1
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Wang R, Wang X, Xie S, Zhang Y, Ji D, Zhang X, Cui C, Jiang J, Tan W. Molecular elements: novel approaches for molecular building. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220024. [PMID: 36633277 PMCID: PMC9835600 DOI: 10.1098/rstb.2022.0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Classically, a molecular element (ME) is a pure substance composed of two or more atoms of the same element. However, MEs, in the context of this review, can be any molecules as elements bonded together into the backbone of synthetic oligonucleotides (ONs) with designed sequences and functions, including natural A, T, C, G, U, and unnatural bases. The use of MEs can facilitate the synthesis of designer molecules and smart materials. In particular, we discuss the landmarks associated with DNA structure and related technologies, as well as the extensive application of ONs, the ideal type of molecules for intervention therapy aimed at correcting disease-causing genetic errors (indels). It is herein concluded that the discovery of ON therapeutics and the fabrication of designer molecules or nanostructures depend on the ME concept that we previously published. Accordingly, ME will be our focal point as we discuss related research directions and perspectives in making molecules and materials. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Ruowen Wang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China,Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | - Xueqiang Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Hangzhou, Zhejiang 310018, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Sitao Xie
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Hangzhou, Zhejiang 310018, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Yanyan Zhang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Dingkun Ji
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Xiaobing Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China,Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | - Jianhui Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China,Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Hangzhou, Zhejiang 310018, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China,Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
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2
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Abstract
In the late 1950s, a number of laboratories took up the study of plasmids once the discovery was made that extrachromosomal antibiotic resistance (R) factors are the responsible agents for the transmissibility of multiple antibiotic resistance among the enterobacteria. The use of incompatibility for the classification of plasmids is now widespread. It seems clear now on the basis of the limited studies to date that the number of incompatibility groups of plasmids will likely be extremely large when one includes plasmids obtained from bacteria that are normal inhabitants of poorly studied natural environments. The presence of both linear chromosomes and linear plasmids is now established for several Streptomyces species. One of the more fascinating developments in plasmid biology was the discovery of linear plasmids in the 1980s. A remarkable feature of the Ti plasmids of Agrobacterium tumefaciens is the presence of two DNA transfer systems. A definitive demonstration that plasmids consisted of duplex DNA came from interspecies conjugal transfer of plasmids followed by separation of plasmid DNA from chromosomal DNA by equilibrium buoyant density centrifugation. The formation of channels for DNA movement and the actual steps involved in DNA transport offer many opportunities for the discovery of proteins with novel activities and for establishing fundamentally new concepts of macromolecular interactions between DNA and specific proteins, membranes, and the peptidoglycan matrix.
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Affiliation(s)
- Donald R. Helinski
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
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3
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Tompkins JD. Discovering DNA Methylation, the History and Future of the Writing on DNA. JOURNAL OF THE HISTORY OF BIOLOGY 2022; 55:865-887. [PMID: 36239862 PMCID: PMC9941238 DOI: 10.1007/s10739-022-09691-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
DNA methylation is a quintessential epigenetic mechanism. Widely considered a stable regulator of gene silencing, it represents a form of "molecular braille," chemically printed on DNA to regulate its structure and the expression of genetic information. However, there was a time when methyl groups simply existed in cells, mysteriously speckled across the cytosine building blocks of DNA. Why was the code of life chemically modified, apparently by "no accident of enzyme action" (Wyatt 1951)? If all cells in a body share the same genome sequence, how do they adopt unique functions and maintain stable developmental states? Do cells remember? In this historical perspective, I review epigenetic history and principles and the tools, key scientists, and concepts that brought us the synthesis and discovery of prokaryotic and eukaryotic methylated DNA. Drawing heavily on Gerard Wyatt's observation of asymmetric levels of methylated DNA across species, as well as to a pair of visionary 1975 DNA methylation papers, 5-methylcytosine is connected to DNA methylating enzymes in bacteria, the maintenance of stable cellular states over development, and to the regulation of gene expression through protein-DNA binding. These works have not only shaped our views on heritability and gene regulation but also remind us that core epigenetic concepts emerged from the intrinsic requirement for epigenetic mechanisms to exist. Driven by observations across prokaryotic and eukaryotic worlds, epigenetic systems function to access and interpret genetic information across all forms of life. Collectively, these works offer many guiding principles for our epigenetic understanding for today, and for the next generation of epigenetic inquiry in a postgenomics world.
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Affiliation(s)
- Joshua D Tompkins
- Arthur Riggs Diabetes Metabolism and Research Institute, City of Hope, 1500 E Duarte Road, Duarte, CA, 91010, USA.
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4
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Feng Y, Ovalle M, Seale JSW, Lee CK, Kim DJ, Astumian RD, Stoddart JF. Molecular Pumps and Motors. J Am Chem Soc 2021; 143:5569-5591. [PMID: 33830744 DOI: 10.1021/jacs.0c13388] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Pumps and motors are essential components of the world as we know it. From the complex proteins that sustain our cells, to the mechanical marvels that power industries, much we take for granted is only possible because of pumps and motors. Although molecular pumps and motors have supported life for eons, it is only recently that chemists have made progress toward designing and building artificial forms of the microscopic machinery present in nature. The advent of artificial molecular machines has granted scientists an unprecedented level of control over the relative motion of components of molecules through the development of kinetically controlled, away-from-thermodynamic equilibrium chemistry. We outline the history of pumps and motors, focusing specifically on the innovations that enable the design and synthesis of the artificial molecular machines central to this Perspective. A key insight connecting biomolecular and artificial molecular machines is that the physical motions by which these machines carry out their function are unambiguously in mechanical equilibrium at every instant. The operation of molecular motors and pumps can be described by trajectory thermodynamics, a theory based on the work of Onsager, which is grounded on the firm foundation of the principle of microscopic reversibility. Free energy derived from thermodynamically non-equilibrium reactions kinetically favors some reaction pathways over others. By designing molecules with kinetic asymmetry, one can engineer potential landscapes to harness external energy to drive the formation and maintenance of geometries of component parts of molecules away-from-equilibrium, that would be impossible to achieve by standard synthetic approaches.
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Affiliation(s)
- Yuanning Feng
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Marco Ovalle
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - James S W Seale
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Christopher K Lee
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Dong Jun Kim
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - R Dean Astumian
- Department of Physics, University of Maine, Orono, Maine 04469, United States
| | - J Fraser Stoddart
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States.,School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia.,Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311215, China
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5
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Abstract
Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry—biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function. Here, we outline research that uses the process of gene circuit engineering to advance biological discovery. Synthetic gene circuit engineering research has not only refined our understanding of cellular regulation but furnished biologists with a toolkit that can be directed at natural systems to exact precision manipulation of network structure. As we discuss, using circuit engineering to predictively reorganize, rewire, and reconstruct cellular regulation serves as the ultimate means of testing and understanding how cellular phenotype emerges from systems-level network function.
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Affiliation(s)
- Caleb J. Bashor
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;,
| | - James J. Collins
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;,
- Harvard–MIT Program in Health Sciences and Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
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6
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Family A and B DNA Polymerases in Cancer: Opportunities for Therapeutic Interventions. BIOLOGY 2018; 7:biology7010005. [PMID: 29301327 PMCID: PMC5872031 DOI: 10.3390/biology7010005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/14/2017] [Accepted: 12/29/2017] [Indexed: 02/07/2023]
Abstract
DNA polymerases are essential for genome replication, DNA repair and translesion DNA synthesis (TLS). Broadly, these enzymes belong to two groups: replicative and non-replicative DNA polymerases. A considerable body of data suggests that both groups of DNA polymerases are associated with cancer. Many mutations in cancer cells are either the result of error-prone DNA synthesis by non-replicative polymerases, or the inability of replicative DNA polymerases to proofread mismatched nucleotides due to mutations in 3'-5' exonuclease activity. Moreover, non-replicative, TLS-capable DNA polymerases can negatively impact cancer treatment by synthesizing DNA past lesions generated from treatments such as cisplatin, oxaliplatin, etoposide, bleomycin, and radiotherapy. Hence, the inhibition of DNA polymerases in tumor cells has the potential to enhance treatment outcomes. Here, we review the association of DNA polymerases in cancer from the A and B families, which participate in lesion bypass, and conduct gene replication. We also discuss possible therapeutic interventions that could be used to maneuver the role of these enzymes in tumorigenesis.
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7
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Yokozawa T, Ohta Y. Transformation of Step-Growth Polymerization into Living Chain-Growth Polymerization. Chem Rev 2015; 116:1950-68. [DOI: 10.1021/acs.chemrev.5b00393] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Tsutomu Yokozawa
- Department
of Material and
Life Chemistry, Kanagawa University, Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Yoshihiro Ohta
- Department
of Material and
Life Chemistry, Kanagawa University, Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
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8
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Laos R, Thomson JM, Benner SA. DNA polymerases engineered by directed evolution to incorporate non-standard nucleotides. Front Microbiol 2014; 5:565. [PMID: 25400626 PMCID: PMC4215692 DOI: 10.3389/fmicb.2014.00565] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 10/07/2014] [Indexed: 11/13/2022] Open
Abstract
DNA polymerases have evolved for billions of years to accept natural nucleoside triphosphate substrates with high fidelity and to exclude closely related structures, such as the analogous ribonucleoside triphosphates. However, polymerases that can accept unnatural nucleoside triphosphates are desired for many applications in biotechnology. The focus of this review is on non-standard nucleotides that expand the genetic "alphabet." This review focuses on experiments that, by directed evolution, have created variants of DNA polymerases that are better able to accept unnatural nucleotides. In many cases, an analysis of past evolution of these polymerases (as inferred by examining multiple sequence alignments) can help explain some of the mutations delivered by directed evolution.
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Affiliation(s)
- Roberto Laos
- Foundation for Applied Molecular Evolution Gainesville, FL, USA
| | | | - Steven A Benner
- Foundation for Applied Molecular Evolution Gainesville, FL, USA
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9
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Wang F, Lu CH, Willner I. From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 2014; 114:2881-941. [PMID: 24576227 DOI: 10.1021/cr400354z] [Citation(s) in RCA: 498] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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10
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Production of pure and functional RNA for in vitro reconstitution experiments. Methods 2013; 65:333-41. [PMID: 24021718 DOI: 10.1016/j.ymeth.2013.08.034] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/30/2013] [Accepted: 08/31/2013] [Indexed: 11/22/2022] Open
Abstract
Reconstitution of protein complexes has been a valuable tool to test molecular functions and to interpret in vivo observations. In recent years, a large number of RNA-protein complexes has been identified to regulate gene expression and to be important for a range of cellular functions. In contrast to protein complexes, in vitro analyses of RNA-protein complexes are hampered by the fact that recombinant expression and purification of RNA molecules is more difficult and less well established than for proteins. Here we review the current state of technology available for in vitro experiments with RNAs. We outline the possibilities to produce and purify large amounts of homogenous RNA and to perform the required quality controls. RNA-specific problems such as degradation, 5' and 3' end heterogeneity, co-existence of different folding states, and prerequisites for reconstituting RNAs with recombinantly expressed proteins are discussed. Additionally a number of techniques for the characterization of direct and indirect RNA-protein interactions are explained.
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11
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Abstract
The discovery of the DNA double helix structure half a century ago immediately suggested a mechanism for its duplication by semi-conservative copying of the nucleotide sequence into two DNA daughter strands. Shortly after, a second fundamental step toward the elucidation of the mechanism of DNA replication was taken with the isolation of the first enzyme able to polymerize DNA from a template. In the subsequent years, the basic mechanism of DNA replication and its enzymatic machinery components were elucidated, mostly through genetic approaches and in vitro biochemistry. Most recently, the spatial and temporal organization of the DNA replication process in vivo within the context of chromatin and inside the intact cell are finally beginning to be elucidated. On the one hand, recent advances in genome-wide high throughput techniques are providing a new wave of information on the progression of genome replication at high spatial resolution. On the other hand, novel super-resolution microscopy techniques are just starting to give us the first glimpses of how DNA replication is organized within the context of single intact cells with high spatial resolution. The integration of these data with time lapse microscopy analysis will give us the ability to film and dissect the replication of the genome in situ and in real time.
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Affiliation(s)
- Vadim O Chagin
- Department of Biology, Technische Universität Darmstadt, Germany
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12
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Yokozawa T, Yokoyama A. Chain-Growth Condensation Polymerization for the Synthesis of Well-Defined Condensation Polymers and π-Conjugated Polymers. Chem Rev 2009; 109:5595-619. [DOI: 10.1021/cr900041c] [Citation(s) in RCA: 310] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tsutomu Yokozawa
- Department of Material and Life Chemistry, Kanagawa University, Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Akihiro Yokoyama
- Department of Material and Life Chemistry, Kanagawa University, Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
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13
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Biology under construction: in vitro reconstitution of cellular function. Nat Rev Mol Cell Biol 2009; 10:644-50. [PMID: 19672276 DOI: 10.1038/nrm2746] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We are much better at taking cells apart than putting them together. Reconstitution of biological processes from component molecules has been a powerful but difficult approach to studying functional organization in biology. Recently, the convergence of biochemical and cell biological advances with new experimental and computational tools is providing the opportunity to reconstitute increasingly complex processes. We predict that this bottom-up strategy will uncover basic processes that guide cellular assembly, advancing both basic and applied sciences.
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14
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Lehman IR. Historical perspective: Arthur Kornberg, a giant of 20th century biochemistry. Trends Biochem Sci 2008; 33:291-6. [PMID: 18467101 DOI: 10.1016/j.tibs.2008.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Revised: 03/19/2008] [Accepted: 03/25/2008] [Indexed: 11/17/2022]
Abstract
For physics, the period from the beginning to the middle of the 20th century was one of great scientific excitement and revolutionary discovery. The analogous era for biochemistry, and its offspring, molecular biology, was the second half of the 20th century. One of the most important and influential leaders of this scientific revolution was Arthur Kornberg. The DNA polymerase, which he discovered in 1955 and showed to have the remarkable capacity to catalyze the template-directed synthesis of DNA, contributed in major ways to the present-day understanding of how DNA is replicated and repaired, and how it is transcribed. The discovery of DNA polymerase also permitted the development of PCR and DNA sequencing, upon which much of modern biotechnology is based. Kornberg's studies of DNA replication, which spanned a period of nearly 30 years, culminated in a detailed biochemical description of the mechanism by which a chromosome is replicated. The final years of Kornberg's life were devoted to the study of polyphosphate, which he was convinced had a crucial role in cellular function.
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Affiliation(s)
- I Robert Lehman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.
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15
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Yokozawa T, Adachi I, Miyakoshi R, Yokoyama A. Catalyst-Transfer Condensation Polymerization for the Synthesis of Well-Defined Polythiophene with Hydrophilic Side Chain and of Diblock Copolythiophene with Hydrophilic and Hydrophobic Side Chains. HIGH PERFORM POLYM 2008. [DOI: 10.1177/0954008307081212] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Chain-growth condensation polymerization of 2-bromo-5-chloromagnesio-3-[2-(2-metho-xyethoxy)ethoxy]methylthiophene (2) with Ni catalysts was studied, and the block copolymer of poly2 and poly(3-hexylthiophene) was synthesized by this polymerization method. The polymerization of 2 depended on the ligands of the Ni catalyst, and poly2 with the lowest polydispersity was obtained when 1,2-bis(diphenylphosphino)ethane (dppe) was used as the ligand. The linear relationships between the conversion of 2 and Mn of the polymer and between the feed ratio of 2 to the Ni catalyst and Mn of the polymer indicate that this polymerization proceeds in a chain-growth polymerization manner via a catalyst-transfer condensation polymerization mechanism. The block copolymerization of 2 and 2-bromo-5-chloromagnesio-3-hexylthiophene (1) was then carried out in four ways by changing the order of polymerization of the two monomers and the catalysts. It turned out that the block copolymer was obtained without the formation of the homopolymers by the polymerization of 1 with Ni(dppe)Cl2 or Ni(dppp)Cl2 (dppp = 1,2-bis(diphenylphosphino)propane), followed by the postpolymerization of 2. Of the two catalysts, Ni(dppe)Cl2 resulted in narrower polydispersity of the block copolymer.
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Affiliation(s)
- Tsutomu Yokozawa
- Department of Material and Life Chemistry, Kanagawa University, Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Isao Adachi
- Department of Material and Life Chemistry, Kanagawa University, Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Ryo Miyakoshi
- Department of Material and Life Chemistry, Kanagawa University, Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Akihiro Yokoyama
- Department of Material and Life Chemistry, Kanagawa University, Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
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16
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Abstract
The physicochemical concepts that underlie our present ideas on the structure and assembly of the "macromolecular machines of gene expression" are developed, starting with the structure and folding of the individual protein and DNA components, the thermodynamics and kinetics of their conformational rearrangements during complex assembly, and the molecular basis of the sequence specificity and recognition interactions of the final assemblies that include the DNA genome. The role of diffusion in reduced dimensions in the kinetics of the assembly of macromolecular machines from their components is also considered, and diffusion-driven reactions are compared with those fueled by ATP binding and hydrolysis, as well as by the specific covalent chemical modifications involved in rearranging chromatin and modifying signal transduction networks in higher organisms.
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Affiliation(s)
- Peter H von Hippel
- Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, Oregon 97403, USA.
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17
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Khalaj-Kondori M, Sadeghizadeh M, Khajeh K, Naderi-Manesh H, Ahadi AM, Emamzadeh A. Cloning, Sequence Analysis and Three-dimensional Structure Prediction of DNA Pol I from Thermophilic Geobacillus sp. MKK Isolated from an Iranian Hot Spring. Appl Biochem Biotechnol 2007; 142:200-8. [DOI: 10.1007/s12010-007-0010-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2006] [Revised: 07/05/2006] [Accepted: 07/07/2006] [Indexed: 10/23/2022]
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18
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Oparin AI. The origin of life and the origin of enzymes. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 27:347-80. [PMID: 4882862 DOI: 10.1002/9780470122723.ch7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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19
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Taylor JH, Haut WF, Tung J. EFFECTS OF FLUORODEOXYURIDINE ON DNA REPLICATION, CHROMOSOME BREAKAGE, AND REUNION. Proc Natl Acad Sci U S A 2006; 48:190-8. [PMID: 16590919 PMCID: PMC220755 DOI: 10.1073/pnas.48.2.190] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- J H Taylor
- DEPARTMENT OF BOTANY, COLUMBIA UNIVERSITY
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20
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21
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Abstract
The identification and partial purification by Arthur Kornberg and his colleagues in 1956 of an enzyme - DNA polymerase I of Escherichia coli - that catalysed the stable incorporation of deoxyribonucleotides into DNA in vitro came as a surprise. At the time, most scientists in the field believed that DNA synthesis was too complicated to be accurately reflected outside the living cell.
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Affiliation(s)
- Errol C Friedberg
- Laboratory of Molecular Pathology, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 79503-9072, USA.
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22
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Ozer BH, Smarsly B, Antonietti M, Faul CFJ. DNA-analogous structures from deoxynucleophosphates and polylysine by ionic self-assembly. SOFT MATTER 2006; 2:329-336. [PMID: 32646130 DOI: 10.1039/b515626b] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Here we show that ionic self-assembly of simple biological tectons can be used to synthesize stable and highly ordered molecular structures. In particular, nucleotides and charged polypeptides can be assembled to form a complex analogous to DNA under relatively benign conditions. The combination of polylysine and pure dGMP leads to a fourfold ladder structure stabilizing an interior G-quartet structure by four polypeptide scaffolds. Making use of the Watson-Crick G∶C base pairing motive leads to double-stranded complexes. Interestingly, these complexes show stable DNA-like organization in aqueous solutions, as proven by gel electrophoresis and intercalation experiments.
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Affiliation(s)
- Byram H Ozer
- Max Planck Institute of Colloids and Interfaces, Research Campus Golm, 14424, Potsdam, Germany
| | - Bernd Smarsly
- Max Planck Institute of Colloids and Interfaces, Research Campus Golm, 14424, Potsdam, Germany
| | - Markus Antonietti
- Max Planck Institute of Colloids and Interfaces, Research Campus Golm, 14424, Potsdam, Germany
| | - Charl F J Faul
- Max Planck Institute of Colloids and Interfaces, Research Campus Golm, 14424, Potsdam, Germany and Inorganic and Materials Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.
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Miyakoshi R, Yokoyama A, Yokozawa T. Catalyst-Transfer Polycondensation. Mechanism of Ni-Catalyzed Chain-Growth Polymerization Leading to Well-Defined Poly(3-hexylthiophene). J Am Chem Soc 2005; 127:17542-7. [PMID: 16332106 DOI: 10.1021/ja0556880] [Citation(s) in RCA: 437] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We studied the mechanism of the chain-growth polymerization of 2-bromo-5-chloromagnesio-3-hexylthiophene (1) with Ni(dppp)Cl2 [dppp = 1,3-bis(diphenylphosphino)propane], in which head-to-tail poly(3-hexylthiophene) (HT-P3HT) with a low polydispersity is obtained and the M(n) is controlled by the feed ratio of the monomer to the Ni catalyst. Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectra showed that the HT-P3HT uniformly had a hydrogen atom at one end of each molecule and a bromine atom at the other. The reaction of the polymer with aryl Grignard reagent gave HT-P3HT with aryl groups at both ends, which indicates that the H-end was derived from the propagating Ni complex. The degree of polymerization and the absolute molecular weight of the polymer could be evaluated from the 1H NMR spectra of the Ar/Ar-ended HT-P3HT, and it was found that one Ni catalyst molecule forms one polymer chain. Furthermore, by reaction of 1 with 50 mol % Ni(dppp)Cl2, the chain initiator was found to be a bithiophene-Ni complex, formed by a coupling reaction of 1 followed by insertion of the Ni(0) catalyst into the C-Br bond of the dimer. On the basis of these results, we propose that this chain-growth polymerization involves the coupling reaction of 1 with the polymer via the Ni catalyst, which is transferred intramolecularly to the terminal C-Br bond of the elongated molecule. We call this mechanism "catalyst-transfer polycondensation".
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Affiliation(s)
- Ryo Miyakoshi
- Department of Applied Chemistry, Kanagawa University, Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
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Yokozawa T, Yokoyama A. Chain-growth polycondensation for well-defined condensation polymers and polymer architecture. CHEM REC 2005; 5:47-57. [PMID: 15806548 DOI: 10.1002/tcr.20032] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The historical development of our research on polycondensation that proceeds in a chain-growth polymerization manner ("chain-growth polycondensation") for well-defined condensation polymers is described. We first studied polycondensation in which change of the substituent effect induced by bond formation drove the reactivity of the polymer end group higher than that of the monomer. In this approach, well-defined aromatic polyamides, polyesters, polyethers, and poly(ether sulfone)s were obtained. The second approach was the study of the phase-transfer polymerization of a solid monomer dispersed in an organic solvent. In this type of polymerization, the solid monomer was physically unable to react with another monomer and was carried with the phase transfer catalyst into the solution phase where it reacted with an initiator and the polymer end group in the solvent in a chain polymerization manner. We also found catalyst-transfer polycondensation as a third approach to chain-growth polycondensation. In the Ni-catalyzed polycondensation of 2-bromo-5-chloromagnesiothiophenes, the Ni catalyst transferred to the polymer end group, and a coupling reaction occurred there to yield a well-defined polythiophene. This chain-growth polycondensation was applied to the synthesis of condensation polymer architectures such as block copolymers, star polymers, graft copolymers, and so on.
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Affiliation(s)
- Tsutomu Yokozawa
- Department of Applied Chemistry, Kanagawa University, Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan.
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Yokozawa T, Yokoyama A. Chain-Growth Polycondensation: Living Polymerization Nature in Polycondensation and Approach to Condensation Polymer Architecture. Polym J 2004. [DOI: 10.1295/polymj.36.65] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Abstract
Past discoveries usually become aggrandized in retrospect, especially at jubilee celebrations, and the double helix is no exception. The historical record reveals a muted response by the scientific community to the proposal of this structure in 1953. Indeed, it was only when the outlines appeared of a mechanism for DNA's involvement in protein synthesis that the biochemical community began to take a serious interest in the structure.
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Affiliation(s)
- Robert Olby
- Department of the History and Philosophy of Science, 1017 Cathedral of Learning, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA. olbyr+@pitt.edu
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27
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Abstract
Knowledge of the structure of DNA enabled scientists to undertake the difficult task of deciphering the detailed molecular mechanisms of two dynamic processes that are central to life: the copying of the genetic information by DNA replication, and its reassortment and repair by DNA recombination. Despite dramatic advances towards this goal over the past five decades, many challenges remain for the next generation of molecular biologists.
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Affiliation(s)
- Bruce Alberts
- National Academy of Sciences, 2101 Constitution Avenue, Washington DC 20418, USA
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28
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Haschke H. A biokinetic model to describe consequences of inhibition/stimulation in DNA-proofreading and repair-1. Development of the model. J Theor Biol 2001; 212:425-56. [PMID: 11597180 DOI: 10.1006/jtbi.2000.2394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A biokinetic model is described which deals with the mathematical consequences of the inhibition or stimulation of DNA proofreading. It demonstrates the development of the number of DNA mismatch-dependent cells (e.g. cells with a malignant phenotype), where such mismatches arise by the in situ interaction of various substances with nucleotides of the DNA. The model can test for consequences by a logic gating on an "if-then" type of analysis in relation to the separate and consecutive processes of proofreading and repair. In particular, the consequences are considered in cases where either (i) the efficacy of proofreading and repair are reduced/prevented (inhibited) or (ii) are increased by some form of stimulation. On the chosen kinetic parameters, the model is accessible to manipulation as new data arising from further investigations become available and are introduced. The model is based on recently published data which show that an increased "mutant fraction" (see note on terms) arises in DNA replication when intracellular nucleotide pools show "asymmetries" (see note on terms). Extraordinarily high mutant fractions can be predicted/have been recorded in the presence of proofreading inhibitors. The model expresses data in mathematical terms of the competition between the development of mismatch-dependent cells and those with authentic genetic information. (Feedback and metastasis-effects and those of wild-type replicates are included.) A computerized (numerical) integration of the corresponding set of differential equations is offered. (A diskette with the program CANCER.xls is available upon request.)
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Affiliation(s)
- H Haschke
- Scientific Board of CONSTANTIA-Group, A-1010 Vienna, Opernring 19, Vienna, Austria
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29
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Rojas Martínez A, Ortiz López R, Delgado Enciso I. [Genetics and molecular medicine in cardiology]. Rev Esp Cardiol 2001; 54:91-108. [PMID: 11141459 DOI: 10.1016/s0300-8932(01)76268-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The discoveries on molecular aspects of cellular function are changing the concepts of health and disease. All medical fields, including cardiology, have been enriched with several diagnostic test to determine predisposition and to detect molecular dysfunctions. This review on the genetic and molecular aspects of cardiovascular diseases is written at the Centenary of the rediscovery of Mendel's principles on heredity and at the time of the announcement of the end of the human genome sequencing task. The review starts with considerations on the pluricellular constitution of the human body, and the principles of genetics with their molecular bases; including a short description of the methods for gene mapping. The following sections give a historic synopsis on the concepts of medical genetics, molecular medicine, and the Human Genome Project. The review ends with a brief description of the spectrum of genetic diseases, using examples of cardiovascular diseases.
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Affiliation(s)
- A Rojas Martínez
- Departamento de Bioquímica. Facultad de Medicina. Universidad Autónoma de Nuevo León. Monterrey. México.
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30
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Yokozawa T, Asai T, Sugi R, Ishigooka S, Hiraoka S. Chain-Growth Polycondensation for Nonbiological Polyamides of Defined Architecture. J Am Chem Soc 2000. [DOI: 10.1021/ja001871b] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tsutomu Yokozawa
- Department of Applied Chemistry Kanagawa University, Rokkakubashi Kanagawa-ku, Yokohama 221-8686, Japan
| | - Toshinobu Asai
- Department of Applied Chemistry Kanagawa University, Rokkakubashi Kanagawa-ku, Yokohama 221-8686, Japan
| | - Ryuji Sugi
- Department of Applied Chemistry Kanagawa University, Rokkakubashi Kanagawa-ku, Yokohama 221-8686, Japan
| | - Shingo Ishigooka
- Department of Applied Chemistry Kanagawa University, Rokkakubashi Kanagawa-ku, Yokohama 221-8686, Japan
| | - Shuichi Hiraoka
- Department of Applied Chemistry Kanagawa University, Rokkakubashi Kanagawa-ku, Yokohama 221-8686, Japan
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31
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Abstract
Human genetics has rapidly evolved from vague impression that descendants resemble their parents, to science which is now of utmost importance to the development of new principles and practice in medicine. It was only in the beginning of this century when it was suggested that chromosomes might carry genetic information. During the two last decades researchers have developed amazing methods to study and manipulate genes. This has created new possibilities to diagnose and cure diseases, but also raised ethical and legal questions. These developments are outlined in the present paper.
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Yokoya A, Watanabe R, Hara T. Single- and double-strand breaks in solid pBR322 DNA induced by ultrasoft X-rays at photon energies of 388, 435 and 573 eV. JOURNAL OF RADIATION RESEARCH 1999; 40:145-158. [PMID: 10494146 DOI: 10.1269/jrr.40.145] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We measured strand breaks of pBR322 plasmid DNA irradiated with ultrasoft X-rays using monochromatic synchrotron radiation as a light source. Three photon energies, 388, 435 and 573 eV, a value below and above the nitrogen K-edge and above the oxygen K-edge, respectively, were chosen for the irradiation experiments as they have an equivalent photon transmittance of the sample. Irradiated DNA was analyzed by agarose gel electrophoresis and the numbers of single- and double-strand breaks (ssb and dsb) were determined by measuring the band intensity on the gel after ethidium bromide staining. The action cross-sections for the ssb and dsb slightly increased with the photon energy. The ratio between 388 and 573 eV was about 1.5 for both forms of strand breaks. The absorbed energy required for a strand break was about 60 eV for ssb and 1 keV for dsb, less than one fifth of the values obtained previously in the 2 keV region. On the other hand, the absorbed energies per strand break, as well as the ratio of the action cross-section for the ssb to that for the dsb, were constant regardless of the photon energy used. The K-shell photoabsorption on carbon, nitrogen and oxygen atoms in the DNA molecule, followed by an Auger cascade, induced DNA strand breaks with a constant efficiency in terms of the absorbed energy. These results indicate that the strand breaks of the DNA molecule in the solid state are mainly caused by the photo- and Auger-electrons and the efficiency of the strand breaks little depends on the atoms ejecting these secondary electrons.
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Affiliation(s)
- A Yokoya
- Department of Synchrotron Radiation Research, Japan Atomic Energy Research Institute, Hyogo.
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RABINOVITCH M, PLAUT W. Cytoplasmic DNA synthesis in Amoeba proteus. I. On the particulate nature of the DNA-containing elements. ACTA ACUST UNITED AC 1998; 15:525-34. [PMID: 13972870 PMCID: PMC2106172 DOI: 10.1083/jcb.15.3.525] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The incorporation of tritiated thymidine in Amoeba proteus was reinvestigated in order to see if it could be associated with microscopically detectable structures. Staining experiments with basic dyes, including the fluorochrome acridine orange, revealed the presence of large numbers of 0.3 to 0.5 micro particles in the cytoplasm of all cells studied. The effect of nuclease digestion on the dye affinity of the particles suggests that they contain DNA as well as RNA. Centrifugation of living cells at 10,000 g leads to the sedimentation of the particles in the centrifugal third of the ameba near the nucleus. Analysis of centrifuged cells which had been incubated with H(3)-thymidine showed a very high degree of correlation between the location of the nucleic acid-containing granules and that of acid-insoluble, deoxyribonuclease-sensitive labeled molecules and leads to the conclusion that cytoplasmic DNA synthesis in Amoeba proteus occurs in association with these particles.
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34
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BASERGA R. A study of nucleic acid synthesis in ascites tumor cells by two-emulsion autoradiography. ACTA ACUST UNITED AC 1998; 12:633-7. [PMID: 13865584 PMCID: PMC2106039 DOI: 10.1083/jcb.12.3.633] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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DAS NK, ALFERT M. Accelerated DNA synthesis in onion root meristem during x-irradiation. Proc Natl Acad Sci U S A 1998; 47:1-6. [PMID: 13719844 PMCID: PMC285220 DOI: 10.1073/pnas.47.1.1] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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36
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TS'O PO, HELMKAMP GK, SANDER C. Interaction of nucleosides and related compounds with nucleic acids as indicated by the change of helix-coil transition temperature. Proc Natl Acad Sci U S A 1998; 48:686-98. [PMID: 13922738 PMCID: PMC220834 DOI: 10.1073/pnas.48.4.686] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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37
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MUNDKUR B. Electron microscopical studies of frozendried yeast. II. The nature of basophile particles and vesicular nuclei in Saccharomyces. Exp Cell Res 1998; 25:1-23. [PMID: 14477192 DOI: 10.1016/0014-4827(61)90303-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38
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OCHOA S, BURMA DP, KROGER H, WEILL JD. Deoxyribonucleic acid-dependent incorporation of nucleotides from nucleoside triphosphates into ribonucleic acid. Proc Natl Acad Sci U S A 1998; 47:670-9. [PMID: 13730224 PMCID: PMC221421 DOI: 10.1073/pnas.47.5.670] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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39
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HOROWITZ NH, MILLER SL. Current theories on the origin of life. FORTSCHRITTE DER CHEMIE ORGANISCHER NATURSTOFFE = PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS. PROGRES DANS LA CHIMIE DES SUBSTANCES ORGANIQUES NATURELLES 1998; 20:423-59. [PMID: 13954989 DOI: 10.1007/978-3-7091-7153-0_10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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40
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41
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Tami JA. The Science of Biotechnology. J Pharm Pract 1998. [DOI: 10.1177/089719009801100105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The quest to understand how genetic information is passed from one generation to the next reached a major milestone in the 1950s with the discovery of the complementary double-helix structure of DNA by Watson and Crick and the demonstration by Kornberg that DNA was capable of self-replication. These breakthroughs provided the stimulus for a flurry of research that culminated in a basic understanding of the genetic code and a statement of the central dogma of molecular biology: DNA goes to RNA goes to protein. In expressing a gene, RNA is formed from the DNA template in a process called transcription. The process of RNA forming protein is known as translation. During translation, amino acids are linked to form protein. The primary structure of proteins is thus determined by the sequence of amino acids. Using x-ray crystallography and computer imaging, it has been possible to determine the three-dimensional structure of many proteins and to design small molecule peptides which can either mimic or block the function of the protein and thus be useful therapeutic agents.
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Affiliation(s)
- Joseph A. Tami
- Drug Development, Isis Pharmaceuticals, 2292 Faraday Avenue, Carlsbad, CA, 92008
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42
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Kiefer JR, Mao C, Hansen CJ, Basehore SL, Hogrefe HH, Braman JC, Beese LS. Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution. Structure 1997; 5:95-108. [PMID: 9016716 DOI: 10.1016/s0969-2126(97)00169-x] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND The study of DNA polymerases in the Pol l family is central to the understanding of DNA replication and repair. DNA polymerases are used in many molecular biology techniques, including PCR, which require a thermostable polymerase. In order to learn about Pol I function and the basis of thermostability, we undertook structural studies of a new thermostable DNA polymerase. RESULTS A DNA polymerase large, Klenow-like, fragment from a recently identified thermostable strain of Bacillus stearothermophilus (BF) was cloned, sequenced, overexpressed and characterized. Its crystal structure was determined to 2.1 A resolution by the method of multiple isomorphous replacement. CONCLUSIONS This structure represents the highest resolution view of a Pol I enzyme obtained to date. Comparison of the three Pol I structures reveals no compelling evidence for many of the specific interactions that have been proposed to induce thermostability, but suggests that thermostability arises from innumerable small changes distributed throughout the protein structure. The polymerase domain is highly conserved in all three proteins. The N-terminal domains are highly divergent in sequence, but retain a common fold. When present, the 3'-5' proofreading exonuclease activity is associated with this domain. Its absence is associated with changes in catalytic residues that coordinate the divalent ions required for activity and in loops connecting homologous secondary structural elements. In BF, these changes result in a blockage of the DNA-binding cleft.
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Affiliation(s)
- J R Kiefer
- Department of Biochemistry, Duke University Medical Centre, Durham, NC 27710, USA
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43
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GRUNBERG-MANAGO M. ENZYMATIC SYNTHESIS OF NUCLEIC ACIDS. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1996; 13:175-239. [PMID: 14135921 DOI: 10.1016/s0079-6107(63)80016-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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44
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ROSENKRANZ HS, ERLANGER BF, TANENBAUM SW, BEISER SM. PURINE- AND PYRIMIDINE-SPECIFIC ANTIBODIES: EFFECT ON THE FERTILIZED SEA URCHIN EGG. Science 1996; 145:282-3. [PMID: 14171573 DOI: 10.1126/science.145.3629.282] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Antiserums from rabbits immunized with several purine- and pyrimidine-containing albumin conjugates can penetrate and become fixed within cells of Arbacia punctulata. All of these specific antiserums were found to inhibit embryonic development of the fertilized sea urchin egg. The stage of arrestment of development was dependent in part upon the dilution of antiserum, and also upon the nature of its specificity. It is suggested that the observed results reflect the interaction of these antiserums with singlestranded DNA within the cell.
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46
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47
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Syvänen AC, Söderlund H. Quantification of polymerase chain reaction products by affinity-based collection. Methods Enzymol 1993; 218:474-90. [PMID: 8389969 DOI: 10.1016/0076-6879(93)18036-c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- A C Syvänen
- Department of Human Molecular Genetics, National Public Health Institute, Helsinki, Finland
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48
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Abstract
The relationship between retroviral genes and oncogenes is described.
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Affiliation(s)
- J M Bishop
- Department of Microbiology and Immunology, G. W. Hooper Research Foundation, University of California, San Francisco 94143
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49
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Bishop JM. Retroviren und Onkogene II (Nobel-Vortrag). Angew Chem Int Ed Engl 1990. [DOI: 10.1002/ange.19901020707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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50
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de Long R. DNA ligase: a site for the immunological destruction of cancer cells. Med Hypotheses 1982; 9:125-7. [PMID: 7132812 DOI: 10.1016/0306-9877(82)90072-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
An hypothesis is presented which could lead to cancer treatment by passive immunotherapy. It is based on the specificity of antigen-antibody reactions. Essential enzymes produced by cancer cells which are involved in the replication and invasiveness of cancer might be nullified by such treatment.
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