1
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Yoo J, Park S, Maffeo C, Ha T, Aksimentiev A. DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles. Nucleic Acids Res 2021; 49:11459-11475. [PMID: 34718725 PMCID: PMC8599915 DOI: 10.1093/nar/gkab967] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 09/27/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic genome and methylome encode DNA fragments' propensity to form nucleosome particles. Although the mechanical properties of DNA possibly orchestrate such encoding, the definite link between 'omics' and DNA energetics has remained elusive. Here, we bridge the divide by examining the sequence-dependent energetics of highly bent DNA. Molecular dynamics simulations of 42 intact DNA minicircles reveal that each DNA minicircle undergoes inside-out conformational transitions with the most likely configuration uniquely prescribed by the nucleotide sequence and methylation of DNA. The minicircles' local geometry consists of straight segments connected by sharp bends compressing the DNA's inward-facing major groove. Such an uneven distribution of the bending stress favors minimum free energy configurations that avoid stiff base pair sequences at inward-facing major grooves. Analysis of the minicircles' inside-out free energy landscapes yields a discrete worm-like chain model of bent DNA energetics that accurately account for its nucleotide sequence and methylation. Experimentally measuring the dependence of the DNA looping time on the DNA sequence validates the model. When applied to a nucleosome-like DNA configuration, the model quantitatively reproduces yeast and human genomes' nucleosome occupancy. Further analyses of the genome-wide chromatin structure data suggest that DNA bending energetics is a fundamental determinant of genome architecture.
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Affiliation(s)
- Jejoong Yoo
- Department of Physics, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sangwoo Park
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Christopher Maffeo
- Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Baltimore, MD 21218, USA
| | - Aleksei Aksimentiev
- Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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2
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Pyne ALB, Noy A, Main KHS, Velasco-Berrelleza V, Piperakis MM, Mitchenall LA, Cugliandolo FM, Beton JG, Stevenson CEM, Hoogenboom BW, Bates AD, Maxwell A, Harris SA. Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides. Nat Commun 2021; 12:1053. [PMID: 33594049 PMCID: PMC7887228 DOI: 10.1038/s41467-021-21243-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 01/16/2021] [Indexed: 12/16/2022] Open
Abstract
In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects the detailed double-helical structure of DNA, largely because of limitations in spatial resolution of the available biophysical tools. Here, we overcome these limitations, by a combination of atomic force microscopy (AFM) and atomistic molecular dynamics (MD) simulations, to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution. We observe that negative superhelical stress induces local variation in the canonical B-form DNA structure by introducing kinks and defects that affect global minicircle structure and flexibility. We probe how these local and global conformational changes affect DNA interactions through the binding of triplex-forming oligonucleotides to DNA minicircles. We show that the energetics of triplex formation is governed by a delicate balance between electrostatics and bonding interactions. Our results provide mechanistic insight into how DNA supercoiling can affect molecular recognition, that may have broader implications for DNA interactions with other molecular species.
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Affiliation(s)
- Alice L B Pyne
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK.
- London Centre for Nanotechnology, University College London, London, UK.
| | - Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, UK.
| | - Kavit H S Main
- London Centre for Nanotechnology, University College London, London, UK
- UCL Cancer Institute, University College London, London, UK
| | | | - Michael M Piperakis
- Department of Biological Chemistry, John Innes Centre, Norwich, UK
- Department of Chemistry, University of Reading, Whiteknights, Reading, UK
| | | | - Fiorella M Cugliandolo
- Department of Biological Chemistry, John Innes Centre, Norwich, UK
- Department of Pathology, Division of Immunology, University of Cambridge, Cambridge, UK
| | - Joseph G Beton
- London Centre for Nanotechnology, University College London, London, UK
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, UK
| | | | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Andrew D Bates
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich, UK
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, Leeds, UK.
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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3
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Meier-Stephenson V, Badmalia MD, Mrozowich T, Lau KCK, Schultz SK, Gemmill DL, Osiowy C, van Marle G, Coffin CS, Patel TR. Identification and characterization of a G-quadruplex structure in the pre-core promoter region of hepatitis B virus covalently closed circular DNA. J Biol Chem 2021; 296:100589. [PMID: 33774051 PMCID: PMC8094906 DOI: 10.1016/j.jbc.2021.100589] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 02/07/2023] Open
Abstract
Approximately 250 million people worldwide are chronically infected with the hepatitis B virus (HBV) and are at increased risk of developing cirrhosis and hepatocellular carcinoma. The HBV genome persists as covalently closed circular DNA (cccDNA), which serves as the template for all HBV mRNA transcripts. Current nucleos(t)ide analogs used to treat HBV do not directly target the HBV cccDNA genome and thus cannot eradicate HBV infection. Here, we report the discovery of a unique G-quadruplex structure in the pre-core promoter region of the HBV genome that is conserved among nearly all genotypes. This region is central to critical steps in the viral life cycle, including the generation of pregenomic RNA, synthesis of core and polymerase proteins, and genome encapsidation; thus, an increased understanding of the HBV pre-core region may lead to the identification of novel anti-HBV cccDNA targets. We utilized biophysical methods (circular dichroism and small-angle X-ray scattering) to characterize the HBV G-quadruplex and the effect of three distinct G to A mutants. We also used microscale thermophoresis to quantify the binding affinity of G-quadruplex and its mutants with a known quadruplex-binding protein (DHX36). To investigate the physiological relevance of HBV G-quadruplex, we employed assays using DHX36 to pull-down cccDNA and compared HBV infection in HepG2 cells transfected with wild-type and mutant HBV plasmids by monitoring the levels of genomic DNA, pregenomic RNA, and antigens. Further evaluation of this critical host-protein interaction site in the HBV cccDNA genome may facilitate the development of novel anti-HBV therapeutics against the resilient cccDNA template.
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Affiliation(s)
- Vanessa Meier-Stephenson
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada; Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada; Department of Medicine, Cumming School of Medicine, Calgary, Alberta, Canada
| | - Maulik D Badmalia
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Tyler Mrozowich
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Keith C K Lau
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Sarah K Schultz
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Darren L Gemmill
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Carla Osiowy
- Viral Hepatitis and Bloodborne Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Guido van Marle
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Carla S Coffin
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada; Department of Medicine, Cumming School of Medicine, Calgary, Alberta, Canada.
| | - Trushar R Patel
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada; Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada; DiscoveryLab, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada.
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4
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Marchetti AL, Guo H. New Insights on Molecular Mechanism of Hepatitis B Virus Covalently Closed Circular DNA Formation. Cells 2020; 9:cells9112430. [PMID: 33172220 PMCID: PMC7694973 DOI: 10.3390/cells9112430] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 12/15/2022] Open
Abstract
The chronic factor of the Hepatitis B Virus (HBV), specifically the covalently closed circular DNA (cccDNA), is a highly stable and active viral episomal genome established in the livers of chronic hepatitis B patients as a constant source of disease. Being able to target and eliminate cccDNA is the end goal for a genuine cure for HBV. Yet how HBV cccDNA is formed from the viral genomic relaxed circular DNA (rcDNA) and by what host factors had been long-standing research questions. It is generally acknowledged that HBV hijacks cellular functions to turn the open circular DNA conformation of rcDNA into cccDNA through DNA repair mechanisms. With great efforts from the HBV research community, there have been several recent leaps in our understanding of cccDNA formation. It is our goal in this review to analyze the recent reports showing evidence of cellular factor's involvement in the molecular pathway of cccDNA biosynthesis.
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Affiliation(s)
- Alexander L. Marchetti
- Department of Microbiology and Immunology, School of Medicine, Indiana University, Indianapolis, IN 46202, USA;
- Cancer Virology Program, Hillman Cancer Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Haitao Guo
- Cancer Virology Program, Hillman Cancer Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Correspondence:
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5
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Prada-Luengo I, Møller HD, Henriksen RA, Gao Q, Larsen C, Alizadeh S, Maretty L, Houseley J, Regenberg B. Replicative aging is associated with loss of genetic heterogeneity from extrachromosomal circular DNA in Saccharomyces cerevisiae. Nucleic Acids Res 2020; 48:7883-7898. [PMID: 32609810 PMCID: PMC7430651 DOI: 10.1093/nar/gkaa545] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 05/28/2020] [Accepted: 06/17/2020] [Indexed: 12/26/2022] Open
Abstract
Circular DNA can arise from all parts of eukaryotic chromosomes. In yeast, circular ribosomal DNA (rDNA) accumulates dramatically as cells age, however little is known about the accumulation of other chromosome-derived circles or the contribution of such circles to genetic variation in aged cells. We profiled circular DNA in Saccharomyces cerevisiae populations sampled when young and after extensive aging. Young cells possessed highly diverse circular DNA populations but 94% of the circular DNA were lost after ∼15 divisions, whereas rDNA circles underwent massive accumulation to >95% of circular DNA. Circles present in both young and old cells were characterized by replication origins including circles from unique regions of the genome and repetitive regions: rDNA and telomeric Y' regions. We further observed that circles can have flexible inheritance patterns: [HXT6/7circle] normally segregates to mother cells but in low glucose is present in up to 50% of cells, the majority of which must have inherited this circle from their mother. Interestingly, [HXT6/7circle] cells are eventually replaced by cells carrying stable chromosomal HXT6 HXT6/7 HXT7 amplifications, suggesting circular DNAs are intermediates in chromosomal amplifications. In conclusion, the heterogeneity of circular DNA offers flexibility in adaptation, but this heterogeneity is remarkably diminished with age.
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Affiliation(s)
- Iñigo Prada-Luengo
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Henrik D Møller
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zurich CH-8093, Switzerland
| | - Rasmus A Henriksen
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Qian Gao
- Epigenetics Programme, The Babraham Institute, Babraham, Cambridge CB22 3-AT, UK
- Adaptimmune Ltd, Oxfordshire OX14 4RX, UK
| | - Camilla Eggert Larsen
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Sefa Alizadeh
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Lasse Maretty
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus DK-8200, Denmark
| | - Jonathan Houseley
- Epigenetics Programme, The Babraham Institute, Babraham, Cambridge CB22 3-AT, UK
| | - Birgitte Regenberg
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
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6
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Krupovic M, Varsani A, Kazlauskas D, Breitbart M, Delwart E, Rosario K, Yutin N, Wolf YI, Harrach B, Zerbini FM, Dolja VV, Kuhn JH, Koonin EV. Cressdnaviricota: a Virus Phylum Unifying Seven Families of Rep-Encoding Viruses with Single-Stranded, Circular DNA Genomes. J Virol 2020; 94:e00582-20. [PMID: 32269128 PMCID: PMC7307096 DOI: 10.1128/jvi.00582-20] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
MESH Headings
- Animals
- DNA Viruses/classification
- DNA Viruses/genetics
- DNA, Circular/chemistry
- DNA, Circular/genetics
- DNA, Circular/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- DNA, Viral/chemistry
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Diatoms/virology
- Genome Size
- Genome, Viral
- Insecta/virology
- Phylogeny
- Plants/virology
- Terminology as Topic
- Viral Proteins/genetics
- Viral Proteins/metabolism
- Virus Replication
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Affiliation(s)
- Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Mya Breitbart
- University of South Florida, College of Marine Science, St. Petersburg, Florida, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, California, USA
- UCSF Department of Laboratory Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Karyna Rosario
- University of South Florida, College of Marine Science, St. Petersburg, Florida, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Balázs Harrach
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - F Murilo Zerbini
- Departamento de Fitopatologia/Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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7
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Wang Y, Guo X, Kou B, Zhang L, Xiao SJ. Small Circular DNA Molecules as Triangular Scaffolds for the Growth of 3D Single Crystals. Biomolecules 2020; 10:biom10060814. [PMID: 32466440 PMCID: PMC7355631 DOI: 10.3390/biom10060814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/14/2020] [Accepted: 05/22/2020] [Indexed: 12/30/2022] Open
Abstract
DNA is a very useful molecule for the programmed self-assembly of 3D (three dimension) nanoscale structures. The organised 3D DNA assemblies and crystals enable scientists to conduct studies for many applications such as enzymatic catalysis, biological immune analysis and photoactivity. The first self-assembled 3D DNA single crystal was reported by Seeman and his colleagues, based on a rigid triangle tile with the tile side length of two turns. Till today, successful designs of 3D single crystals by means of programmed self-assembly are countable, and still remain as the most challenging task in DNA nanotechnology, due to the highly constrained conditions for rigid tiles and precise packing. We reported here the use of small circular DNA molecules instead of linear ones as the core triangle scaffold to grow 3D single crystals. Several crystallisation parameters were screened, DNA concentration, incubation time, water-vapour exchange speed, and pH of the sampling buffer. Several kinds of DNA single crystals with different morphologies were achieved in macroscale. The crystals can provide internal porosities for hosting guest molecules of Cy3 and Cy5 labelled triplex-forming oligonucleotides (TFOs). Success of small circular DNA molecules in self-assembling 3D single crystals encourages their use in DNA nanotechnology regarding the advantage of rigidity, stability, and flexibility of circular tiles.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China; (Y.W.); (X.G.); (L.Z.)
| | - Xin Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China; (Y.W.); (X.G.); (L.Z.)
| | - Bo Kou
- School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing 211167, China;
| | - Ling Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China; (Y.W.); (X.G.); (L.Z.)
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China; (Y.W.); (X.G.); (L.Z.)
- Correspondence:
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8
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Peddireddy KR, Lee M, Zhou Y, Adalbert S, Anderson S, Schroeder CM, Robertson-Anderson RM. Unexpected entanglement dynamics in semidilute blends of supercoiled and ring DNA. Soft Matter 2020; 16:152-161. [PMID: 31774103 DOI: 10.1039/c9sm01767d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of producing polymers of different topologies, the dynamics of topological polymer blends remains poorly understood. We address this void by using both passive and active microrheology to characterize the linear and nonlinear rheological properties of blends of relaxed circular and supercoiled DNA. We characterize the dynamics as we vary the concentration from below the overlap concentration c* to above (0.5c* to 2c*). Surprisingly, despite working at the dilute-semidilute crossover, entanglement dynamics, such as elastic plateaus and multiple relaxation modes, emerge. Finally, blends exhibit an unexpected sustained elastic response to nonlinear strains not previously observed even in well-entangled linear polymer solutions.
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Affiliation(s)
- Karthik R Peddireddy
- Department of Physics and Biophysics, University of San Diego, 5998 Alcala Park, San Diego, CA 92110, USA.
| | - Megan Lee
- Department of Physics and Biophysics, University of San Diego, 5998 Alcala Park, San Diego, CA 92110, USA.
| | - Yuecheng Zhou
- Department of Materials Science and Engineering, Beckman Institute for Advanced Science and Technology & Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Serenity Adalbert
- Department of Physics and Biophysics, University of San Diego, 5998 Alcala Park, San Diego, CA 92110, USA.
| | - Sylas Anderson
- Department of Physics and Biophysics, University of San Diego, 5998 Alcala Park, San Diego, CA 92110, USA.
| | - Charles M Schroeder
- Department of Materials Science and Engineering, Beckman Institute for Advanced Science and Technology & Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rae M Robertson-Anderson
- Department of Physics and Biophysics, University of San Diego, 5998 Alcala Park, San Diego, CA 92110, USA.
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9
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Ohtsuki S, Shiba Y, Maezawa T, Hidaka K, Sugiyama H, Endo M, Takahashi Y, Takakura Y, Nishikawa M. Folding of single-stranded circular DNA into rigid rectangular DNA accelerates its cellular uptake. Nanoscale 2019; 11:23416-23422. [PMID: 31799532 DOI: 10.1039/c9nr08695a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Despite the importance of the interaction between DNA and cells for its biological activity, little is known about exactly how DNA interacts with cells. To elucidate the relationship between the structural properties of DNA and its cellular uptake, a single-stranded circular DNA of 1801 bases was designed and folded into a series of rectangular DNA (RecDNA) nanostructures with different rigidities using DNA origami technology. Interactions between these structures and cells were evaluated using mouse macrophage-like RAW264.7 cells. RecDNA with 50 staple DNAs, including four that were Alexa Fluor 488-labeled, was designed. RecDNA with fewer staples, down to four staples (all Alexa Fluor 488-labeled), was also prepared. Electrophoresis and atomic force microscopy showed that all DNA nanostructures were successfully obtained with a sufficiently high yield. Flow cytometry analysis showed that folding of the single-stranded circular DNA into RecDNA significantly increased its cellular uptake. In addition, there was a positive correlation between uptake and the number of staples. These results indicate that highly folded DNA nanostructures interact more efficiently with RAW264.7 cells than loosely folded structures do. Based on these results, it was concluded that the interaction of DNA with cells can be controlled by folding using DNA origami technology.
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Affiliation(s)
- Shozo Ohtsuki
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Yukako Shiba
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Tatsuoki Maezawa
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan and Institute for Integrated Cell-Material Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan and Institute for Integrated Cell-Material Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Makiya Nishikawa
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan. and Laboratory of Biopharmaceutics, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
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10
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Xu M, Zhang S, Xuan Z, Wu J, Dong P, Zhou Y, Li R, Cao M. Molecular characterization of a new badnavirus infecting green Sichuan pepper (Zanthoxylum schinifolium). Arch Virol 2019; 164:2613-2616. [PMID: 31321586 DOI: 10.1007/s00705-019-04357-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/26/2019] [Indexed: 11/25/2022]
Abstract
A new virus with a circular double-stranded DNA genome was discovered in green Sichuan pepper with vein clearing symptoms. Its complete genome of 8,014 bp contains three open reading frames (ORF) on the plus strand, which is typical of members of the genus Badnavirus in the family Caulimoviridae. Sequence comparisons revealed that the new virus has the highest nucleotide sequence identity with grapevine vein-clearing virus (GVCV). In particular, the identity of the two viruses in the ORF3 RT-RNase H region is 71.9%, which is below the species demarcation cutoff of 80% for badnaviruses. Phylogenetic analysis also placed the new virus with GVCV in a cluster. The virus was tentatively named "green Sichuan pepper vein clearing-associated virus" (GSPVCaV). The geographical distribution and genetic diversity of GSPVCaV were studied. Another isolate was found to be highly divergent.
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Affiliation(s)
- Min Xu
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Song Zhang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Zhiyou Xuan
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Jiaxing Wu
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Peng Dong
- Chongqing Agricultural Technology Extension Station, Chongqing, 401121, China
| | - Yan Zhou
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Ruhui Li
- National Germplasm Resources Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
| | - Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
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11
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Wu F, Japaridze A, Zheng X, Wiktor J, Kerssemakers JWJ, Dekker C. Direct imaging of the circular chromosome in a live bacterium. Nat Commun 2019; 10:2194. [PMID: 31097704 PMCID: PMC6522522 DOI: 10.1038/s41467-019-10221-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 04/26/2019] [Indexed: 01/08/2023] Open
Abstract
Although the physical properties of chromosomes, including their morphology, mechanics, and dynamics are crucial for their biological function, many basic questions remain unresolved. Here we directly image the circular chromosome in live E. coli with a broadened cell shape. We find that it exhibits a torus topology with, on average, a lower-density origin of replication and an ultrathin flexible string of DNA at the terminus of replication. At the single-cell level, the torus is strikingly heterogeneous, with blob-like Mbp-size domains that undergo major dynamic rearrangements, splitting and merging at a minute timescale. Our data show a domain organization underlying the chromosome structure of E. coli, where MatP proteins induce site-specific persistent domain boundaries at Ori/Ter, while transcription regulators HU and Fis induce weaker transient domain boundaries throughout the genome. These findings provide an architectural basis for the understanding of the dynamic spatial organization of bacterial genomes in live cells.
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MESH Headings
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Bacterial/chemistry
- Chromosomes, Bacterial/metabolism
- DNA Replication
- DNA, Bacterial/chemistry
- DNA, Bacterial/metabolism
- DNA, Circular/chemistry
- DNA, Circular/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/metabolism
- Genome, Bacterial
- Intravital Microscopy/instrumentation
- Intravital Microscopy/methods
- Microscopy, Fluorescence/instrumentation
- Microscopy, Fluorescence/methods
- Nucleic Acid Conformation
- Single-Cell Analysis/instrumentation
- Single-Cell Analysis/methods
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Affiliation(s)
- Fabai Wu
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| | - Aleksandre Japaridze
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Xuan Zheng
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jakub Wiktor
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jacob W J Kerssemakers
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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12
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Abstract
From the original sequencing of the human genome, it was found that about 98.5% of the genome did not code for proteins. Subsequent studies have now revealed that a much larger portion of the genome is related to short or long noncoding RNAs that regulate cellular activities. In addition to the milestones of chemical and protein drugs, it has been proposed that RNA drugs or drugs targeting RNA will become the third milestone in drug development ( Shu , Y. ; Adv. Drug Deliv. Rev. 2014 , 66 , 74 . ). Currently, the yield and cost for RNA nanoparticle or RNA drug production requires improvement in order to advance the RNA field in both research and clinical translation by reducing the multiple tedious manufacturing steps. For example, with 98.5% incorporation efficiency of chemical synthesis of a 100 nucleotide RNA strand, RNA oligos will result with 78% contamination of aborted byproducts. Thus, RNA nanotechnology is one of the remedies, because large RNA can be assembled from small RNA fragments via bottom-up self-assembly. Here we report the one-pot production of RNA nanoparticles via automated processing and self-assembly. The continuous production of RNA by rolling circle transcription (RCT) using a circular dsDNA template is coupled with self-cleaving ribozymes encoded in the concatemeric RNA transcripts. Production was monitored in real-time. Automatic production of RNA fragments enabled their assembly either in situ or via one-pot co-transcription to obtain RNA nanoparticles of desired motifs and functionalities from bottom-up assembly of multiple RNA fragments. In combination with the RNA nanoparticle construction process, a purification method using a large-scale electrophoresis column was also developed.
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Affiliation(s)
| | | | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; Dorothy M. Davis Heart and Lung Research Institute; and James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
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13
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Iric K, Subramanian M, Oertel J, Agarwal NP, Matthies M, Periole X, Sakmar TP, Huber T, Fahmy K, Schmidt TL. DNA-encircled lipid bilayers. Nanoscale 2018; 10:18463-18467. [PMID: 30272763 DOI: 10.1039/c8nr06505e] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Lipid bilayers and lipid-associated proteins play crucial roles in biology. As in vivo studies and manipulation are inherently difficult, membrane-mimetic systems are useful for the investigation of lipidic phases, lipid-protein interactions, membrane protein function and membrane structure in vitro. In this work, we describe a route to leverage the programmability of DNA nanotechnology and create DNA-encircled bilayers (DEBs). DEBs are made of multiple copies of an alkylated oligonucleotide hybridized to a single-stranded minicircle, in which up to two alkyl chains per helical turn point to the inside of the toroidal DNA ring. When phospholipids are added, a bilayer is observed to self-assemble within the ring such that the alkyl chains of the oligonucleotides stabilize the hydrophobic rim of the bilayer to prevent formation of vesicles and support thermotropic lipid phase transitions. The DEBs are completely free of protein and can be synthesized from commercially available components using routine equipment. The diameter of DEBs can be varied in a predictable manner. The well-established toolbox from structural DNA nanotechnology, will ultimately enable the rational design of DEBs so that their size, shape or functionalization can be adapted to the specific needs of biophysical investigations of lipidic phases and the properties of membrane proteins embedded into DEB nanoparticle bilayers.
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Affiliation(s)
- Katarina Iric
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062 Dresden, Germany.
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14
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Abstract
Recent work indicates that twist-bend coupling plays an important role in DNA micromechanics. Here we investigate its effect on bent DNA. We provide an analytical solution of the minimum-energy shape of circular DNA, showing that twist-bend coupling induces sinusoidal twist waves. This solution is in excellent agreement with both coarse-grained simulations of minicircles and nucleosomal DNA data, which is bent and wrapped around histone proteins in a superhelical conformation. Our analysis shows that the observed twist oscillation in nucleosomal DNA, so far attributed to the interaction with the histone proteins, is an intrinsic feature of free bent DNA, and should be observable in other protein-DNA complexes.
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Affiliation(s)
- Enrico Skoruppa
- KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Stefanos K Nomidis
- KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium
- Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol, Belgium
| | - John F Marko
- Department of Physics and Astronomy, and Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Enrico Carlon
- KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium
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15
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Monachino E, Ghodke H, Spinks RR, Hoatson BS, Jergic S, Xu ZQ, Dixon NE, van Oijen AM. Design of DNA rolling-circle templates with controlled fork topology to study mechanisms of DNA replication. Anal Biochem 2018; 557:42-45. [PMID: 30016625 DOI: 10.1016/j.ab.2018.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/12/2018] [Accepted: 07/13/2018] [Indexed: 11/19/2022]
Abstract
Rolling-circle DNA amplification is a powerful tool employed in biotechnology to produce large from small amounts of DNA. This mode of DNA replication proceeds via a DNA topology that resembles a replication fork, thus also providing experimental access to the molecular mechanisms of DNA replication. However, conventional templates do not allow controlled access to multiple fork topologies, which is an important factor in mechanistic studies. Here we present the design and production of a rolling-circle substrate with a tunable length of both the gap and the overhang, and we show its application to the bacterial DNA-replication reaction.
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Affiliation(s)
- Enrico Monachino
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia; Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Harshad Ghodke
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Richard R Spinks
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Ben S Hoatson
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia.
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16
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Valero J, Pal N, Dhakal S, Walter NG, Famulok M. A bio-hybrid DNA rotor-stator nanoengine that moves along predefined tracks. Nat Nanotechnol 2018; 13:496-503. [PMID: 29632399 PMCID: PMC5994166 DOI: 10.1038/s41565-018-0109-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/01/2018] [Indexed: 05/25/2023]
Abstract
Biological motors are highly complex protein assemblies that generate linear or rotary motion, powered by chemical energy. Synthetic motors based on DNA nanostructures, bio-hybrid designs or synthetic organic chemistry have been assembled. However, unidirectionally rotating biomimetic wheel motors with rotor-stator units that consume chemical energy are elusive. Here, we report a bio-hybrid nanoengine consisting of a catalytic stator that unidirectionally rotates an interlocked DNA wheel, powered by NTP hydrolysis. The engine consists of an engineered T7 RNA polymerase (T7RNAP-ZIF) attached to a dsDNA nanoring that is catenated to a rigid rotating dsDNA wheel. The wheel motor produces long, repetitive RNA transcripts that remain attached to the engine and are used to guide its movement along predefined ssDNA tracks arranged on a DNA nanotube. The simplicity of the design renders this walking nanoengine adaptable to other biological nanoarchitectures, facilitating the construction of complex bio-hybrid structures that achieve NTP-driven locomotion.
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Affiliation(s)
- Julián Valero
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Bonn, Germany
- Center of Advanced European Studies and Research (CAESAR), Bonn, Germany
| | - Nibedita Pal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Soma Dhakal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Michael Famulok
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Bonn, Germany.
- Center of Advanced European Studies and Research (CAESAR), Bonn, Germany.
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17
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Nguyen NPD, Deshpande V, Luebeck J, Mischel PS, Bafna V. ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer. Nucleic Acids Res 2018; 46:3309-3325. [PMID: 29579309 PMCID: PMC6283451 DOI: 10.1093/nar/gky180] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 02/12/2018] [Accepted: 03/05/2018] [Indexed: 12/20/2022] Open
Abstract
The integration of viral sequences into the host genome is an important driver of tumorigenesis in many viral mediated cancers, notably cervical cancer and hepatocellular carcinoma. We present ViFi, a computational method that combines phylogenetic methods with reference-based read mapping to detect viral integrations. In contrast with read-based reference mapping approaches, ViFi is faster, and shows high precision and sensitivity on both simulated and biological data, even when the integrated virus is a novel strain or highly mutated. We applied ViFi to matched genomic and mRNA data from 68 cervical cancer samples from TCGA and found high concordance between the two. Surprisingly, viral integration resulted in a dramatic transcriptional upregulation in all proximal elements, including LINEs and LTRs that are not normally transcribed. This upregulation is highly correlated with the presence of a viral gene fused with a downstream human element. Moreover, genomic rearrangements suggest the formation of apparent circular extrachromosomal (ecDNA) human-viral structures. Our results suggest the presence of apparent small circular fusion viral/human ecDNA, which correlates with indiscriminate and unregulated expression of proximal genomic elements, potentially contributing to the pathogenesis of HPV-associated cervical cancers. ViFi is available at https://github.com/namphuon/ViFi.
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Affiliation(s)
- Nam-phuong D Nguyen
- Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Viraj Deshpande
- Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Jens Luebeck
- Bioinformatics and Systems Biology Program, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
- Department of Pathology, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
- Moores Cancer Center, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Vineet Bafna
- Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
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18
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Paulsen T, Kumar P, Koseoglu MM, Dutta A. Discoveries of Extrachromosomal Circles of DNA in Normal and Tumor Cells. Trends Genet 2018; 34:270-278. [PMID: 29329720 PMCID: PMC5881399 DOI: 10.1016/j.tig.2017.12.010] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/24/2017] [Accepted: 12/13/2017] [Indexed: 10/18/2022]
Abstract
While the vast majority of cellular DNA in eukaryotes is contained in long linear strands in chromosomes, we have long recognized some exceptions like mitochondrial DNA, plasmids in yeasts, and double minutes (DMs) in cancer cells where the DNA is present in extrachromosomal circles. In addition, specialized extrachromosomal circles of DNA (eccDNA) have been noted to arise from repetitive genomic sequences like telomeric DNA or rDNA. Recently eccDNA arising from unique (nonrepetitive) DNA have been discovered in normal and malignant cells, raising interesting questions about their biogenesis, function and clinical utility. Here, we review recent results and future directions of inquiry on these new forms of eccDNA.
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MESH Headings
- Animals
- Chromosomes, Human/chemistry
- Chromosomes, Human/metabolism
- DNA, Chloroplast/chemistry
- DNA, Chloroplast/genetics
- DNA, Chloroplast/metabolism
- DNA, Circular/chemistry
- DNA, Circular/genetics
- DNA, Circular/metabolism
- DNA, Kinetoplast/chemistry
- DNA, Kinetoplast/genetics
- DNA, Kinetoplast/metabolism
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- DNA, Neoplasm/chemistry
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Eukaryotic Cells/chemistry
- Eukaryotic Cells/metabolism
- Humans
- Kinetoplastida/genetics
- Kinetoplastida/metabolism
- Neoplasms/genetics
- Neoplasms/metabolism
- Neoplasms/pathology
- Neoplastic Cells, Circulating/chemistry
- Neoplastic Cells, Circulating/metabolism
- Plants/genetics
- Plants/metabolism
- Plasmids/chemistry
- Plasmids/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Telomere/chemistry
- Telomere/metabolism
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Affiliation(s)
- Teressa Paulsen
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - M Murat Koseoglu
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
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19
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Wang L, Meng Z, Martina F, Shao H, Shao F. Fabrication of circular assemblies with DNA tetrahedrons: from static structures to a dynamic rotary motor. Nucleic Acids Res 2017; 45:12090-12099. [PMID: 29126166 PMCID: PMC5716610 DOI: 10.1093/nar/gkx1045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 01/07/2023] Open
Abstract
DNA tetrahedron as the simplest 3D DNA nanostructure has been applied widely in biomedicine and biosensing. Herein, we design and fabricate a series of circular assemblies of DNA tetrahedron with high purity and decent yields. These circular nanostructures are confirmed by endonuclease digestion, gel electrophoresis and atomic force microscopy. Inspired by rotary protein motor, we demonstrate these circular architectures can serve as a stator for a rotary DNA motor to achieve the circular rotation. The DNA motor can rotate on the stators for several cycles, and the locomotion of the motor is monitored by the real-time fluorescent measurements.
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Affiliation(s)
- Liying Wang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Zhenyu Meng
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Felicia Martina
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Huilin Shao
- Biomedical Institute of Global Heath Research and Technology, Departments of Biomedical Engineering and Surgery, National University of Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Fangwei Shao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
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20
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Afshan N, Ali M, Wang M, Baig MMFA, Xiao SJ. DNA nanotubes assembled from tensegrity triangle tiles with circular DNA scaffolds. Nanoscale 2017; 9:17181-17185. [PMID: 29091094 DOI: 10.1039/c7nr04869f] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Using small circular DNA molecules of different lengths as scaffolds, we successfully synthesised DNA nanotubes consisting of Mao's DNA tensegrity triangle tiles with four-arm junctions (Holliday junctions) at all vertices. Due to the intrinsic curvature of the triangle tile and the consecutive tile alignment, the 2D arrays are organised in the form of nanotubes. Two sized triangle tiles with equilateral side lengths of 1.5 and 2.5 full helical turns are connected by the sticky ended cohesion of a duplex with a length of 2.5 helical turns respectively, and their parallel lozenge tiling lattices were demonstrated by high resolution AFM images, where the former lozenge unit cell has a lattice constant of 13.6 nm, and the latter has a larger lattice constant of 17.0 nm. Modification of the triangle tile with infinitesimal disturbance on side lengths and insertion of one thymine single stranded loop at every vertex resulted in comparably similar nanotubes.
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Affiliation(s)
- Noshin Afshan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, Jiangsu, China.
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21
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Le BH, Seo YJ. Highly sensitive MicroRNA 146a detection using a gold nanoparticle-based CTG repeat probing system and isothermal amplification. Anal Chim Acta 2017; 999:155-160. [PMID: 29254567 DOI: 10.1016/j.aca.2017.11.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 10/10/2017] [Accepted: 11/09/2017] [Indexed: 12/13/2022]
Abstract
We have developed a gold nanoparticle (AuNP)-based CTG repeat probing system displaying high quenching capability and combined it with isothermal amplification for the detection of miRNA 146a. This method of using a AuNP-based CTG repeat probing system with isothermal amplification allowed the highly sensitive (14 aM) and selective detection of miRNA 146a. A AuNP-based CTG repeat probing system having a hairpin structure and a dTF fluorophore exhibited highly efficient quenching because the CTG repeat-based stable hairpin structure imposed a close distance between the AuNP and the dTF residue. A small amount of miRNA 146a induced multiple copies of the CAG repeat sequence during rolling circle amplification; the AuNP-based CTG repeat probing system then bound to the complementary multiple-copy CAG repeat sequence, thereby inducing a structural change from a hairpin to a linear structure with amplified fluorescence. This AuNP-based CTG probing system combined with isothermal amplification could also discriminate target miRNA 146a from one- and two-base-mismatched miRNAs (ORN 1 and ORN 2, respectively). This simple AuNP-based CTG probing system, combined with isothermal amplification to induce a highly sensitive change in fluorescence, allows the detection of miRNA 146a with high sensitivity (14 aM) and selectivity.
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Affiliation(s)
- Binh Huy Le
- Department of Bioactive Material Sciences, Research Center of Bioactive Materials Chonbuk National University, Jeonju 561-756, South Korea
| | - Young Jun Seo
- Department of Bioactive Material Sciences, Research Center of Bioactive Materials Chonbuk National University, Jeonju 561-756, South Korea; Department of Chemistry, Chonbuk National University, Jeonju 561-756, South Korea.
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22
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Wang Q, Irobalieva RN, Chiu W, Schmid MF, Fogg JM, Zechiedrich L, Pettitt BM. Influence of DNA sequence on the structure of minicircles under torsional stress. Nucleic Acids Res 2017; 45:7633-7642. [PMID: 28609782 PMCID: PMC5737869 DOI: 10.1093/nar/gkx516] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 05/26/2017] [Accepted: 06/01/2017] [Indexed: 01/09/2023] Open
Abstract
The sequence dependence of the conformational distribution of DNA under various levels of torsional stress is an important unsolved problem. Combining theory and coarse-grained simulations shows that the DNA sequence and a structural correlation due to topology constraints of a circle are the main factors that dictate the 3D structure of a 336 bp DNA minicircle under torsional stress. We found that DNA minicircle topoisomers can have multiple bend locations under high torsional stress and that the positions of these sharp bends are determined by the sequence, and by a positive mechanical correlation along the sequence. We showed that simulations and theory are able to provide sequence-specific information about individual DNA minicircles observed by cryo-electron tomography (cryo-ET). We provided a sequence-specific cryo-ET tomogram fitting of DNA minicircles, registering the sequence within the geometric features. Our results indicate that the conformational distribution of minicircles under torsional stress can be designed, which has important implications for using minicircle DNA for gene therapy.
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Affiliation(s)
- Qian Wang
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Rossitza N. Irobalieva
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wah Chiu
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael F. Schmid
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jonathan M. Fogg
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston TX, 77030, USA
| | - Lynn Zechiedrich
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston TX, 77030, USA
| | - B. Montgomery Pettitt
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
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23
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Delaney AM, Adams CF, Fernandes AR, Al-Shakli AF, Sen J, Carwardine DR, Granger N, Chari DM. A fusion of minicircle DNA and nanoparticle delivery technologies facilitates therapeutic genetic engineering of autologous canine olfactory mucosal cells. Nanoscale 2017; 9:8560-8566. [PMID: 28613324 DOI: 10.1039/c7nr00811b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Olfactory ensheathing cells (OECs) promote axonal regeneration and improve locomotor function when transplanted into the injured spinal cord. A recent clinical trial demonstrated improved motor function in domestic dogs with spinal injury following autologous OEC transplantation. Their utility in canines offers promise for human translation, as dogs are comparable to humans in terms of clinical management and genetic/environmental variation. Moreover, the autologous, minimally invasive derivation of OECs makes them viable for human spinal injury investigation. Genetic engineering of transplant populations may augment their therapeutic potential, but relies heavily on viral methods which have several drawbacks for clinical translation. We present here the first proof that magnetic particles deployed with applied magnetic fields and advanced DNA minicircle vectors can safely bioengineer OECs to secrete a key neurotrophic factor, with an efficiency approaching that of viral vectors. We suggest that our alternative approach offers high translational potential for the delivery of augmented clinical cell therapies.
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Affiliation(s)
- Alexander M Delaney
- Cellular and Neural Engineering Group, Institute for Science and Technology in Medicine, Keele University, Keele, Staffordshire ST5 5BG, UK.
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24
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Japaridze A, Orlandini E, Smith KB, Gmür L, Valle F, Micheletti C, Dietler G. Spatial confinement induces hairpins in nicked circular DNA. Nucleic Acids Res 2017; 45:4905-4914. [PMID: 28201616 PMCID: PMC5605231 DOI: 10.1093/nar/gkx098] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/25/2017] [Accepted: 02/06/2017] [Indexed: 01/05/2023] Open
Abstract
In living cells, DNA is highly confined in space with the help of condensing agents, DNA binding proteins and high levels of supercoiling. Due to challenges associated with experimentally studying DNA under confinement, little is known about the impact of spatial confinement on the local structure of the DNA. Here, we have used well characterized slits of different sizes to collect high resolution atomic force microscopy images of confined circular DNA with the aim of assessing the impact of the spatial confinement on global and local conformational properties of DNA. Our findings, supported by numerical simulations, indicate that confinement imposes a large mechanical stress on the DNA as evidenced by a pronounced anisotropy and tangent-tangent correlation function with respect to non-constrained DNA. For the strongest confinement we observed nanometer sized hairpins and interwound structures associated with the nicked sites in the DNA sequence. Based on these findings, we propose that spatial DNA confinement in vivo can promote the formation of localized defects at mechanically weak sites that could be co-opted for biological regulatory functions.
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Affiliation(s)
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Universita di Padova, Via Marzolo 8, 35131 Padova, Italy
| | | | - Lucas Gmür
- Laboratory of Physics of Living Matter, EPFL, 1015 Lausanne, Switzerland
| | - Francesco Valle
- Consiglio Nazionale delle Ricerche (CNR), Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Via P.Gobetti 101, Bologna 40129, Italy
| | - Cristian Micheletti
- SISSA - Scuola Internazionale Superiore di Studi Avanzati and CNR-IOM Democritos, Via Bonomea 265, 34136 Trieste, Italy
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter, EPFL, 1015 Lausanne, Switzerland
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25
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Abstract
Nucleic acid amplification is a hugely important technology for biology and medicine. While the polymerase chain reaction (PCR) has been highly useful and effective, its reliance on heating and cooling cycles places some constraints on its utility. For example, the heating step of PCR can destroy biological molecules under investigation and heat/cool cycles are not applicable in living systems. Thus, isothermal approaches to DNA and RNA amplification are under widespread study. Perhaps the simplest of these are the rolling circle approaches, including rolling circle amplification (RCA) and rolling circle transcription (RCT). In this strategy, a very small circular oligonucleotide (e.g., 25-100 nucleotides in length) acts as a template for a DNA or an RNA polymerase, producing long repeating product strands that serve as amplified copies of the circle sequence. Here we describe the early developments and studies involving circular oligonucleotides that ultimately led to the burgeoning rolling circle technologies currently under development. This Account starts with our studies on the design of circular oligonucleotides as novel DNA- and RNA-binding motifs. We describe how we developed chemical and biochemical strategies for synthesis of well-defined circular oligonucleotides having defined sequence and open (unpaired) structure, and we outline the unusual ways in which circular DNAs can interact with other nucleic acids. We proceed next to the discovery of DNA and RNA polymerase activity on these very small cyclic DNAs. DNA polymerase "rolling circle" activities were discovered concurrently in our laboratory and that of Andrew Fire. We describe the surprising efficiency of this process even on shockingly small circular DNAs, producing repeating DNAs thousands of nucleotides in length. RNA polymerase activity on circular oligonucleotides was first documented in our group in 1995; especially surprising in this case was the finding that the process occurs efficiently even without promoter sequences in the circle. We describe how one can encode cleavable sites into the product DNAs and RNAs from RCA/RCT, which can then be resolved into large quantities of almost pure oligonucleotides. Our Account then proceeds with a summary describing a broad variety of tools and methods built in many laboratories around the rolling circle concept. Among the important developments are the discovery of highly efficient DNA polymerases for RCA; the invention of exponential ("hyperbranched") RCA amplification made possible by use of a second primer; the development of the "padlock" process for detection of nucleic acids and proteins coupled with RCA; the use of circular oligonucleotides as vectors in cells to encode biologically active RNAs via RCT; and the use of small DNA circles to encode and extend human telomeres. Finally, we finish with some ideas about where the field may go in the future.
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Affiliation(s)
- Michael G Mohsen
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Eric T Kool
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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Hu Y, Ren J, Lu CH, Willner I. Programmed pH-Driven Reversible Association and Dissociation of Interconnected Circular DNA Dimer Nanostructures. Nano Lett 2016; 16:4590-4594. [PMID: 27225955 DOI: 10.1021/acs.nanolett.6b01891] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The switchable pH-driven reversible assembly and dissociation of interlocked circular DNA dimers is presented. The circular DNA dimers are interconnected by pH-responsive nucleic acid bridges. In one configuration, the two-ring nanostructure is separated at pH = 5.0 to individual rings by reconfiguring the interlocking bridges into C-G·C(+) triplex units, and the two-ring assembly is reformed at pH = 7.0. In the second configuration, the dimer of circular DNAs is bridged at pH = 7.0 by the T-A·T triplex bridging units that are separated at pH = 10.0, leading to the dissociation of the dimer to single circular DNA nanostructures. The two circular DNA units are also interconnected by two pH-responsive locks. The pH-programmed opening of the locks at pH = 5.0 or pH = 10.0 yields two isomeric dimer structures composed of two circular DNAs. The switchable reconfigured states of the circular DNA nanostructures are followed by time-dependent fluorescence changes of fluorophore/quencher labeled systems and by complementary gel electrophoresis experiments. The dimer circular DNA structures are further implemented as scaffolds for the assembly of Au nanoparticle dimers exhibiting controlled spatial separation.
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Affiliation(s)
- Yuwei Hu
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Jiangtao Ren
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Chun-Hua Lu
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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27
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Luo X, Huang Y, Chen Y, Tu Z, Hu J, Tavis JE, Huang A, Hu Y. Association of Hepatitis B Virus Covalently Closed Circular DNA and Human APOBEC3B in Hepatitis B Virus-Related Hepatocellular Carcinoma. PLoS One 2016; 11:e0157708. [PMID: 27310677 PMCID: PMC4911053 DOI: 10.1371/journal.pone.0157708] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 04/18/2016] [Indexed: 12/13/2022] Open
Abstract
Chronic Hepatitis B Virus (HBV) infections can progresses to liver cirrhosis and hepatocellular carcinoma (HCC). The HBV covalently-closed circular DNA cccDNA is a key to HBV persistence, and its degradation can be induced by the cellular deaminase APOBEC3. This study aimed to measure the distribution of intrahepatic cccDNA levels and evaluate the association between levels of cccDNA and APOBEC3 in HCC patients. Among 49 HCC patients, 35 matched cancerous and contiguous noncancerous liver tissues had detectable cccDNA, and the median intrahepatic cccDNA in the cancerous tissues (CT) was significantly lower than in the contiguous noncancerous tissues (CNCT) (p = 0.0033). RCA (rolling circle amplification), followed by 3D-PCR identified positive amplification in 27 matched HCC patients. Sequence analysis indicated G to A mutations accumulated to higher levels in CT samples compared to CNCT samples, and the dinucleotide context showed preferred editing in the GpA context. Among 7 APOBEC3 genes, APOBEC3B was the only one up-regulated in cancerous tissues both at the transcriptional and protein levels (p < 0.05). This implies APOBEC3B may contribute to cccDNA editing and subsequent degradation in cancerous tissues.
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MESH Headings
- Adult
- Aged
- Antigens, Viral/genetics
- Antigens, Viral/metabolism
- Carcinoma, Hepatocellular/enzymology
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/virology
- Case-Control Studies
- Cytidine Deaminase/genetics
- Cytidine Deaminase/metabolism
- DNA, Circular/chemistry
- DNA, Circular/genetics
- DNA, Circular/metabolism
- DNA, Viral/chemistry
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Gene Expression
- Hepatitis B virus/genetics
- Hepatitis B virus/metabolism
- Hepatitis B, Chronic/complications
- Host-Pathogen Interactions
- Humans
- Hydrolysis
- Liver/enzymology
- Liver/pathology
- Liver/virology
- Liver Neoplasms/enzymology
- Liver Neoplasms/genetics
- Liver Neoplasms/virology
- Male
- Middle Aged
- Minor Histocompatibility Antigens/genetics
- Minor Histocompatibility Antigens/metabolism
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Affiliation(s)
- Xuan Luo
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Institute for Viral Hepatitis, Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Yao Huang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Institute for Viral Hepatitis, Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Yanmeng Chen
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Institute for Viral Hepatitis, Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Zeng Tu
- Department of Microbiology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Jieli Hu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Institute for Viral Hepatitis, Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, People’s Republic of China
| | - John E. Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University Liver Center, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Ailong Huang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Institute for Viral Hepatitis, Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, People’s Republic of China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, People’s Republic of China
- * E-mail: (AH); (YH)
| | - Yuan Hu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Institute for Viral Hepatitis, Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, People’s Republic of China
- * E-mail: (AH); (YH)
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28
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Azim MAR, Iliopoulos CS, Rahman MS, Samiruzzaman M. A Simple, Fast, Filter-Based Algorithm for Approximate Circular Pattern Matching. IEEE Trans Nanobioscience 2016; 15:93-100. [PMID: 26992174 DOI: 10.1109/tnb.2016.2542062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This paper deals with the approximate version of the circular pattern matching (ACPM) problem, which appears as an interesting problem in many biological contexts. The circular pattern matching problem consists in finding all occurrences of the rotations of a pattern P of length m in a text T of length n. In ACPM, we consider occurrences with k -mismatches under the Hamming distance model. In this paper, we present a simple and fast filter-based algorithm to solve the ACPM problem. We compare our algorithm with the state of the art algorithms and the results are found to be excellent. In particular, our algorithm runs almost twice as fast than the state of the art. Much of the efficiency of our algorithm can be attributed to its filters that are effective but extremely simple and lightweight.
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29
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Abstract
Understanding how the sequence of a DNA molecule affects its dynamic properties is a central problem affecting biochemistry and biotechnology. The process of cyclizing short DNA, as a critical step in molecular cloning, lacks a comprehensive picture of the kinetic process containing sequence information. We have elucidated this process by using coarse-grained simulations, enhanced sampling methods, and recent theoretical advances. We are able to identify the types and positions of structural defects during the looping process at a base-pair level. Correlations along a DNA molecule dictate critical sequence positions that can affect the looping rate. Structural defects change the bending elasticity of the DNA molecule from a harmonic to subharmonic potential with respect to bending angles. We explore the subelastic chain as a possible model in loop formation kinetics. A sequence-dependent model is developed to qualitatively predict the relative loop formation time as a function of DNA sequence.
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30
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Abstract
We present a self-avoiding polygon (SAP) model for circular DNA in which the radius of impermeable cylindrical segments corresponds to the screening length of double-stranded DNA surrounded by counter ions. For the model we evaluate the probability for a generated SAP with N segments having a given knot K through simulation. We call it the knotting probability of a knot K with N segments for the SAP model. We show that when N is large the most significant factor in the knotting probability is given by the exponentially decaying part exp(-N/NK), where the estimates of parameter NK are consistent with the same value for all the different knots we investigated. We thus call it the characteristic length of the knotting probability. We give formulae expressing the characteristic length as a function of the cylindrical radius rex, i.e. the screening length of double-stranded DNA.
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Affiliation(s)
- Erica Uehara
- Department of Physics, Graduate School of Humanities and Sciences, Ochanomizu University 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
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31
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Abstract
Teleaulax amphioxeia is a photosynthetic unicellular cryptophyte alga that is distributed throughout marine habitats worldwide. This alga is an important plastid donor to the dinoflagellate Dinophysis caudata through the ciliate Mesodinium rubrum in the marine food web. To better understand the genomic characteristics of T. amphioxeia, we have sequenced and analyzed its plastid genome. The plastid genome sequence of T. amphioxeia is similar to that of Rhodomonas salina, and they share significant synteny. This sequence exhibits less similarity to that of Guillardia theta, the representative plastid genome of photosynthetic cryptophytes. The gene content and order of the three photosynthetic cryptomonad plastid genomes studied is highly conserved. The plastid genome of T. amphioxeia is composed of 129,772 bp and includes 143 protein-coding genes, 2 rRNA operons and 30 tRNA sequences. The DNA polymerase III gene (dnaX) was most likely acquired via lateral gene transfer (LGT) from a firmicute bacterium, identical to what occurred in R. salina. On the other hand, the psbN gene was independently encoded by the plastid genome without a reverse transcriptase gene as an intron. To clarify the phylogenetic relationships of the algae with red-algal derived plastids, phylogenetic analyses of 32 taxa were performed, including three previously sequenced cryptophyte plastid genomes containing 93 protein-coding genes. The stramenopiles were found to have branched out from the Chromista taxa (cryptophytes, haptophytes, and stramenopiles), while the cryptophytes and haptophytes were consistently grouped into sister relationships with high resolution.
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Affiliation(s)
- Jong Im Kim
- Department of Biology, Chungnam National University, Daejeon, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Gangman Yi
- Department of Computer Science, Gangneung-Wonju National University, Wonju, Korea
| | - Hyung Seop Kim
- Department of Marine Biotechnology, Kunsan National University, Kunsan, Korea
| | - Wonho Yih
- Department of Marine Biotechnology, Kunsan National University, Kunsan, Korea
- * E-mail: (WY); (WS)
| | - Woongghi Shin
- Department of Biology, Chungnam National University, Daejeon, Korea
- * E-mail: (WY); (WS)
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32
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Abstract
DNA hemicatenanes, one of the simplest possible junctions between two double stranded DNA molecules, have frequently been mentioned in the literature for their possible function in DNA replication, recombination, repair, and organization in chromosomes. They have been little studied experimentally, however, due to the lack of an appropriate method for their preparation. Here we have designed a method to build hemicatenanes from two small circular DNA molecules. The method involves, first, the assembly of two linear single strands and their circularization to form a catenane of two single stranded circles, and, second, the addition and base-pairing of the two single stranded circles complementary to the first ones, followed by their annealing using DNA topoisomerase I. The product was purified by gel electrophoresis and characterized. The arrangement of strands was as expected for a hemicatenane and clearly distinct from a full catenane. In addition, each circle was unwound by an average of half a double helical turn, also in excellent agreement with the structure of a hemicatenane. It was also observed that hemicatenanes are quickly destabilized by a single cut on either of the two strands passing inside the junction, strongly suggesting that DNA strands are able to slide easily inside the hemicatenane. This method should make it possible to study the biochemical properties of hemicatenanes and to test some of the hypotheses that have been proposed about their function, including a possible role for this structure in the organization of complex genomes in loops and chromosomal domains.
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33
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Koussa MA, Halvorsen K, Ward A, Wong WP. DNA nanoswitches: a quantitative platform for gel-based biomolecular interaction analysis. Nat Methods 2015; 12:123-126. [PMID: 25486062 PMCID: PMC4336243 DOI: 10.1038/nmeth.3209] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 10/17/2014] [Indexed: 11/16/2022]
Abstract
We introduce a nanoscale experimental platform that enables kinetic and equilibrium measurements of a wide range of molecular interactions using a gel electrophoresis readout. Programmable, self-assembled DNA nanoswitches serve both as templates for positioning molecules and as sensitive, quantitative reporters of molecular association and dissociation. We demonstrated this low-cost, versatile, 'lab-on-a-molecule' system by characterizing ten different interactions, including a complex four-body interaction with five discernible states.
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Affiliation(s)
- Mounir A Koussa
- Program in Neuroscience, Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Ken Halvorsen
- The RNA Institute, University at Albany, Albany, NY, United States
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, United States
| | - Andrew Ward
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, United States
| | - Wesley P Wong
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
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34
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Paprotka T, Deuschle K, Pilartz M, Jeske H. Form follows function in geminiviral minichromosome architecture. Virus Res 2015; 196:44-55. [PMID: 25445344 DOI: 10.1016/j.virusres.2014.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 10/24/2022]
Abstract
A comprehensive survey on the viral minichromosomes of the begomoviruses Abutilon mosaic virus, tomato yellow leaf curl Sardinia virus, African cassava mosaic virus, Indian cassava mosaic virus (family Geminiviridae) during the course of infections in Nicotiana benthamiana is summarized. Using optimized one-dimensional and two-dimensional gel systems combined with blot hybridization and a standardized evaluation, discrete and heterogeneous virus-specific signals with different DNA forms were compared to trace functions of viral multiplication with inactive/active replication and/or transcription. A quantitative approach to compare the distantly related viruses during the course of infection with the aim to generalize the conclusions for geminiviruses has been developed. Focussing on the distribution of topoisomers of viral supercoiled DNA, which reflect minichromosomal stages, predominant minichromosomes with 12 nucleosomes, less with 13 nucleosomes and no with 11 nucleosomes were found. These results indicate that chromatin with only one open gap to bind transcription factors is the favourite form. The dynamics during infections in dependence on the experimental conditions is discussed with reference to the design of experiments for resistance breeding and molecular analyses.
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Affiliation(s)
- Tobias Paprotka
- Institut für Biomaterialien und biomolekulare Systeme, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Kathrin Deuschle
- Institut für Biomaterialien und biomolekulare Systeme, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Marcel Pilartz
- Institut für Biomaterialien und biomolekulare Systeme, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Holger Jeske
- Institut für Biomaterialien und biomolekulare Systeme, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany.
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35
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Cuartas PE, Barrera GP, Belaich MN, Barreto E, Ghiringhelli PD, Villamizar LF. The complete sequence of the first Spodoptera frugiperda Betabaculovirus genome: a natural multiple recombinant virus. Viruses 2015; 7:394-421. [PMID: 25609309 PMCID: PMC4306845 DOI: 10.3390/v7010394] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 12/26/2014] [Indexed: 01/08/2023] Open
Abstract
Spodoptera frugiperda (Lepidoptera: Noctuidae) is a major pest in maize crops in Colombia, and affects several regions in America. A granulovirus isolated from S. frugiperda (SfGV VG008) has potential as an enhancer of insecticidal activity of previously described nucleopolyhedrovirus from the same insect species (SfMNPV). The SfGV VG008 genome was sequenced and analyzed showing circular double stranded DNA of 140,913 bp encoding 146 putative ORFs that include 37 Baculoviridae core genes, 88 shared with betabaculoviruses, two shared only with betabaculoviruses from Noctuide insects, two shared with alphabaculoviruses, three copies of own genes (paralogs) and the other 14 corresponding to unique genes without representation in the other baculovirus species. Particularly, the genome encodes for important virulence factors such as 4 chitinases and 2 enhancins. The sequence analysis revealed the existence of eight homologous regions (hrs) and also suggests processes of gene acquisition by horizontal transfer including the SfGV VG008 ORFs 046/047 (paralogs), 059, 089 and 099. The bioinformatics evidence indicates that the genome donors of mentioned genes could be alpha- and/or betabaculovirus species. The previous reported ability of SfGV VG008 to naturally co-infect the same host with other virus show a possible mechanism to capture genes and thus improve its fitness.
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Affiliation(s)
- Paola E Cuartas
- Centro de investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria CORPOICA, Km 14 Vía Mosquera 250047, Cundinamarca, Colombia.
| | - Gloria P Barrera
- Centro de investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria CORPOICA, Km 14 Vía Mosquera 250047, Cundinamarca, Colombia.
| | - Mariano N Belaich
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Dto. de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Saenz Peña 352, Bernal, Provincia de Buenos Aires, 1876, Argentina.
| | - Emiliano Barreto
- Centro de Bioinformática, Instituto de Biotecnología, Universidad Nacional de Colombia. Avenida Carrera 30 # 45, Bogotá 11001000, Cundinamarca, Colombia.
| | - Pablo D Ghiringhelli
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Dto. de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Saenz Peña 352, Bernal, Provincia de Buenos Aires, 1876, Argentina.
| | - Laura F Villamizar
- Centro de investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria CORPOICA, Km 14 Vía Mosquera 250047, Cundinamarca, Colombia.
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36
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Abstract
YOYO-1 is a green fluorescent dye which is widely used to image single DNA molecules in solution for biophysical studies. However, the question of whether the intercalation of YOYO-1 affects the mechanical properties of DNA is still not clearly answered. Investigators have put forth contradicting data on the changes in persistence length of DNA. Here, we use atomic force microscopy to systematically study the changes in the mechanical properties of DNA due to the intercalation of YOYO-1. We first measured the persistence length, contour length and the bending angle distribution of the DNA-YOYO-1 complex. We find that the persistence length of DNA remains unaffected with the intercalation of YOYO-1. However the contour length increases linearly with about 38% increase at full saturation of 1 YOYO-1 per 4 base pairs of DNA. Next we measured the change in topology of relaxed closed circular DNA after the intercalation of YOYO-1. We find that YOYO-1 introduces supercoiling in closed circular DNA. Our observations indicate that the intercalation of YOYO-1 results in the underwinding of DNA duplex, but does not significantly change the persistence length.
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Affiliation(s)
- Binu Kundukad
- BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), Singapore.
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37
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Bhattacherjee A, Levy Y. Search by proteins for their DNA target site: 2. The effect of DNA conformation on the dynamics of multidomain proteins. Nucleic Acids Res 2014; 42:12415-24. [PMID: 25324311 PMCID: PMC4227779 DOI: 10.1093/nar/gku933] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 11/14/2022] Open
Abstract
Multidomain transcription factors, which are especially abundant in eukaryotic genomes, are advantageous to accelerate the search kinetics for target site because they can follow the intersegment transfer via the monkey-bar mechanism in which the protein forms a bridged intermediate between two distant DNA regions. Monkey-bar dynamics highly depends on the properties of the multidomain protein (the affinity of each of the constituent domains to the DNA and the length of the linker) and the DNA molecules (their inter-distance and inter-angle). In this study, we investigate using coarse-grained molecular dynamics simulations how the local conformation of the DNA may affect the DNA search performed by a multidomain protein Pax6 in comparison to that of the isolated domains. Our results suggest that in addition to the common rotation-coupled translation along the DNA major groove, for curved DNA the tethered domains may slide in a rotation-decoupled sliding mode. Furthermore, the multidomain proteins move by longer jumps on curved DNA compared with those performed by the single domain protein. The long jumps originate from the DNA curvature bringing two sequentially distant DNA sites into close proximity with each other and they suggest that multidomain proteins may move on highly curved DNA faster than linear DNA.
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Affiliation(s)
- Arnab Bhattacherjee
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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Fueller E, Schaefer D, Fischer U, Krell PFI, Stanulla M, Borkhardt A, Slany RK. Genomic inverse PCR for exploration of ligated breakpoints (GIPFEL), a new method to detect translocations in leukemia. PLoS One 2014; 9:e104419. [PMID: 25137060 PMCID: PMC4138100 DOI: 10.1371/journal.pone.0104419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 07/09/2014] [Indexed: 11/18/2022] Open
Abstract
Here we present a novel method “Genomic inverse PCR for exploration of ligated breakpoints” (GIPFEL) that allows the sensitive detection of recurrent chromosomal translocations. This technique utilizes limited amounts of DNA as starting material and relies on PCR based quantification of unique DNA sequences that are created by circular ligation of restricted genomic DNA from translocation bearing cells. Because the complete potential breakpoint region is interrogated, a prior knowledge of the individual, specific interchromosomal fusion site is not required. We validated GIPFEL for the five most common gene fusions associated with childhood leukemia (MLL-AF4, MLL-AF9, MLL-ENL, ETV6-RUNX1, and TCF3-PBX1). A workflow of restriction digest, purification, ligation, removal of linear fragments and precipitation enriching for circular DNA was developed. GIPFEL allowed detection of translocation specific signature sequences down to a 10−4 dilution which is close to the theoretical limit. In a blinded proof-of-principle study utilizing DNA from cell lines and 144 children with B-precursor-ALL associated translocations this method was 100% specific with no false positive results. Sensitivity was 83%, 65%, and 24% for t(4;11), t(9;11) and t(11;19) respectively. Translocation t(12;21) was correctly detected in 64% and t(1;19) in 39% of the cases. In contrast to other methods, the characteristics of GIPFEL make it particularly attractive for prospective studies.
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MESH Headings
- Child
- Chromosome Breakpoints
- Chromosomes, Human, Pair 11
- Chromosomes, Human, Pair 12
- Chromosomes, Human, Pair 19
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Pair 4
- Chromosomes, Human, Pair 9
- Core Binding Factor Alpha 2 Subunit/genetics
- DNA, Circular/chemistry
- DNA, Circular/genetics
- Humans
- Myeloid-Lymphoid Leukemia Protein/genetics
- Oncogene Proteins, Fusion/genetics
- Polymerase Chain Reaction/methods
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/diagnosis
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Sensitivity and Specificity
- Translocation, Genetic
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Affiliation(s)
- Elisa Fueller
- Department of Genetics, Friedrich Alexander University, Erlangen, Germany
| | - Daniel Schaefer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Pina F. I. Krell
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Martin Stanulla
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- * E-mail: (AB); (RKS)
| | - Robert K. Slany
- Department of Genetics, Friedrich Alexander University, Erlangen, Germany
- * E-mail: (AB); (RKS)
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Østerberg FW, Rizzi G, Donolato M, Bejhed RS, Mezger A, Strömberg M, Nilsson M, Strømme M, Svedlindh P, Hansen MF. On-chip detection of rolling circle amplified DNA molecules from Bacillus globigii spores and Vibrio cholerae. Small 2014; 10:2877-2882. [PMID: 24616417 DOI: 10.1002/smll.201303325] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/10/2014] [Indexed: 06/03/2023]
Abstract
For the first time DNA coils formed by rolling circle amplification are quantified on-chip by Brownian relaxation measurements on magnetic nanobeads using a magnetoresistive sensor. No external magnetic fields are required besides the magnetic field arising from the current through the sensor, which makes the setup very compact. Limits of detection down to 500 Bacillus globigii spores and 2 pM of Vibrio cholerae are demonstrated, which are on the same order of magnitude or lower than those achieved previously using a commercial macro-scale AC susceptometer. The chip-based readout is an important step towards the realization of field tests based on rolling circle amplification molecular analyses.
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Affiliation(s)
- Frederik W Østerberg
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800, Kongens Lyngby, Denmark
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40
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Abstract
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with ∼100 base pairs, is addressed. Three minicircles with different radii and almost equal contents of AT and GC pairs are investigated. The DNA sequences are modeled by a mesoscopic Hamiltonian which describes the essential interactions in the helix at the level of the base pair and incorporates twisting and bending degrees of freedom. Helix unwinding and bubble formation patterns are consistently computed by a path integral method that sums over a large number of molecule configurations compatible with the model potential. The path ensembles are determined, as a function of temperature, by minimizing the free energy of the system. Fluctuational openings appear along the helix to release the stress due to the bending of the molecule backbone. In agreement with the experimental findings, base pair disruptions are found with larger probability in the smallest minicircle of 66 bps whose bending angle is ∼6°. For this minicircle, a sizeable untwisting is obtained with the helical repeat showing a step-like increase at T = 315 K. The method can be generalized to determine the bubble probability profiles of open ends linear sequences.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology - CNISM, Università di Camerino, I-62032 Camerino, Italy.
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Liu M, Song J, Shuang S, Dong C, Brennan JD, Li Y. A graphene-based biosensing platform based on the release of DNA probes and rolling circle amplification. ACS Nano 2014; 8:5564-5573. [PMID: 24857187 DOI: 10.1021/nn5007418] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We report a versatile biosensing platform capable of achieving ultrasensitive detection of both small-molecule and macromolecular targets. The system features three components: reduced graphene oxide for its ability to adsorb single-stranded DNA molecules nonspecifically, DNA aptamers for their ability to bind reduced graphene oxide but undergo target-induced conformational changes that facilitate their release from the reduced graphene oxide surface, and rolling circle amplification (RCA) for its ability to amplify a primer-template recognition event into repetitive sequence units that can be easily detected. The key to the design is the tagging of a short primer to an aptamer sequence, which results in a small DNA probe that allows for both effective probe adsorption onto the reduced graphene oxide surface to mask the primer domain in the absence of the target, as well as efficient probe release in the presence of the target to make the primer available for template binding and RCA. We also made an observation that the circular template, which on its own does not cause a detectable level of probe release from the reduced graphene oxide, augments target-induced probe release. The synergistic release of DNA probes is interpreted to be a contributing factor for the high detection sensitivity. The broad utility of the platform is illustrated though engineering three different sensors that are capable of achieving ultrasensitive detection of a protein target, a DNA sequence and a small-molecule analyte. We envision that the approach described herein will find useful applications in the biological, medical, and environmental fields.
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Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main Street West, Hamilton, Ontario, L8S 4K1 Canada
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42
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Fernández-Durán JJ, Gregorio-Domínguez MM. Modeling angles in proteins and circular genomes using multivariate angular distributions based on multiple nonnegative trigonometric sums. Stat Appl Genet Mol Biol 2014; 13:1-18. [PMID: 24391194 DOI: 10.1515/sagmb-2012-0012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Fernández-Durán, J. J. (2004): "Circular distributions based on nonnegative trigonometric sums," Biometrics, 60, 499-503, developed a family of univariate circular distributions based on nonnegative trigonometric sums. In this work, we extend this family of distributions to the multivariate case by using multiple nonnegative trigonometric sums to model the joint distribution of a vector of angular random variables. Practical examples of vectors of angular random variables include the wind direction at different monitoring stations, the directions taken by an animal on different occasions, the times at which a person performs different daily activities, and the dihedral angles of a protein molecule. We apply the proposed new family of multivariate distributions to three real data-sets: two for the study of protein structure and one for genomics. The first is related to the study of a bivariate vector of dihedral angles in proteins. In the second real data-set, we compare the fit of the proposed multivariate model with the bivariate generalized von Mises model of [Shieh, G. S., S. Zheng, R. A. Johnson, Y.-F. Chang, K. Shimizu, C.-C. Wang, and S.-L. Tang (2011): "Modeling and comparing the organization of circular genomes," Bioinformatics, 27(7), 912-918.] in a problem related to orthologous genes in pairs of circular genomes. The third real data-set consists of observed values of three dihedral angles in γ-turns in a protein and serves as an example of trivariate angular data. In addition, a simulation algorithm is presented to generate realizations from the proposed multivariate angular distribution.
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Venturini C, Hassan KA, Roy Chowdhury P, Paulsen IT, Walker MJ, Djordjevic SP. Sequences of two related multiple antibiotic resistance virulence plasmids sharing a unique IS26-related molecular signature isolated from different Escherichia coli pathotypes from different hosts. PLoS One 2013; 8:e78862. [PMID: 24223859 PMCID: PMC3817090 DOI: 10.1371/journal.pone.0078862] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/23/2013] [Indexed: 02/07/2023] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) and atypical enteropathogenic E. coli (aEPEC) are important zoonotic pathogens that increasingly are becoming resistant to multiple antibiotics. Here we describe two plasmids, pO26-CRL125 (125 kb) from a human O26:H- EHEC, and pO111-CRL115 (115kb) from a bovine O111 aEPEC, that impart resistance to ampicillin, kanamycin, neomycin, streptomycin, sulfathiazole, trimethoprim and tetracycline and both contain atypical class 1 integrons with an identical IS26-mediated deletion in their 3´-conserved segment. Complete sequence analysis showed that pO26-CRL125 and pO111-CRL115 are essentially identical except for a 9.7 kb fragment, present in the backbone of pO26-CRL125 but absent in pO111-CRL115, and several indels. The 9.7 kb fragment encodes IncI-associated genes involved in plasmid stability during conjugation, a putative transposase gene and three imperfect repeats. Contiguous sequence identical to regions within these pO26-CRL125 imperfect repeats was identified in pO111-CRL115 precisely where the 9.7 kb fragment is missing, suggesting it may be mobile. Sequences shared between the plasmids include a complete IncZ replicon, a unique toxin/antitoxin system, IncI stability and maintenance genes, a novel putative serine protease autotransporter, and an IncI1 transfer system including a unique shufflon. Both plasmids carry a derivate Tn21 transposon with an atypical class 1 integron comprising a dfrA5 gene cassette encoding resistance to trimethoprim, and 24 bp of the 3´-conserved segment followed by Tn6026, which encodes resistance to ampicillin, kanymycin, neomycin, streptomycin and sulfathiazole. The Tn21-derivative transposon is linked to a truncated Tn1721, encoding resistance to tetracycline, via a region containing the IncP-1α oriV. Absence of the 5 bp direct repeats flanking Tn3-family transposons, indicates that homologous recombination events played a key role in the formation of this complex antibiotic resistance gene locus. Comparative sequence analysis of these closely related plasmids reveals aspects of plasmid evolution in pathogenic E. coli from different hosts.
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Affiliation(s)
- Carola Venturini
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, the University of Queensland, Brisbane, Queensland, Australia
| | - Karl A. Hassan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Macquarie Park, New South Wales, Australia
| | - Piklu Roy Chowdhury
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Macquarie Park, New South Wales, Australia
- NSW Department of Primary Industries, Camden, New South Wales, Australia
- The ithree Institute - Infection. Immunity. Innovation, University of Technology, Sydney, New South Wales, Australia
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Macquarie Park, New South Wales, Australia
| | - Mark J. Walker
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, the University of Queensland, Brisbane, Queensland, Australia
| | - Steven P. Djordjevic
- The ithree Institute - Infection. Immunity. Innovation, University of Technology, Sydney, New South Wales, Australia
- * . E-mail:
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44
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Bohr J, Olsen KW. Total positive curvature of circular DNA. Phys Rev E Stat Nonlin Soft Matter Phys 2013; 88:052714. [PMID: 24329303 DOI: 10.1103/physreve.88.052714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 08/15/2013] [Indexed: 06/03/2023]
Abstract
The properties of double-stranded DNA and other chiral molecules depend on the local geometry, i.e., on curvature and torsion, yet the paths of closed chain molecules are globally restricted by topology. When both of these characteristics are to be incorporated in the description of circular chain molecules, e.g., plasmids, it is shown to have implications for the total positive curvature integral. For small circular micro-DNAs it follows as a consequence of Fenchel's inequality that there must exist a minimum length for the circular plasmids to be double stranded. It also follows that all circular micro-DNAs longer than the minimum length must be concave, a result that is consistent with typical atomic force microscopy images of plasmids. Predictions for the total positive curvature of circular micro-DNAs are given as a function of length, and comparisons with circular DNAs from the literature are presented.
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Affiliation(s)
- Jakob Bohr
- DTU Nanotech, Building 345Ø, Ørsteds Plads, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Kasper W Olsen
- DTU Nanotech, Building 345Ø, Ørsteds Plads, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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45
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Ji C, Zhang L, Wang PY. Quantitative analysis of the flexibility effect of cisplatin on circular DNA. Phys Rev E Stat Nonlin Soft Matter Phys 2013; 88:042703. [PMID: 24229209 DOI: 10.1103/physreve.88.042703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 09/15/2013] [Indexed: 06/02/2023]
Abstract
We study the effects of cisplatin on the circular configuration of DNA using atomic force microscopy (AFM) and observe that the DNA gradually transforms to a complex configuration with an intersection and interwound structures from a circlelike structure. An algorithm is developed to extract the configuration profiles of circular DNA from AFM images and the radius of gyration is used to describe the flexibility of circular DNA. The quantitative analysis of the circular DNA demonstrates that the radius of gyration gradually decreases and two processes on the change of flexibility of circular DNA are found as the cisplatin concentration increases. Furthermore, a model is proposed and discussed to explain the mechanism for understanding the complicated interaction between DNA and cisplatin.
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Affiliation(s)
- Chao Ji
- Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
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46
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Uchiya KI, Takahashi H, Yagi T, Moriyama M, Inagaki T, Ichikawa K, Nakagawa T, Nikai T, Ogawa K. Comparative genome analysis of Mycobacterium avium revealed genetic diversity in strains that cause pulmonary and disseminated disease. PLoS One 2013; 8:e71831. [PMID: 23990995 PMCID: PMC3749206 DOI: 10.1371/journal.pone.0071831] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 07/02/2013] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium avium complex (MAC) infection causes disseminated disease in immunocompromised hosts, such as human immunodeficiency virus (HIV)-positive patients, and pulmonary disease in persons without systemic immunosuppression, which has been increasing in many countries. In Japan, the incidence of pulmonary MAC disease caused by M. avium is about 7 times higher than that caused by M. intracellulare. To explore the bacterial factors that affect the pathological state of MAC disease caused by M. avium, we determined the complete genome sequence of the previously unreported M. avium subsp. hominissuis strain TH135 isolated from a HIV-negative patient with pulmonary MAC disease and compared it with the known genomic sequence of M. avium strain 104 derived from an acquired immunodeficiency syndrome patient with MAC disease. The genome of strain TH135 consists of a 4,951,217-bp circular chromosome with 4,636 coding sequences. Comparative analysis revealed that 4,012 genes are shared between the two strains, and strains TH135 and 104 have 624 and 1,108 unique genes, respectively. Many strain-specific regions including virulence-associated genes were found in genomes of both strains, and except for some regions, the G+C content in the specific regions was low compared with the mean G+C content of the corresponding chromosome. Screening of clinical isolates for genes located in the strain-specific regions revealed that the detection rates of strain TH135-specific genes were relatively high in specimens isolated from pulmonary MAC disease patients, while, those of strain 104-specific genes were relatively high in those from HIV-positive patients. Collectively, M. avium strains that cause pulmonary and disseminated disease possess genetically distinct features, and it suggests that the acquisition of specific genes during strain evolution has played an important role in the pathological manifestations of MAC disease.
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Affiliation(s)
- Kei-ichi Uchiya
- Department of Microbiology, Faculty of Pharmacy, Meijo University, Nagoya, Japan
- * E-mail:
| | - Hiroyasu Takahashi
- Department of Pharmacy, Kainan Hospital Aichi Prefectural Welfare Federation of Agricultural Cooperatives, Yatomi, Japan
| | - Tetsuya Yagi
- Department of Infectious Diseases, Center of National University Hospital for Infection Control, Nagoya University Hospital, Nagoya, Japan
| | - Makoto Moriyama
- Department of Microbiology, Faculty of Pharmacy, Meijo University, Nagoya, Japan
- Department of Pharmacy, National Hospital Organization, Nagoya Medical Center, Nagoya, Japan
| | - Takayuki Inagaki
- Department of Microbiology, Faculty of Pharmacy, Meijo University, Nagoya, Japan
- Department of Pharmacy, Takayama Red Cross Hospital, Takayama, Japan
- Department of Clinical Research, National Hospital Organization, Higashinagoya National Hospital, Nagoya, Japan
| | - Kazuya Ichikawa
- Department of Pharmacy, Nagoya University Hospital, Nagoya, Japan
| | - Taku Nakagawa
- Department of Clinical Research, National Hospital Organization, Higashinagoya National Hospital, Nagoya, Japan
- Department of Pulmonary Medicine, National Hospital Organization, Higashinagoya National Hospital, Nagoya, Japan
| | - Toshiaki Nikai
- Department of Microbiology, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Kenji Ogawa
- Department of Clinical Research, National Hospital Organization, Higashinagoya National Hospital, Nagoya, Japan
- Department of Pulmonary Medicine, National Hospital Organization, Higashinagoya National Hospital, Nagoya, Japan
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Chandel M, Sharma U, Kumar N, Singh B, Kaur S. Antioxidant activity and identification of bioactive compounds from leaves of Anthocephalus cadamba by ultra-performance liquid chromatography/electrospray ionization quadrupole time of flight mass spectrometry. ASIAN PAC J TROP MED 2013. [PMID: 23199718 DOI: 10.1016/s1995-7645(12)60186-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE To evaluate the antioxidant potential of different extract/fractions of Anthocephalus cadamba (A. cadamba) (Roxb.) Miq. (Rubiaceae) and study the tentative identification of their active constituents. METHODS The extract/fractions were screened for antioxidant activity using various in vitro assays viz. DPPH assay, ABTS assay, superoxide anion radical scavenging assay, reducing power assay and plasmid DNA nicking assay. Total phenolic content of extract/fractions was determined by colorimetric method. An ultra-performance LC-electrospray-quadrupole-time of flight mass spectrometry method was used to analyse the active constituents of extract/fractions of A. cadamba. RESULTS The ethyl acetate fraction was found to be most active fraction in all the assays as compared to other extract/fractions. The IC(50) value of ethyl acetate fraction (ETAC fraction) was 21.24 μg/mL, 1.12 μg/mL, 9.68 μg/mL and 57.81 μg/mL in DPPH assay, ABTS assay, reducing power assay and superoxide scavenging assay respectively. All the extract/fractions also showed the potential to protect the plasmid DNA (pBR322) against the attack of hydroxyl radicals generated by Fentońs reagent. The bioactive compounds were identified by UPLC-ESI-QTOF-MS, by comparing the mass and λ(max) with literature values. CONCLUSIONS The potential of the extract/fractions to scavenge different free radicals in different systems indicated that they may be useful therapeutic agents for treating radical-related pathologic damage.
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Affiliation(s)
- Madhu Chandel
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar-143005 India
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Jędrzejewska B, Bajorek A, Moraczewska J. Interaction of carbocyanine dyes with DNA: synthesis and spectroscopic studies. Appl Spectrosc 2013; 67:672-680. [PMID: 23735253 DOI: 10.1366/12-06887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Six carbocyanine dyes have been synthesized and their interactions with DNA have been investigated for their prospective use as fluorescent markers in molecular biology. The noncovalent binding of the compounds with DNA was explored by fluorescence spectroscopy, ultraviolet/visible spectrophotometry, and photobleaching. The electron-withdrawing ability of the substituents in N-position of free thio- and selenocarbocyanines strongly affected their photostabilities. Changes in the experimental conditions, such as the presence or absence of oxygen, had an impact on the rate of photobleaching. In the presence of DNA, absorbance photofading and fluorescence photobleaching occurred. It appears that the reduction of fluorescence intensity was due to quenching of the dye fluorescence by interaction with DNA.
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Affiliation(s)
- Beata Jędrzejewska
- Faculty of Chemical Technology and Engineering, University of Technology and Life Sciences, Seminaryjna 3, 85-326 Bydgoszcz, Poland.
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Kurz V, Nelson EM, Shim J, Timp G. Direct visualization of single-molecule translocations through synthetic nanopores comparable in size to a molecule. ACS Nano 2013; 7:4057-69. [PMID: 23607372 DOI: 10.1021/nn400182s] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A nanopore is the ultimate analytical tool. It can be used to detect DNA, RNA, oligonucleotides, and proteins with submolecular sensitivity. This extreme sensitivity is derived from the electric signal associated with the occlusion that develops during the translocation of the analyte across a membrane through a pore immersed in electrolyte. A larger occluded volume results in an improvement in the signal-to-noise ratio, and so the pore geometry should be made comparable to the size of the target molecule. However, the pore geometry also affects the electric field, the charge density, the electro-osmotic flow, the capture volume, and the response time. Seeking an optimal pore geometry, we tracked the molecular motion in three dimensions with high resolution, visualizing with confocal microscopy the fluorescence associated with DNA translocating through nanopores with diameters comparable to the double helix, while simultaneously measuring the pore current. Measurements reveal single molecules translocating across the membrane through the pore commensurate with the observation of a current blockade. To explain the motion of the molecule near the pore, finite-element simulations were employed that account for diffusion, electrophoresis, and the electro-osmotic flow. According to this analysis, detection using a nanopore comparable in diameter to the double helix represents a compromise between sensitivity, capture volume, the minimum detectable concentration, and response time.
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Affiliation(s)
- Volker Kurz
- Departments of Electrical Engineering and Biological Science, University of Notre Dame, Notre Dame, Indiana 46556, United States
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50
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Abstract
We have used scanning force microscopy (SFM) to elucidate the dynamic behavior of open (torsionally unconstrained) circular and long linear DNA molecules during the relaxation process following adsorption onto mica. We find that bending stress and excluded volume effects drive the conformational equilibration via segmental out-of-plane dynamics.
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Affiliation(s)
- Willem Vanderlinden
- Laboratory of Photochemistry and Spectroscopy, Division of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium.
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