrix RW, Casjens SR, Kaiser AD. Host participation in bacteriophage lambda head assembly. J Mol Biol 1973; 76:45-60. [PMID: 4578100 DOI: 10.1016/0022-2836(73)90080-6] [Citation(s) in RCA: 311] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Dityatkin SY, Lisovskaya KV, Panzhava NN, Iliashenko BN. Frozen-thawed bacteria as recipients of isolated coliphage DNA. BIOCHIMICA ET BIOPHYSICA ACTA 1972; 281:319-23. [PMID: 4565238 DOI: 10.1016/0005-2787(72)90444-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Abstract
Denaturation and renaturation of the adenovirus-2 chromosome (a duplex rod) generates single-stranded circles of unit length. These circles can be opened into linear DNA molecules by digestion with exonuclease III, indicating that hydrogen bonding between the two ends of an adenovirus strand is responsible for maintaining the rod in a circular state.The formation of adenovirus single-stranded circles, and their sensitivity to exonuclease III, indicate that the mature adenovirus-2 DNA molecule contains an inverted terminal repetition. That is, the base sequence at one end of the molecule is inverted and appears again at the other end of the molecule. This is the first example of such a structure, and its function is unknown.
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Higa A, Mandel M. Factors influencing competence of Escherichia coli for lambda-phage deoxyribonucleic acid infection. JAPANESE JOURNAL OF MICROBIOLOGY 1972; 16:251-7. [PMID: 4569211 DOI: 10.1111/j.1348-0421.1972.tb00657.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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37
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Casjens S, Horn T, Kaiser AD. Head assembly steps controlled by genes F and W in bacteriophage lambda. J Mol Biol 1972; 64:551-63. [PMID: 5022189 DOI: 10.1016/0022-2836(72)90082-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Masamune Y, Fleischman RA, Richardson CC. Enzymatic Removal and Replacement of Nucleotides at Single Strand Breaks in Deoxyribonucleic Acid. J Biol Chem 1971. [DOI: 10.1016/s0021-9258(18)62340-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Polito L, Graziani F, Boncinelli E, Malva C, Ritossa F. DNA circularization: a molecular approach for the detection and isolation of tandemly duplicated genes. NATURE: NEW BIOLOGY 1971; 229:84-6. [PMID: 5280341 DOI: 10.1038/newbio229084a0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Dressler D. The rolling circle for phiX DNA replication. II. Synthesis of single-stranded circles. Proc Natl Acad Sci U S A 1970; 67:1934-42. [PMID: 5276153 PMCID: PMC283450 DOI: 10.1073/pnas.67.4.1934] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
varphiX-infected cells have been allowed to incorporate tritiated thymidine late in the phage life cycle when single-stranded circles are the product of DNA synthesis. Virtually all of the radioactivity is recovered in a continuum of actively replicating viral DNA molecules. These molecules are termed rolling circle intermediates because they are characterized by three structural properties. They possess positive strands that are longer than the length of a mature viral genome, and negative strands that are covalently closed single-stranded circles. The 3' termini of the long positive strands lie upon the template rings, while the 5' ends are free in solution. From these experimental data, the basic mode of synthesis is deduced to involve the continuous elongation of the open positive strand by endless copying around the circular negative strand template. As new bases are added to the template-bound (3') end of the positive strand, the distal (5') end is displaced from the template ring as a single-stranded tail of increasing length. It is the tail which serves as the source of material for progeny chromosomes. These data confirm our characterization of this varphiX intermediate, which initially was based only on the possession of long positive strands, and extend this characterization to include experimental statements about the circular nature of the template DNA strand, and the 5' to 3' direction of polynucleotide chain growth within the intermediate. Moreover, the description can now be applied to all of the molecules which acquire label during a pulse.
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DNA replication in Escherichia coli: location of recently incorporated thymidine within molecules of high molecular weight DNA. Proc Natl Acad Sci U S A 1970; 67:629-36. [PMID: 4943176 PMCID: PMC283252 DOI: 10.1073/pnas.67.2.629] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
More than 50% of the [(3)H]thymidine incorporated during short pulses into the DNA of Escherichia coli 15T(-) can be extracted by alkali as high molecular weight DNA. Density gradient centrifugation and digestion with exonuclease I suggest that these large pieces of DNA are composed of newly synthesized DNA attached to pre-existing material at the 3' end of the molecule.
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Dressler D, Wolfson J. The rolling circle for phi X DNA replication. 3. Synthesis of supercoiled duplex rings. Proc Natl Acad Sci U S A 1970; 67:456-63. [PMID: 5272326 PMCID: PMC283226 DOI: 10.1073/pnas.67.1.456] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
During varphiX duplex ring synthesis, the first supercoils to acquire radioactivity after the addition of tritiated thymidine are labeled only in their negative strands. In longer pulses, this asymmetry of labeling progressively disappears. This finding supports the rolling circle model for DNA replication due to the structural asymmetry of its replicating intermediate, but is not predicted by the Cairns or Yoshikawa models.
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Greene R, Korn D. Partial Purification and Characterization of Deoxyribonucleic Acid Polymerase from KB Cells. J Biol Chem 1970. [DOI: 10.1016/s0021-9258(18)63389-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Lark KG. Role of deoxynucleotide strand age or polarity in determining asymmetric chromosome replication after thymine starvation of Escherichia coli 15T - . J Mol Biol 1969; 44:217-31. [PMID: 4940917 DOI: 10.1016/0022-2836(69)90171-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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