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Rodriguez EL, Poddar S, Iftekhar S, Suh K, Woolfork AG, Ovbude S, Pekarek A, Walters M, Lott S, Hage DS. Affinity chromatography: A review of trends and developments over the past 50 years. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1157:122332. [PMID: 32871378 PMCID: PMC7584770 DOI: 10.1016/j.jchromb.2020.122332] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 12/16/2022]
Abstract
The field of affinity chromatography, which employs a biologically-related agent as the stationary phase, has seen significant growth since the modern era of this method began in 1968. This review examines the major developments and trends that have occurred in this technique over the past five decades. The basic principles and history of this area are first discussed. This is followed by an overview of the various supports, immobilization strategies, and types of binding agents that have been used in this field. The general types of applications and fields of use that have appeared for affinity chromatography are also considered. A survey of the literature is used to identify major trends in these topics and important areas of use for affinity chromatography in the separation, analysis, or characterization of chemicals and biochemicals.
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Affiliation(s)
| | - Saumen Poddar
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Sazia Iftekhar
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Kyungah Suh
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Ashley G Woolfork
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Susan Ovbude
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Allegra Pekarek
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Morgan Walters
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Shae Lott
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA.
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Scherrer K. Primary transcripts: From the discovery of RNA processing to current concepts of gene expression - Review. Exp Cell Res 2018; 373:1-33. [PMID: 30266658 DOI: 10.1016/j.yexcr.2018.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/12/2018] [Accepted: 09/17/2018] [Indexed: 12/15/2022]
Abstract
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.
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Affiliation(s)
- Klaus Scherrer
- Institute Jacques Monod, CNRS, University Paris Diderot, Paris, France.
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Douarche C, Cortès R, Roser SJ, Sikorav JL, Braslau A. DNA Adsorption at Liquid/Solid Interfaces. J Phys Chem B 2008; 112:13676-9. [DOI: 10.1021/jp807759d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Carine Douarche
- Physique de la Matière Condensée École Polytechnique, CNRS, 91128 Palaiseau, France, Institut de Recherche Interdisciplinaire, Cité Scientifique, Avenue Poincaré BP 60069, 59652 Villeneuve d’Ascq Cedex, France, Department of Chemistry, University of Bath, Bath, Avon, U.K. BA2 7AY, Service de Biologie Intégrative et de Génétique Moléculaire, Institut de Physique Théorique, CNRS URA 2306, and Service de Physique de l′État Condensé, CNRS URA 2464, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Robert Cortès
- Physique de la Matière Condensée École Polytechnique, CNRS, 91128 Palaiseau, France, Institut de Recherche Interdisciplinaire, Cité Scientifique, Avenue Poincaré BP 60069, 59652 Villeneuve d’Ascq Cedex, France, Department of Chemistry, University of Bath, Bath, Avon, U.K. BA2 7AY, Service de Biologie Intégrative et de Génétique Moléculaire, Institut de Physique Théorique, CNRS URA 2306, and Service de Physique de l′État Condensé, CNRS URA 2464, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Steven J. Roser
- Physique de la Matière Condensée École Polytechnique, CNRS, 91128 Palaiseau, France, Institut de Recherche Interdisciplinaire, Cité Scientifique, Avenue Poincaré BP 60069, 59652 Villeneuve d’Ascq Cedex, France, Department of Chemistry, University of Bath, Bath, Avon, U.K. BA2 7AY, Service de Biologie Intégrative et de Génétique Moléculaire, Institut de Physique Théorique, CNRS URA 2306, and Service de Physique de l′État Condensé, CNRS URA 2464, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Jean-Louis Sikorav
- Physique de la Matière Condensée École Polytechnique, CNRS, 91128 Palaiseau, France, Institut de Recherche Interdisciplinaire, Cité Scientifique, Avenue Poincaré BP 60069, 59652 Villeneuve d’Ascq Cedex, France, Department of Chemistry, University of Bath, Bath, Avon, U.K. BA2 7AY, Service de Biologie Intégrative et de Génétique Moléculaire, Institut de Physique Théorique, CNRS URA 2306, and Service de Physique de l′État Condensé, CNRS URA 2464, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Alan Braslau
- Physique de la Matière Condensée École Polytechnique, CNRS, 91128 Palaiseau, France, Institut de Recherche Interdisciplinaire, Cité Scientifique, Avenue Poincaré BP 60069, 59652 Villeneuve d’Ascq Cedex, France, Department of Chemistry, University of Bath, Bath, Avon, U.K. BA2 7AY, Service de Biologie Intégrative et de Génétique Moléculaire, Institut de Physique Théorique, CNRS URA 2306, and Service de Physique de l′État Condensé, CNRS URA 2464, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France
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Satterfield BC, Stern S, Caplan MR, Hukari KW, West JAA. Microfluidic purification and preconcentration of mRNA by flow-through polymeric monolith. Anal Chem 2007; 79:6230-5. [PMID: 17625914 DOI: 10.1021/ac0709201] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficient and rapid isolation of mRNA is important in the field of genomics as well as in the clinical and pharmaceutical arena. We have developed UV-initiated methacrylate-based porous polymer monoliths (PPM) for microfluidic trapping and concentration of eukaryotic mRNA. PPM are cast-to-shape and are tunable for functionalization using a variety of amine-terminated molecules. Efficient isolation of eukaryotic mRNA from total RNA was first mathematically modeled and then achieved using PPM in capillaries. Purification protocols using oligo dT's, locked nucleic acid substituted dT's, and tetramethylammonium chloride salts were characterized. mRNA yield and purity were compared with mRNA isolated by commercial kits with statistically equivalent yields and purities (determined by qPCR ratio of 18s rRNA and Gusb mRNA markers). Even after extracting 16 microg of mRNA from 315 microg of total RNA, the 0.4-microL volume monolith showed no signs of saturation. Elution volumes were below 20 microL with concentrations up to 1 microg/microL. In addition, the polymeric material exhibited exceptional stability in a range of conditions (pH, temperature, dryness) and was stable for a period of months. All of these characteristics make porous polymer monoliths good candidates for potential microfluidic sample preconcentrators and purifiers.
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Cuatrecasas P. Affinity chromatography of macromolecules. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 36:29-89. [PMID: 4561014 DOI: 10.1002/9780470122815.ch2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Penman S, Scherrer K, Becker Y, Darnell JE. POLYRIBOSOMES IN NORMAL AND POLIOVIRUS-INFECTED HELA CELLS AND THEIR RELATIONSHIP TO MESSENGER-RNA. Proc Natl Acad Sci U S A 2006; 49:654-62. [PMID: 16591084 PMCID: PMC299946 DOI: 10.1073/pnas.49.5.654] [Citation(s) in RCA: 372] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- S Penman
- DEPARTMENT OF BIOLOGY, MASSACHUSETTS INSTITUTE OF TECHNOLOGY
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Abstract
In some aspects, homogeneous (all-in-solution) nucleic acid hybridization assays are superior to the traditionally used heterogeneous (solution-to-surface) alternatives. Profluorescent probes, which reveal fluorescence enhancement or fluorescence polarization upon their binding to DNA and RNA targets, are a paradigm for the real-time sequence-specific homogeneous detection of nucleic acids. A variety of such DNA or RNA-derived probes of different constructs has already been developed with numerous applications. However, the recent additions to the field - locked nucleic acids (LNAs) and peptide nucleic acids (PNAs) - significantly increase the potential of profluorescent probes and provide a robust impulse for their new uses.
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Affiliation(s)
- Vadim V Demidov
- Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA.
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JUKES TH. Relations between mutations and base sequences in the amino acid code. Proc Natl Acad Sci U S A 1998; 48:1809-15. [PMID: 14029847 PMCID: PMC221044 DOI: 10.1073/pnas.48.10.1809] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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CHAMPE SP, BENZER S. Reversal of mutant phenotypes by 5-fluorouracil: an approach to nucleotide sequences in messenger-RNA. Proc Natl Acad Sci U S A 1998; 48:532-46. [PMID: 13877975 PMCID: PMC220814 DOI: 10.1073/pnas.48.4.532] [Citation(s) in RCA: 222] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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BOLTON ET, McCARTHY BJ. A general method for the isolation of RNA complementary to DNA. Proc Natl Acad Sci U S A 1998; 48:1390-7. [PMID: 13870855 PMCID: PMC220964 DOI: 10.1073/pnas.48.8.1390] [Citation(s) in RCA: 231] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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LANNI F. Biological validity of amino acid codes deduced with synthetic ribonucleotide polymers. Proc Natl Acad Sci U S A 1998; 48:1623-30. [PMID: 14462206 PMCID: PMC221011 DOI: 10.1073/pnas.48.9.1623] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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RITOSSA FM, SPIEGELMAN S. LOCALIZATION OF DNA COMPLEMENTARY TO RIBOSOMAL RNA IN THE NUCLEOLUS ORGANIZER REGION OF DROSOPHILA MELANOGASTER. Proc Natl Acad Sci U S A 1996; 53:737-45. [PMID: 14324529 PMCID: PMC221060 DOI: 10.1073/pnas.53.4.737] [Citation(s) in RCA: 438] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Abstract
Poliovirus-infected HeLa cells contain a small amount of an RNA that sediments slightly faster than 16S. This RNA is less dense than viral RNA and resists digestion by ribonuclease. It is therefore, considered to be a double-stranded form of poliovirus RNA. A significant amount of this material is found in association with a membranous virus-specific particulate.
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ERHAN S, NORTHRUP LG, LEACH FR. A METHOD POTENTIALLY USEFUL FOR ESTABLISHING BASE SEQUENCES IN CODEWORDS. Proc Natl Acad Sci U S A 1996; 53:646-52. [PMID: 14338247 PMCID: PMC336991 DOI: 10.1073/pnas.53.3.646] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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HAYASHI MN, HAYASHI M, SPIEGELMAN S. CHROMATOGRAPHIC SEPARATION OF ANNEALED AND ENZYMATICALLY SYNTHESIZED RNA-DNA HYBRIDS. Biophys J 1996; 5:231-46. [PMID: 14268956 PMCID: PMC1367720 DOI: 10.1016/s0006-3495(65)86713-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
A procedure is described for the chromatographic detection and isolation of DNA-RNA hybrids on columns of methylated albumin coated on kieselguhr (MAK). Its use is illustrated with both annealed and enzymatically synthesized hybrids. The method has the advantage of a wide range in capacity and resolution and permits actual isolation of the hybrid structure. It is uniquely effective in experiments involving hybridization with small DNA fragments.
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GEIDUSCHEK EP, TOCCHINI-VALENTINI GP, SARNAT MT. ASYMMETRIC SYNTHESIS OF RNA IN VITRO: DEPENDENCE OF DNA CONTINUITY AND CONFORMATION. Proc Natl Acad Sci U S A 1996; 52:486-93. [PMID: 14206614 PMCID: PMC300303 DOI: 10.1073/pnas.52.2.486] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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HOLLAND JJ, MCCARTHY BJ. STIMULATION OF PROTEIN SYNTHESIS IN VITRO BY DENATURED DNA. Proc Natl Acad Sci U S A 1996; 52:1554-61. [PMID: 14243532 PMCID: PMC300485 DOI: 10.1073/pnas.52.6.1554] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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HAYASHI M, HAYASHI MN, SPIEGELMAN S. RESTRICTION OF IN VIVO GENETIC TRANSCRIPTION TO ONE OF THE COMPLEMENTARY STRANDS OF DNA. Proc Natl Acad Sci U S A 1996; 50:664-72. [PMID: 14077495 PMCID: PMC221243 DOI: 10.1073/pnas.50.4.664] [Citation(s) in RCA: 136] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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COX RA, ARNSTEIN HR. THE ISOLATION, CHARACTERIZATION AND ACID-BASE PROPERTIES OF RIBONUCLEIC ACID FROM RABBIT-RETICULOCYTE RIBOSOMES. Biochem J 1996; 89:574-84. [PMID: 14101978 PMCID: PMC1202465 DOI: 10.1042/bj0890574] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Bacteriophage T4 infection mechanisms. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/b978-0-444-80400-6.50013-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Macdougall AJ, Brown JR, Plumbridge TW. Immobilization of DNA for affinity chromatography and drug-binding studies. Biochem J 1980; 191:855-8. [PMID: 7283977 PMCID: PMC1162286 DOI: 10.1042/bj1910855] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A method is described in which double-stranded DNA is alkylated with 4-bis-(2-chloroethyl)amino-L-phenylalanine and the product immobilized on an insoluble support via the primary amino group of the phenylalanine moiety. The DNA is hence irreversibly bound to the matrix by both strands at a limited number of points.
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Kempf J, Pfleger N, Egly J. Coupling of nucleic acids to agarose: A biospecific support for the purification and/or study of the interactions of related compounds. J Chromatogr A 1978. [DOI: 10.1016/s0021-9673(00)85131-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gilboa E, Prives CL, Aviv H. Purification of SV-40 messenger RNA by hybridization to SV-40 DNA covalently bound to Sepharose. Biochemistry 1975; 14:4215-20. [PMID: 170957 DOI: 10.1021/bi00690a010] [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: 12/13/2022]
Abstract
SV-40 DNA sheared form was coupled in a stable covalent bond to cyanogen bromide activated Sepharose. Under the conditions used at least 80% of the DNA was bound to Sepharose. The T 1/2 of hybridization of 0.5 mug/ml of SV-40 cRNA to SV-40 DNA-Sepharose was 1 hr. This rate of hybridization is sufficiently rapid to purify SV-40 sequences from solutions containing as little as 0.05-0.1 mug/ml. Nonspecific hybridization of RNA is in the range of 0.1-0.2% of the total input RNA. The DNA-Sepharose is fairly stable and can be reused several times to purify RNA. The SV-40 DNA-Sepharose was used to select large quantities of virus specific RNA from SV-40 infected BS-C-1 cells. The virus specific RNA when added to cell-free extracts from wheat germ was shown to direct the synthesis of the major viral structural protein VP-1.
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Arndt-Jovin DJ, Jovin TM, Bähr W, Frischauf AM, Marquardt M. Covalent attachment of DNA to agarose. Improved synthesis and use in affinity chromatography. EUROPEAN JOURNAL OF BIOCHEMISTRY 1975; 54:411-8. [PMID: 1100376 DOI: 10.1111/j.1432-1033.1975.tb04151.x] [Citation(s) in RCA: 176] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DNA has been covalently linked to insoluble matrices of agarose (Sepharose) in high yield using cyanogen bromide activation. Both double-stranded and single-stranded DNA have been coupled with yields up to 225 nmol/mg dry weight Sepharose or 3-8 mumol nucleotide phosphate/ml bed volume. The DNA-Sepharose has been used for (a) the affinity chromatography of various enzymes (Escherichia coli DNA polymerase I and RNA polymerase) from crude extracts or after initial purification steps, resulting in high yields and degrees of purification, and for (b) nucleic acid hybridization. The DNA-Sepharose is stable to high temperature, prolonged storage, and in the case of single-stranded DNA, can be washed with NaOH to destroy nuclease activity and to release any digested oligonucleotides or mononucleotides.
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Cooper TG, Whitney P, Magasanik B. Reaction of lac-specific Ribonucleic Acid from Escherichia coli with lac Deoxyribonucleic Acid. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42191-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Mosch WHM, Huttinga H, Rast ATB. Some chemical and physical properties of 18 tobacco mosaic virus isolates from tomato. ACTA ACUST UNITED AC 1973. [DOI: 10.1007/bf01976684] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Carter BJ, Khoury G, Rose JA. Adenovirus-associated virus multiplication. IX. Extent of transcription of the viral genome in vivo. J Virol 1972; 10:1118-25. [PMID: 4345491 PMCID: PMC356591 DOI: 10.1128/jvi.10.6.1118-1125.1972] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Nucleic acid hybridization procedures were used to measure the extent of transcription of adenovirus-associated virus (AAV) deoxyribonucleic acid (DNA) in KB cells in the presence of either adenovirus or herpes simplex virus as the helper. Annealing of AAV ribonucleic acid to AAV DNA was monitored by a hybridization inhibition assay on nitrocellulose filters or by hydroxyapatite chromatography. These experiments confirmed the previous observation that, in the presence of either type of helper virus, only one strand of AAV DNA (the thymidine-rich or "minus" strand) is transcribed in vivo. However, it was found that only 70 to 80% of this strand appears to be transcribed in vivo. Furthermore, studies with minus strands employing hydroxyapatite chromatography and nuclease S(1), which specifically degrades single-stranded DNA, indicated that up to 20% of the minus strand is self-complementary. It seems likely that these self-complementary sequences account for the bulk of that portion of the minus strand (20 to 30%) which is not transcribed in vivo.
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Abstract
Frogs were injected intraperitoneally with bacteria, and the RNA of the brains (which have protective barriers against the bacteria used) was extracted. Part of the RNA was bacterial RNA apparently resulting from the transcription of DNA transferred from bacteria to the brain cells.
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Orth HD, Brümmer W. Carrier-bound biologically active substances and their applications. Angew Chem Int Ed Engl 1972; 11:249-60. [PMID: 4626419 DOI: 10.1002/anie.197202491] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Orth HD, Brümmer W. Träger-gebundene, biologisch aktive Substanzen und ihre Anwendung. Angew Chem Int Ed Engl 1972. [DOI: 10.1002/ange.19720840802] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Boguslaski RC, Smith RS, Mhatre NS. Applications of bound biopolymers in enzymology and immunology. Curr Top Microbiol Immunol 1972; 58:1-68. [PMID: 4559087 DOI: 10.1007/978-3-642-65357-5_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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42
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Lee-Huang S, Ochoa S. Messenger discriminating species of initiation factor F3. NATURE: NEW BIOLOGY 1971; 234:236-9. [PMID: 4942987 DOI: 10.1038/newbio234236a0] [Citation(s) in RCA: 83] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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43
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Abstract
The nucleotide composition of the ribonucleic acid of three strains of rabies virus was determined and found to be similar to that of vesicular stomatitis virus.
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44
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Rose JA, Koczot F. Adenovirus-associated virus multiplication. VI. Base compostion of the deoxyribonucleic acid strand species and strand-specific in vivo transcription. J Virol 1971; 8:771-7. [PMID: 5132698 PMCID: PMC376259 DOI: 10.1128/jvi.8.5.771-777.1971] [Citation(s) in RCA: 27] [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
The two complementary strand species of 5-bromodeoxyuridine-substituted, adenovirus-associated virus type 2 (AAV-2) deoxyribonucleic acid were preparatively separated in CsCl density gradients and further purified by sedimentation through 5 to 20% sucrose. The base composition of each strand species was determined, and it was found that the species banding at a greater density in CsCl (heavy strands) had an expected higher thymidine content (26.5%) than that 21.7%) of the less dense species (light strands). Furthermore, the base composition of in vivo-synthesized, AAV-specific ribonucleic acid was similar to that of light-strand deoxyribonucleic acid, and this ribonucleic acid apparently hybridized only with heavy strands. These observations indicate that the heavy-strand species alone serves as the transcriptional template in vivo. This study represents the first instance in which the base composition and specificity of in vivo transcription have been determined for each of the complementary strands of an animal virus deoxyribonucleic acid.
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Witmer HJ. In Vitro Transcription of T4 Deoxyribonucleic Acid by Escherichia coli Ribonucleic Acid Polymerase. J Biol Chem 1971. [DOI: 10.1016/s0021-9258(18)61897-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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46
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Feinstein G. Affinity chromatography of biological macromolecules. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 1971; 58:389-96. [PMID: 5315495 DOI: 10.1007/bf00591519] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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47
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Stroun M, Anker P. Bacterial RNA synthesis in animal cells following bacterial contact. FEBS Lett 1971; 16:114-116. [PMID: 11945916 DOI: 10.1016/0014-5793(71)80346-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- M Stroun
- Laboratoire de Physiologie végétale, Université Genève, Suisse, Switzerland
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48
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Stroun M, Anker P, Cattaneo A, Rossier A. Effect of the extent of DNA transcription of plant cells and bacteria on the transcription in plant cells of DNA released from bacteria. FEBS Lett 1971; 13:161-164. [PMID: 11945657 DOI: 10.1016/0014-5793(71)80225-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Maurice Stroun
- Département de Physiologie végétale, Université, Genève, Switzerland
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50
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Stroun M, Anker P. Bacterial nucleic acid synthesis in plants following bacterial contact. MOLECULAR & GENERAL GENETICS : MGG 1971; 113:92-8. [PMID: 5135994 DOI: 10.1007/bf00335008] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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