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Rajendran A, Krishnamurthy K, Park S, Nakata E, Kwon Y, Morii T. Topologically‐Interlocked Minicircles as Probes of DNA Topology and DNA‐Protein Interactions. Chemistry 2022; 28:e202200108. [DOI: 10.1002/chem.202200108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Indexed: 12/30/2022]
Affiliation(s)
| | | | - Seojeong Park
- College of Pharmacy Ewha Womans University Seoul 120-750 Republic of Korea
| | - Eiji Nakata
- Institute of Advanced Energy Kyoto University Uji Kyoto, 611–0011 Japan
| | - Youngjoo Kwon
- College of Pharmacy Ewha Womans University Seoul 120-750 Republic of Korea
| | - Takashi Morii
- Institute of Advanced Energy Kyoto University Uji Kyoto, 611–0011 Japan
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Abrosimova LA, Kuznetsov NA, Astafurova NA, Samsonova AR, Karpov AS, Perevyazova TA, Oretskaya TS, Fedorova OS, Kubareva EA. Kinetic Analysis of the Interaction of Nicking Endonuclease BspD6I with DNA. Biomolecules 2021; 11:1420. [PMID: 34680052 PMCID: PMC8533099 DOI: 10.3390/biom11101420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/03/2022] Open
Abstract
Nicking endonucleases (NEs) are enzymes that incise only one strand of the duplex to produce a DNA molecule that is 'nicked' rather than cleaved in two. Since these precision tools are used in genetic engineering and genome editing, information about their mechanism of action at all stages of DNA recognition and phosphodiester bond hydrolysis is essential. For the first time, fast kinetics of the Nt.BspD6I interaction with DNA were studied by the stopped-flow technique, and changes of optical characteristics were registered for the enzyme or DNA molecules. The role of divalent metal cations was estimated at all steps of Nt.BspD6I-DNA complex formation. It was demonstrated that divalent metal ions are not required for the formation of a non-specific complex of the protein with DNA. Nt.BspD6I bound five-fold more efficiently to its recognition site in DNA than to a random DNA. DNA bending was confirmed during the specific binding of Nt.BspD6I to a substrate. The optimal size of Nt.BspD6I's binding site in DNA as determined in this work should be taken into account in methods of detection of nucleic acid sequences and/or even various base modifications by means of NEs.
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Affiliation(s)
- Liudmila A. Abrosimova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (N.A.A.); (A.S.K.)
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia;
| | - Natalia A. Astafurova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (N.A.A.); (A.S.K.)
| | | | - Andrey S. Karpov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (N.A.A.); (A.S.K.)
| | - Tatiana A. Perevyazova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya Str. 3, 142290 Puschino, Russia;
| | - Tatiana S. Oretskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (T.S.O.); (E.A.K.)
| | - Olga S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia;
| | - Elena A. Kubareva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (T.S.O.); (E.A.K.)
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3
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Das B, Banerjee K, Gangopadhyay G. On the Role of Magnesium Ions in the DNA-Scissoring Activity of the Restriction Endonuclease ApaI: Stochastic Kinetics from a Single Molecule to Mesoscopic Paradigm. J Phys Chem B 2021; 125:4099-4107. [PMID: 33861609 DOI: 10.1021/acs.jpcb.0c10643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biochemical reactions occurring inside cells have significant stochastic signatures due to the low copy number of reacting species. Kinetics of DNA cleavage by restriction endonucleases are no exception as established by single-molecule experiments. Here, we propose a simple reaction scheme to understand the role of the cofactor magnesium ion in the action of the endonuclease ApaI. The methodology is based on the waiting time distribution of cleavage product formation that enables us to determine the corresponding rate both analytically and numerically. The theory is developed at the single-molecule level and then generalized to the biologically relevant case of a population of DNA-endonuclease complexes present inside a cell. The theoretical rate versus cofactor concentration curve is matched with relevant single-molecule experimental data that reveals positive cooperativity of cofactor binding and provides a reliable estimate of model parameters. Furthermore, a parameter range is identified where the dispersion of the waiting time, measured using the coefficient of variation, is significantly lower than the Poisson limit and becomes minimum at the in vivo magnesium ion concentration level. Such low dispersion can play a role in the robust DNA-scissoring activity of ApaI under in vivo conditions.
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Affiliation(s)
- Biswajit Das
- S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake City, Kolkata 700106, India
| | - Kinshuk Banerjee
- Department of Chemistry, Acharya Jagadish Chandra Bose College, Kolkata 700020, India
| | - Gautam Gangopadhyay
- S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake City, Kolkata 700106, India
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4
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Ferreira RM, Ware AD, Matozel E, Price AC. Salt concentration modulates the DNA target search strategy of NdeI. Biochem Biophys Res Commun 2020; 534:1059-1063. [PMID: 33121681 DOI: 10.1016/j.bbrc.2020.10.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 10/14/2020] [Indexed: 11/29/2022]
Abstract
DNA target search is a key step in cellular transactions that access genomic information. How DNA binding proteins combine 3D diffusion, sliding and hopping into an overall search strategy remains poorly understood. Here we report the use of a single molecule DNA tethering method to characterize the target search kinetics of the type II restriction endonuclease NdeI. The measured search rate depends strongly on DNA length as well as salt concentration. Using roadblocks, we show that there are significant changes in the DNA sliding length over the salt concentrations in our study. To explain our results, we propose a model including cycles of 3D and 1D search in which salt concentration modulates the strategy by varying the length of DNA probed per 1D scan. At low salt NdeI makes a single non-specific encounter with DNA followed by an effective and complete 1D scan. At higher salt, NdeI must execute multiple cycles of target search due to the reduced efficacy of 1D search.
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Affiliation(s)
- Raquel M Ferreira
- Department of Biology, Emmanuel College, 400 the Fenway, Boston, MA, 02115, United States
| | - Anna D Ware
- Department of Biology, Emmanuel College, 400 the Fenway, Boston, MA, 02115, United States
| | - Emily Matozel
- Department of Biology, Emmanuel College, 400 the Fenway, Boston, MA, 02115, United States
| | - Allen C Price
- Department of Chemistry and Physics, Emmanuel College, 400 the Fenway, Boston, MA, 02115, United States.
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5
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Piatt SC, Loparo JJ, Price AC. The Role of Noncognate Sites in the 1D Search Mechanism of EcoRI. Biophys J 2019; 116:2367-2377. [PMID: 31113551 PMCID: PMC6588823 DOI: 10.1016/j.bpj.2019.04.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 04/18/2019] [Accepted: 04/29/2019] [Indexed: 02/02/2023] Open
Abstract
A one-dimensional (1D) search is an essential step in DNA target recognition. Theoretical studies have suggested that the sequence dependence of 1D diffusion can help resolve the competing demands of a fast search and high target affinity, a conflict known as the speed-selectivity paradox. The resolution requires that the diffusion energy landscape is correlated with the underlying specific binding energies. In this work, we report observations of a 1D search by quantum dot-labeled EcoRI. Our data supports the view that proteins search DNA via rotation-coupled sliding over a corrugated energy landscape. We observed that whereas EcoRI primarily slides along DNA at low salt concentrations, at higher concentrations, its diffusion is a combination of sliding and hopping. We also observed long-lived pauses at genomic star sites, which differ by a single nucleotide from the target sequence. To reconcile these observations with prior biochemical and structural data, we propose a model of search in which the protein slides over a sequence-independent energy landscape during fast search but rapidly interconverts with a "hemispecific" binding mode in which a half site is probed. This half site interaction stabilizes the transition to a fully specific mode of binding, which can then lead to target recognition.
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Affiliation(s)
- Sadie C Piatt
- Department of Chemistry and Physics, Emmanuel College, Boston, Massachusetts
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts.
| | - Allen C Price
- Department of Chemistry and Physics, Emmanuel College, Boston, Massachusetts.
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6
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Pikin SA, Pikina ES. On DNA Motions under Action of Enzymes of Different Types. II. CRYSTALLOGR REP+ 2019. [DOI: 10.1134/s106377451901019x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Štěpán J, Kabelka I, Koča J, Kulhánek P. Behavior of BsoBI endonuclease in the presence and absence of DNA. J Mol Model 2017; 24:22. [PMID: 29264670 DOI: 10.1007/s00894-017-3557-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/01/2017] [Indexed: 11/28/2022]
Abstract
BsoBI is a type II restriction endonuclease belonging to the EcoRI family. There is only one previously published X-ray structure for this endonuclease: it shows a homodimer of BsoBI completely encircling DNA in a tunnel. In this work, molecular dynamics simulations were employed to elucidate possible ways in which DNA is loaded into this complex prior to its cleavage. We found that the dimer does not open spontaneously when DNA is removed from the complex on the timescale of our simulations (~ 0.5 μs). A biased simulation had to be used to facilitate the opening, which revealed a possible way for the two catalytic domains to separate. The α-helices connecting the catalytic and helical domains were found to act as a hinge during the separation. In addition, we found that the opening of the BsoBI dimer was influenced by the type of counterions present in the environment. A reference simulation of the BsoBI/DNA complex further showed spontaneous reorganization of the active sites due to the binding of solvent ions, which led to an active-site structure consistent with other experimental structures of type II restriction endonucleases determined in the presence of metal ions.
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Affiliation(s)
- Jakub Štěpán
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Ivo Kabelka
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Jaroslav Koča
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Petr Kulhánek
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic. .,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
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8
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Wang D, Miyazono KI, Tanokura M. Tetrameric structure of the restriction DNA glycosylase R.PabI in complex with nonspecific double-stranded DNA. Sci Rep 2016; 6:35197. [PMID: 27731370 PMCID: PMC5059719 DOI: 10.1038/srep35197] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/26/2016] [Indexed: 02/06/2023] Open
Abstract
R.PabI is a type II restriction enzyme that recognizes the 5′-GTAC-3′ sequence and belongs to the HALFPIPE superfamily. Although most restriction enzymes cleave phosphodiester bonds at specific sites by hydrolysis, R.PabI flips the guanine and adenine bases of the recognition sequence out of the DNA helix and hydrolyzes the N-glycosidic bond of the flipped adenine in a similar manner to DNA glycosylases. In this study, we determined the structure of R.PabI in complex with double-stranded DNA without the R.PabI recognition sequence by X-ray crystallography. The 1.9 Å resolution structure of the complex showed that R.PabI forms a tetrameric structure to sandwich the double-stranded DNA and the tetrameric structure is stabilized by four salt bridges. DNA binding and DNA glycosylase assays of the R.PabI mutants showed that the residues that form the salt bridges (R70 and D71) are essential for R.PabI to find the recognition sequence from the sea of nonspecific sequences. R.PabI is predicted to utilize the tetrameric structure to bind nonspecific double-stranded DNA weakly and slide along it to find the recognition sequence.
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Affiliation(s)
- Delong Wang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ken-Ichi Miyazono
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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9
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Mechetin GV, Zharkov DO. Mechanisms of diffusional search for specific targets by DNA-dependent proteins. BIOCHEMISTRY (MOSCOW) 2015; 79:496-505. [PMID: 25100007 DOI: 10.1134/s0006297914060029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
To perform their functions, many DNA-dependent proteins have to quickly locate specific targets against the vast excess of nonspecific DNA. Although this problem was first formulated over 40 years ago, the mechanism of such search remains one of the unsolved fundamental problems in the field of protein-DNA interactions. Several complementary mechanisms have been suggested: sliding, based on one-dimensional random diffusion along the DNA contour; hopping, in which the protein "jumps" between the closely located DNA fragments; macroscopic association-dissociation of the protein-DNA complex; and intersegmental transfer. This review covers the modern state of the problem of target DNA search, theoretical descriptions, and methods of research at the macroscopic (molecule ensembles) and microscopic (individual molecules) levels. Almost all studied DNA-dependent proteins search for specific targets by combined three-dimensional diffusion and one-dimensional diffusion along the DNA contour.
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Affiliation(s)
- G V Mechetin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
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10
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Pingoud A, Wilson GG, Wende W. Type II restriction endonucleases--a historical perspective and more. Nucleic Acids Res 2014; 42:7489-527. [PMID: 24878924 PMCID: PMC4081073 DOI: 10.1093/nar/gku447] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/02/2014] [Accepted: 05/07/2014] [Indexed: 12/17/2022] Open
Abstract
This article continues the series of Surveys and Summaries on restriction endonucleases (REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II' REases, the kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what they do, and how they do it. Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby. The discoveries of these enzymes in the 1970s, and of the uses to which they could be put, have since impacted every corner of the life sciences. They became the enabling tools of molecular biology, genetics and biotechnology, and made analysis at the most fundamental levels routine. Hundreds of different REases have been discovered and are available commercially. Their genes have been cloned, sequenced and overexpressed. Most have been characterized to some extent, but few have been studied in depth. Here, we describe the original discoveries in this field, and the properties of the first Type II REases investigated. We discuss the mechanisms of sequence recognition and catalysis, and the varied oligomeric modes in which Type II REases act. We describe the surprising heterogeneity revealed by comparisons of their sequences and structures.
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Affiliation(s)
- Alfred Pingoud
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - Geoffrey G Wilson
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938-2723, USA
| | - Wolfgang Wende
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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11
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Naganathan AN, Orozco M. The Conformational Landscape of an Intrinsically Disordered DNA-Binding Domain of a Transcription Regulator. J Phys Chem B 2013; 117:13842-50. [DOI: 10.1021/jp408350v] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Athi N. Naganathan
- Department
of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
| | - Modesto Orozco
- IRB-BSC
Joint Research Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain
- Department
of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain
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12
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Kanev I, Mei WN, Mizuno A, DeHaai K, Sanmann J, Hess M, Starr L, Grove J, Dave B, Sanger W. Searching for electrical properties, phenomena and mechanisms in the construction and function of chromosomes. Comput Struct Biotechnol J 2013; 6:e201303007. [PMID: 24688715 PMCID: PMC3962117 DOI: 10.5936/csbj.201303007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 06/09/2013] [Accepted: 06/13/2013] [Indexed: 12/22/2022] Open
Abstract
OUR STUDIES REVEAL PREVIOUSLY UNIDENTIFIED ELECTRICAL PROPERTIES OF CHROMOSOMES: (1) chromosomes are amazingly similar in construction and function to electrical transformers; (2) chromosomes possess in their construction and function, components similar to those of electric generators, conductors, condensers, switches, and other components of electrical circuits; (3) chromosomes demonstrate in nano-scale level electromagnetic interactions, resonance, fusion and other phenomena similar to those described by equations in classical physics. These electrical properties and phenomena provide a possible explanation for unclear and poorly understood mechanisms in clinical genetics including: (a) electrically based mechanisms responsible for breaks, translocations, fusions, and other chromosomal abnormalities associated with cancer, intellectual disability, infertility, pregnancy loss, Down syndrome, and other genetic disorders; (b) electrically based mechanisms involved in crossing over, non-disjunction and other events during meiosis and mitosis; (c) mechanisms demonstrating heterochromatin to be electrically active and genetically important.
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Affiliation(s)
- Ivan Kanev
- Human Genetics Laboratory, Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5440, USA
| | - Wai-Ning Mei
- Department of physics, University of Nebraska at Omaha, Nebraska, 68182, USA
| | - Akira Mizuno
- Applied Electrostatics Laboratory, Department of Environmental and Life Sciences, Toyohashi University of Technology, Tempaku-cyo, Toyohashi, Aichi, 441-8580, Japan
| | - Kristi DeHaai
- Human Genetics Laboratory, Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5440, USA
| | - Jennifer Sanmann
- Human Genetics Laboratory, Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5440, USA
| | - Michelle Hess
- Human Genetics Laboratory, Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5440, USA
| | - Lois Starr
- Human Genetics Laboratory, Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5440, USA
| | - Jennifer Grove
- Human Genetics Laboratory, Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5440, USA
| | - Bhavana Dave
- Human Genetics Laboratory, Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5440, USA
| | - Warren Sanger
- Human Genetics Laboratory, Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5440, USA
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13
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Malygin EG, Hattman S. DNA methyltransferases: mechanistic models derived from kinetic analysis. Crit Rev Biochem Mol Biol 2012; 47:97-193. [PMID: 22260147 DOI: 10.3109/10409238.2011.620942] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The sequence-specific transfer of methyl groups from donor S-adenosyl-L-methionine (AdoMet) to certain positions of DNA-adenine or -cytosine residues by DNA methyltransferases (MTases) is a major form of epigenetic modification. It is virtually ubiquitous, except for some notable exceptions. Site-specific methylation can be regarded as a means to increase DNA information capacity and is involved in a large spectrum of biological processes. The importance of these functions necessitates a deeper understanding of the enzymatic mechanism(s) of DNA methylation. DNA MTases fall into one of two general classes; viz. amino-MTases and [C5-cytosine]-MTases. Amino-MTases, common in prokaryotes and lower eukaryotes, catalyze methylation of the exocyclic amino group of adenine ([N6-adenine]-MTase) or cytosine ([N4-cytosine]-MTase). In contrast, [C5-cytosine]-MTases methylate the cyclic carbon-5 atom of cytosine. Characteristics of DNA MTases are highly variable, differing in their affinity to their substrates or reaction products, their kinetic parameters, or other characteristics (order of substrate binding, rate limiting step in the overall reaction). It is not possible to present a unifying account of the published kinetic analyses of DNA methylation because different authors have used different substrate DNAs and/or reaction conditions. Nevertheless, it would be useful to describe those kinetic data and the mechanistic models that have been derived from them. Thus, this review considers in turn studies carried out with the most consistently and extensively investigated [N6-adenine]-, [N4-cytosine]- and [C5-cytosine]-DNA MTases.
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Affiliation(s)
- Ernst G Malygin
- Institute of Molecular Biology, State Research Center of Virology and Biotechnology Vector, Novosibirsk, Russia
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14
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Ramakrishnan V, Rajagopalan R. Dynamics and thermodynamics of water around EcoRI bound to a minimally mutated DNA chain. Phys Chem Chem Phys 2012; 14:12277-84. [DOI: 10.1039/c2cp41638g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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15
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Uyar A, Kurkcuoglu O, Nilsson L, Doruker P. The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases. Phys Biol 2011; 8:056001. [PMID: 21791727 DOI: 10.1088/1478-3975/8/5/056001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The vibrational dynamics of various type II restriction endonucleases, in complex with cognate/non-cognate DNA and in the apo form, are investigated with the elastic network model in order to reveal common functional mechanisms in this enzyme family. Scissor-like and tong-like motions observed in the slowest modes of all enzymes and their complexes point to common DNA recognition and cleavage mechanisms. Normal mode analysis further points out that the scissor-like motion has an important role in differentiating between cognate and non-cognate sequences at the recognition site, thus implying its catalytic relevance. Flexible regions observed around the DNA-binding site of the enzyme usually concentrate on the highly conserved β-strands, especially after DNA binding. These β-strands may have a structurally stabilizing role in functional dynamics for target site recognition and cleavage. In addition, hot spot residues based on high-frequency modes reveal possible communication pathways between the two distant cleavage sites in the enzyme family. Some of these hot spots also exist on the shortest path between the catalytic sites and are highly conserved.
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Affiliation(s)
- A Uyar
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, 34342 Bebek, Istanbul, Turkey
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16
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Sasnauskas G, Kostiuk G, Tamulaitis G, Siksnys V. Target site cleavage by the monomeric restriction enzyme BcnI requires translocation to a random DNA sequence and a switch in enzyme orientation. Nucleic Acids Res 2011; 39:8844-56. [PMID: 21771860 PMCID: PMC3203586 DOI: 10.1093/nar/gkr588] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Endonucleases that generate double-strand breaks in DNA often possess two identical subunits related by rotational symmetry, arranged so that the active sites from each subunit act on opposite DNA strands. In contrast to many endonucleases, Type IIP restriction enzyme BcnI, which recognizes the pseudopalindromic sequence 5′-CCSGG-3′ (where S stands for C or G) and cuts both DNA strands after the second C, is a monomer and possesses a single catalytic center. We show here that to generate a double-strand break BcnI nicks one DNA strand, switches its orientation on DNA to match the polarity of the second strand and then cuts the phosphodiester bond on the second DNA strand. Surprisingly, we find that an enzyme flip required for the second DNA strand cleavage occurs without an excursion into bulk solution, as the same BcnI molecule acts processively on both DNA strands. We provide evidence that after cleavage of the first DNA strand, BcnI remains associated with the nicked intermediate and relocates to the opposite strand by a short range diffusive hopping on DNA.
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Affiliation(s)
- Giedrius Sasnauskas
- Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
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17
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Suzuki Y, Yokokawa M, Yoshimura SH, Takeyasu K. Biological Application of Fast-Scanning Atomic Force Microscopy. SCANNING PROBE MICROSCOPY IN NANOSCIENCE AND NANOTECHNOLOGY 2 2011. [DOI: 10.1007/978-3-642-10497-8_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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18
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Rau DC, Sidorova NY. Diffusion of the restriction nuclease EcoRI along DNA. J Mol Biol 2009; 395:408-16. [PMID: 19874828 DOI: 10.1016/j.jmb.2009.10.049] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 10/20/2009] [Accepted: 10/22/2009] [Indexed: 10/20/2022]
Abstract
Many specific sequence DNA binding proteins locate their target sequence by first binding to DNA nonspecifically, then by linearly diffusing or hopping along DNA until either the protein dissociates from the DNA or it finds the recognition sequence. We have devised a method for measuring one-dimensional diffusion along DNA based on the ratio of the dissociation rate of protein from DNA fragments containing one specific binding site to the dissociation rate from DNA fragments containing two specific binding sites. Our extensive measurements of dissociation rates and specific-nonspecific relative binding constants of the restriction nuclease EcoRI enable us to determine the diffusion rate of nonspecifically bound protein along the DNA. By varying the distance between the two binding sites, we confirm a linear diffusion mechanism. The sliding rate is relatively insensitive to salt concentration and osmotic pressure, indicating that the protein moves smoothly along the DNA probably following the helical phosphate-sugar backbone of DNA. We calculate a diffusion coefficient for EcoRI of 3 x 10(4) bp(2) s(-)(1) EcoRI is able to diffuse approximately 150 bp, on average, along the DNA in 1 s. This diffusion rate is about 2000-fold slower than the diffusion of free protein in solution. A factor of 40-50 can be accounted for by rotational friction resulting from following the helical path of the DNA backbone. Two possibilities could account for the remaining activation energy: salt bridges between the DNA and the protein are transiently broken, or the water structure at the protein-DNA interface is disrupted as the two surfaces move past each other.
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Affiliation(s)
- Donald C Rau
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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19
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Keum JW, Bermudez H. Enhanced resistance of DNA nanostructures to enzymatic digestion. Chem Commun (Camb) 2009:7036-8. [PMID: 19904386 DOI: 10.1039/b917661f] [Citation(s) in RCA: 198] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The ability of nucleases to perform their catalytic functions depends on the sequence and structural features of target DNA substrates. Due to their size and shape, several DNA tetrahedra are resistant to the action of specific and non-specific nucleases. Such enhanced stability is a key requirement for DNA nanostructures to be useful as delivery vehicles.
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Affiliation(s)
- Jung-Won Keum
- Department of Chemical Engineering, University of Massachusetts, Amherst, MA, USA
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20
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Pikin SA. On the distinction of the mechanisms of DNA cleavage by restriction enzymes—The I-, II-, and III-type molecular motors. CRYSTALLOGR REP+ 2008. [DOI: 10.1134/s1063774508050222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Bonnet I, Biebricher A, Porté PL, Loverdo C, Bénichou O, Voituriez R, Escudé C, Wende W, Pingoud A, Desbiolles P. Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA. Nucleic Acids Res 2008; 36:4118-27. [PMID: 18544605 PMCID: PMC2475641 DOI: 10.1093/nar/gkn376] [Citation(s) in RCA: 151] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The restriction endonuclease EcoRV can rapidly locate a short recognition site within long non-cognate DNA using 'facilitated diffusion'. This process has long been attributed to a sliding mechanism, in which the enzyme first binds to the DNA via nonspecific interaction and then moves along the DNA by 1D diffusion. Recent studies, however, provided evidence that 3D translocations (hopping/jumping) also help EcoRV to locate its target site. Here we report the first direct observation of sliding and jumping of individual EcoRV molecules along nonspecific DNA. Using fluorescence microscopy, we could distinguish between a slow 1D diffusion of the enzyme and a fast translocation mechanism that was demonstrated to stem from 3D jumps. Salt effects on both sliding and jumping were investigated, and we developed numerical simulations to account for both the jump frequency and the jump length distribution. We deduced from our study the 1D diffusion coefficient of EcoRV, and we estimated the number of jumps occurring during an interaction event with nonspecific DNA. Our results substantiate that sliding alternates with hopping/jumping during the facilitated diffusion of EcoRV and, furthermore, set up a framework for the investigation of target site location by other DNA-binding proteins.
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Affiliation(s)
- Isabelle Bonnet
- Laboratoire Kastler Brossel, ENS, UPMC-Paris 6, CNRS UMR 8552, France
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22
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A spectroscopic method to determine the activity of the restriction endonuclease EcoRV that involves a single reaction. Anal Biochem 2008; 497:103-5. [PMID: 18489897 DOI: 10.1016/j.ab.2008.04.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Revised: 04/20/2008] [Accepted: 04/24/2008] [Indexed: 11/23/2022]
Abstract
A one-step protocol is presented to determine the activity of EcoRV as a model of restriction enzymes. The protocol involved a molecular beacon as DNA substrate, with the target sequence recognized by EcoRV in the stem. EcoRV cleaved the stem forming two fragments, one of which contained the fluorophore and quencher, initially bound by 3 bp. This shorter fragment rapidly dissociated at 37 °C, causing an increase of fluorescence intensity that was used to gauge the reaction kinetics. The reaction can be described using the Michaelis-Menten mechanism, and the kinetic parameters obtained were compared with literature values involving other protocols.
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23
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Rezania V, Tuszynski J, Hendzel M. Modeling transcription factor binding events to DNA using a random walker/jumper representation on a 1D/2D lattice with different affinity sites. Phys Biol 2007; 4:256-67. [PMID: 18185004 DOI: 10.1088/1478-3975/4/4/003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Surviving in a diverse environment requires corresponding organism responses. At the cellular level, such adjustment relies on the transcription factors (TFs) which must rapidly find their target sequences amidst a vast amount of non-relevant sequences on DNA molecules. Whether these transcription factors locate their target sites through a 1D or 3D pathway is still a matter of speculation. It has been suggested that the optimum search time is when the protein equally shares its search time between 1D and 3D diffusions. In this paper, we study the above problem using Monte Carlo simulations by considering a simple physical model. A 1D strip, representing a DNA, with a number of low affinity sites, corresponding to non-target sites, and high affinity sites, corresponding to target sites, is considered and later extended to a 2D strip. We study the 1D and 3D exploration pathways, and combinations thereof by considering three different types of molecules: a walker that randomly walks along the strip with no dissociation; a jumper that represents dissociation and then re-association of a TF with the strip at later time at a distant site; and a hopper that is similar to the jumper but it dissociates and then re-associates at a faster rate than the jumper. We analyze the final probability distribution of molecules for each case and find that TFs can locate their targets on the experimental time scale even if they spend only 15% of their search time diffusing freely in the solution. This agrees with recent experimental results obtained by Elf et al (2007 Science 316 1191) and is in contrast to previously reported theoretical predictions. Our results also agree with the experimental evidence for the role of chaperons and proteasomes in stabilizing and destabilizing TFs binding, respectively, during the regulation process. Therefore, the results of our manuscript can provide a refined theoretical framework for the process.
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Affiliation(s)
- Vahid Rezania
- Division of Experimental Oncology, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada.
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24
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25
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26
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Steiniger M, Adams CD, Marko JF, Reznikoff WS. Defining characteristics of Tn5 Transposase non-specific DNA binding. Nucleic Acids Res 2006; 34:2820-32. [PMID: 16717287 PMCID: PMC1464417 DOI: 10.1093/nar/gkl179] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
While non-specific DNA plays a role in target localization for many recombinases, transcription factors and restriction enzymes, the importance of non-specific DNA interactions for transposases has not been investigated. Here, we discuss non-specific DNA-Tn5 Transposase (Tnp) interactions and suggest how they stabilize the Tnp and modulate Tnp localization of the 19 bp Tnp recognition end sequences (ESes). DNA protection assays indicate that full-length Tnp interacts efficiently with supercoiled DNA that does not contain ESes. These interactions significantly prolong the lifetime of Tnp, in vitro. The balance between non-specific DNA bound and free Tnp is affected by DNA topology, yet, intermolecular transfer of active Tnp occurs with both supercoiled and linear non-specific DNA. Experiments with substrates of varying lengths show that Tn5 Tnp can utilize non-specific DNA to facilitate localization of an intramolecular ES over distances less than 464 bp. Finally, synaptic complex formation is inhibited in the presence of increasing concentrations of supercoiled and linear pUC19. These experiments strongly suggest that Tn5 Tnp has a robust non-specific DNA binding activity, that non-specific DNA modulates ES sequence localization within the global DNA, most likely through a direct transfer mechanism, and that non-specific DNA binding may play a role in the cis bias manifested by Tn5 transposition.
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Affiliation(s)
| | | | - John F. Marko
- Department of Physics, University of Illinois at ChicagoChicago, IL 60607, USA
| | - William S. Reznikoff
- To whom correspondence should be addressed. Tel: +1 608 262 3608; Fax: +1 608 265 2603;
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27
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Hu T, Grosberg AY, Shklovskii BI. How proteins search for their specific sites on DNA: the role of DNA conformation. Biophys J 2006; 90:2731-44. [PMID: 16461402 PMCID: PMC1414577 DOI: 10.1529/biophysj.105.078162] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is known since the early days of molecular biology that proteins locate their specific targets on DNA up to two orders-of-magnitude faster than the Smoluchowski three-dimensional diffusion rate. An accepted explanation of this fact is that proteins are nonspecifically adsorbed on DNA, and sliding along DNA provides for the faster one-dimensional search. Surprisingly, the role of DNA conformation was never considered in this context. In this article, we explicitly address the relative role of three-dimensional diffusion and one-dimensional sliding along coiled or globular DNA and the possibility of correlated readsorption of desorbed proteins. We have identified a wealth of new different scaling regimes. We also found the maximal possible acceleration of the reaction due to sliding. We found that the maximum on the rate-versus-ionic strength curve is asymmetric, and that sliding can lead not only to acceleration, but also in some regimes to dramatic deceleration of the reaction.
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Affiliation(s)
- Tao Hu
- Department of Physics, and William I. Fine Theoretical Physics Institute, University of Minnesota, Minneapolis, USA
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28
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Kampmann M. Facilitated diffusion in chromatin lattices: mechanistic diversity and regulatory potential. Mol Microbiol 2005; 57:889-99. [PMID: 16091032 DOI: 10.1111/j.1365-2958.2005.04707.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The interaction between a protein and a specific DNA site is the molecular basis for vital processes in all organisms. Location of the DNA target site by the protein commonly involves facilitated diffusion. Mechanisms of facilitated diffusion vary among proteins; they include one- and two-dimensional sliding along DNA, direct transfer between uncorrelated sites, as well as combinations of these mechanisms. Facilitated diffusion has almost exclusively been studied in vitro. This review discusses facilitated diffusion in the context of the living cell and proposes a theoretical model for facilitated diffusion in chromatin lattices. Chromatin structure differentially affects proteins in different modes of diffusion. The interplay of facilitated diffusion and chromatin structure can determine the rate of protein association with the target site, the frequency of association-dissociation events at the target site, and, under particular conditions, the occupancy of the target site. Facilitated diffusion is required in vivo for efficient DNA repair and bacteriophage restriction and has potential roles in fine-tuning gene regulatory networks and kinetically compartmentalizing the eukaryotic nucleus.
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Affiliation(s)
- Martin Kampmann
- The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.
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29
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Zharkov DO, Grollman AP. The DNA trackwalkers: principles of lesion search and recognition by DNA glycosylases. Mutat Res 2005; 577:24-54. [PMID: 15939442 DOI: 10.1016/j.mrfmmm.2005.03.011] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Revised: 03/28/2005] [Accepted: 03/29/2005] [Indexed: 11/24/2022]
Abstract
DNA glycosylases, the pivotal enzymes in base excision repair, are faced with the difficult task of recognizing their substrates in a large excess of unmodified DNA. We present here a kinetic analysis of DNA glycosylase substrate specificity, based on the probability of error. This novel approach to this subject explains many features of DNA surveillance and catalysis of lesion excision by DNA glycosylases. This approach also is applicable to the general issue of substrate specificity. We discuss determinants of substrate specificity in damaged DNA and in the enzyme, as well as methods by which these determinants can be identified.
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Affiliation(s)
- Dmitry O Zharkov
- Laboratory of Repair Enzymes, SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.
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30
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Sidorova NY, Rau DC. Differences between EcoRI nonspecific and "star" sequence complexes revealed by osmotic stress. Biophys J 2004; 87:2564-76. [PMID: 15454451 PMCID: PMC1304675 DOI: 10.1529/biophysj.104.042390] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2004] [Accepted: 07/26/2004] [Indexed: 11/18/2022] Open
Abstract
The binding of the restriction endonuclease EcoRI to DNA is exceptionally specific. Even a single basepair change ("star" sequence) from the recognition sequence, GAATTC, decreases the binding free energy of EcoRI to values nearly indistinguishable from nonspecific binding. The difference in the number of waters sequestered by the protein-DNA complexes of the "star" sequences TAATTC and CAATTC and by the specific sequence complex determined from the dependence of binding free energy on water activity is also practically indistinguishable at low osmotic pressures from the 110 water molecules sequestered by nonspecific sequence complexes. Novel measurements of the dissociation rates of noncognate sequence complexes and competition equilibrium show that sequestered water can be removed from "star" sequence complexes by high osmotic pressure, but not from a nonspecific complex. By 5 Osm, the TAATTC "star" sequence complex has lost almost 90 of the approximately 110 waters initially present. It is more difficult to remove water from the CAATTC "star" sequence complex. The sequence dependence of water loss correlates with the known sequence dependence of "star" cleavage activity.
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Affiliation(s)
- Nina Y Sidorova
- Laboratory of Physical and Structural Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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31
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Belotserkovskii BP, Zarling DA. Analysis of a one-dimensional random walk with irreversible losses at each step: applications for protein movement on DNA. J Theor Biol 2004; 226:195-203. [PMID: 14643189 DOI: 10.1016/j.jtbi.2003.08.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We analysed a one-dimensional random walk between two points when the migrating particle could be irreversibly lost (dissociated) from the system at each step of the process. We show that in the case of losses at each step the average number of steps made by the particle that reaches the final point does not obey quadratic dependence on the distance between the starting and the final points: for long distances this dependence is linear. This is because losses "select" for shorter pathways between the starting and the final points. We applied this analysis to protein translocations within long DNA molecules.
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32
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33
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Randell JC, Coen DM. Linear diffusion on DNA despite high-affinity binding by a DNA polymerase processivity factor. Mol Cell 2001; 8:911-20. [PMID: 11684025 DOI: 10.1016/s1097-2765(01)00355-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The oligomeric "sliding clamp" processivity factors, such as PCNA, are thought to rely on a loose, topological association with DNA to slide freely along dsDNA. Unlike PCNA, the processivity subunit of the herpes simplex virus DNA polymerase, UL42, is a monomer and has an intrinsic affinity for dsDNA that is remarkably high for a sequence-independent DNA binding protein. Using a DNase footprinting assay, we demonstrate that UL42 translocates with the catalytic subunit of the polymerase during chain elongation. In addition, footprinting and electrophoretic mobility shift assays show that, despite its tight DNA binding, UL42 is capable of linear diffusion on DNA at a rate of between 17 and 47 bp/s. Our results thus suggest that, despite profound biochemical differences with the sliding clamps, UL42 can freely slide downstream with the catalytic subunit during DNA replication.
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Affiliation(s)
- J C Randell
- Committee on Virology and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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34
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Sidorova NY, Rau DC. Linkage of EcoRI dissociation from its specific DNA recognition site to water activity, salt concentration, and pH: separating their roles in specific and non-specific binding. J Mol Biol 2001; 310:801-16. [PMID: 11453689 DOI: 10.1006/jmbi.2001.4781] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have measured the dependencies of both the dissociation rate of specifically bound EcoRI endonuclease and the ratio of non-specific and specific association constants on water activity, salt concentration, and pH in order to distinguish the contributions of these solution components to specific and non-specific binding. For proteins such as EcoRI that locate their specific recognition site efficiently by diffusing along non-specific DNA, the specific site dissociation rate can be separated into two steps: an equilibrium between non-specific and specific binding of the enzyme to DNA, and the dissociation of non-specifically bound protein. We demonstrated previously that the osmotic dependence of the dissociation rate is dominated by the equilibrium between specific and non-specific binding that is independent of the osmolyte nature. The remaining osmotic sensitivity linked to the dissociation of non-specifically bound protein depends significantly on the particular osmolyte used, indicating a change in solute-accessible surface area. In contrast, the dissociation of non-specifically bound enzyme accounts for almost all the pH and salt-dependencies. We observed virtually no pH-dependence of the equilibrium between specific and non-specific binding measured by the competition assay. The observed weak salt-sensitivity of the ratio of specific and non-specific association constants is consistent with an osmotic, rather than electrostatic, action. The seeming lack of a dependence on viscosity suggests the rate-limiting step in dissociation of non-specifically bound protein is a discrete conformational change rather than a general diffusion of the protein away from the DNA.
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Affiliation(s)
- N Y Sidorova
- Laboratory of Physical and Structural Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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35
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Burdzy K, Hołyst R. Mechanisms for facilitated target location and the optimal number of molecules in the diffusion search process. PHYSICAL REVIEW E 2001; 64:011914. [PMID: 11461295 DOI: 10.1103/physreve.64.011914] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2001] [Indexed: 11/07/2022]
Abstract
We investigate the number N of molecules needed to perform independent diffusion in order to achieve bonding of a single molecule to a specific site in time t(0). For a certain range of values of t(0), an increase from N to kN molecules (k>1) results in the decrease of search time from t(0) to t(0)/k. In this regime, increasing the number of molecules is an effective way of speeding up the search process. However when N> or =N0 (optimal number of N) the reduction of time from t(0) to t(0)/k can be achieved only by an exponentially large increase in the number of molecules [from N to N exp(ck) for some c>0].
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Affiliation(s)
- K Burdzy
- Department of Mathematics, University of Washington, Box 354350, Seattle, Washington 98195-4350, USA.
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36
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Gowher H, Jeltsch A. Molecular enzymology of the EcoRV DNA-(Adenine-N (6))-methyltransferase: kinetics of DNA binding and bending, kinetic mechanism and linear diffusion of the enzyme on DNA. J Mol Biol 2000; 303:93-110. [PMID: 11021972 DOI: 10.1006/jmbi.2000.4127] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The EcoRV DNA-(adenine-N(6))-methyltransferase recognizes GATATC sequences and modifies the first adenine residue within this site. We show here, that the enzyme binds to the DNA and the cofactor S-adenosylmethionine (AdoMet) in an ordered bi-bi fashion, with AdoMet being bound first. M.EcoRV binds DNA in a non-specific manner and the enzyme searches for its recognition site by linear diffusion with a range of approximately 1800 bp. During linear diffusion the enzyme continuously scans the DNA for the presence of recognition sites. Upon specific M.EcoRV-DNA complex formation a strong increase in the fluorescence of an oligonucleotide containing a 2-aminopurine base analogue at the GAT-2AP-TC position is observed which, most likely, is correlated with DNA bending. In contrast to the GAT-2AP-TC substrate, a G-2AP-TATC substrate in which the target base is replaced by 2-aminopurine does not show an increase in fluorescence upon M.EcoRV binding, demonstrating that 2-aminopurine is not a general tool to detect base flipping. Stopped-flow experiments show that DNA bending is a fast process with rate constants >10 s(-1). In the presence of cofactor, the specific complex adopts a second conformation, in which the target sequence is more tightly contacted by the enzyme. M.EcoRV exists in an open and in a closed state that are in slow equilibrium. Closing the open state is a slow process (rate constant approximately 0.7 min(-1)) that limits the rate of DNA methylation under single turnover conditions. Product release requires opening of the closed complex which is very slow (rate constant approximately 0.05-0.1 min(-1)) and limits the rate of DNA methylation under multiple turnover conditions. M.EcoRV methylates DNA sequences containing more than one recognition sites in a distributive manner. Since the dissociation rate from non-specific DNA does not depend on the length of the DNA fragment, DNA dissociation does not preferentially occur at the ends of the DNA.
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Affiliation(s)
- H Gowher
- Institut für Biochemie, Fachbereich 8, Giessen, 35392, Germany
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37
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Abstract
This paper considers how enzymes that catalyze reactions at specific DNA sites have been engineered to overcome the problem of competitive inhibition by excess nonspecific binding sites on DNA. The formation of a specific protein-DNA recognition complex is discussed from both structural and thermodynamic perspectives, and contrasted with formation of nonspecific complexes. Evidence (from EcoRI and BamHI endonucleases) is presented that a wide variety of perturbations of the DNA substrate alter binding free energy but do not affect the free energy of activation for the chemical step; that is, many energetic factors contribute equally to the recognition complex and the transition-state complex. This implies that the specific recognition complex bears a close resemblance to the transition-state complex, such that very tight binding to the recognition site on the DNA substrate does not inhibit catalysis, but instead provides energy that is efficiently utilized along the path to the transition state. It is suggested that this view can be usefully extended to "noncatalytic" site-specific DNA-binding proteins like transcriptional activators and general transcription factors.
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Affiliation(s)
- L Jen-Jacobson
- Department of Biological Sciences, University of Pittsburgh, PA 15260, USA
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38
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Abstract
The central problem faced by DNA binding proteins is how to select the correct DNA sequence from the sea of nonspecific sequences in a cell. The problem is particularly acute for bacterial restriction enzymes because cleavage at an incorrect DNA site could be lethal. To understand the basis of this selectivity, we report here the crystal structure of endonuclease BamHI bound to noncognate DNA. We show that, despite only a single base pair change in the recognition sequence, the enzyme adopts an open configuration that is on the pathway between free and specifically bound forms of the enzyme. Surprisingly, the DNA drops out of the binding cleft with a total loss of base-specific and backbone contacts. Taken together, the structure provides a remarkable snapshot of an enzyme poised for linear diffusion (rather than cleavage) along the DNA.
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Affiliation(s)
- H Viadiu
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
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39
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Abstract
Steady-state parameters governing cleavage of pBR322 DNA by EcoRI endonuclease are highly sensitive to ionic environment, with K(m) and k(cat) increasing 1,000-fold and 15-fold, respectively, when ionic strength is increased from 0.059 to 0.23 M. By contrast, pre-steady-state analysis has shown that recognition, as well as first and second strand cleavage events that occur once the enzyme has arrived at the EcoRI site, are essentially insensitive to ionic strength, and has demonstrated that the rate-limiting step for endonuclease turnover occurs after double-strand cleavage under all conditions tested. Furthermore, processive cleavage of a pBR322 variant bearing two closely spaced EcoRI sites is governed by the same turnover number as hydrolysis of parental pBR322, which contains only a single EcoRI sequence, ruling out slow release of the enzyme from the cleaved site or a slow conformational change subsequent to double-strand cleavage. We attribute the effects of ionic strength on steady-state parameters to nonspecific endonuclease.DNA interactions, reflecting facilitated diffusion processes, that occur prior to EcoRI sequence recognition and subsequent to DNA cleavage.
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Affiliation(s)
- D J Wright
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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40
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Lambert MW, Lambert WC. DNA repair and chromatin structure in genetic diseases. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1999; 63:257-310. [PMID: 10506834 DOI: 10.1016/s0079-6603(08)60725-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Interaction of DNA repair proteins with damaged DNA in eukaryotic cells is influenced by the packaging of DNA into chromatin. The basic repeating unit of chromatin, the nucleosome, plays an important role in regulating accessibility of repair proteins to sites of damage in DNA. There are a number of different pathways fundamental to the DNA repair process. Elucidation of the proteins involved in these pathways and the mechanisms they utilize for interacting with damaged nucleosomal and nonnucleosomal DNA has been aided by studies of genetic diseases where there are defects in the DNA repair process. Two of these diseases are xeroderma pigmentosum (XP) and Fanconi anemia (FA). Cells from patients with these disorders are similar in that they have defects in the initial steps of the repair process. However, there are a number of important differences in the nature of these defects. One of these is in the ability of repair proteins from XP and FA cells to interact with damaged nucleosomal DNA. In XP complementation group A (XPA) cells, for example, endonucleases present in a chromatin-associated protein complex involved in the initial steps in the repair process are defective in their ability to incise damaged nucleosomal DNA, but, like the normal complexes, can incise damaged naked DNA. In contrast, in FA complementation group A (FA-A) cells, these complexes are equally deficient in their ability to incise damaged naked and similarly damaged nucleosomal DNA. This ability to interact with damaged nucleosomal DNA correlates with the mechanism of action these endonucleases use for locating sites of damage. Whereas the FA-A and normal endonucleases act by a processive mechanism of action, the XPA endonucleases locate sites of damage distributively. Thus the mechanism of action utilized by a DNA repair enzyme may be of critical importance in its ability to interact with damaged nucleosomal DNA.
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Affiliation(s)
- M W Lambert
- Department of Pathology, UMDNJ-New Jersey Medical School, Newark 07103, USA
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41
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Shimamoto N. One-dimensional diffusion of proteins along DNA. Its biological and chemical significance revealed by single-molecule measurements. J Biol Chem 1999; 274:15293-6. [PMID: 10336412 DOI: 10.1074/jbc.274.22.15293] [Citation(s) in RCA: 143] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- N Shimamoto
- Structural Biology Center, National Institute of Genetics, Mishima, Japan 411-8540, USA.
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Malin G, Iakobashvili R, Lapidot A. Effect of tetrahydropyrimidine derivatives on protein-nucleic acids interaction. Type II restriction endonucleases as a model system. J Biol Chem 1999; 274:6920-9. [PMID: 10066745 DOI: 10.1074/jbc.274.11.6920] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
2-Methyl-4-carboxy,5-hydroxy-3,4,5,6-tetrahydropyri- midine (THP(A) or hydroxyectoine) and 2-methyl,4-carboxy-3,4,5, 6-tetrahydropyrimidine (THP(B) or ectoine) are now recognized as ubiquitous bacterial osmoprotectants. To evaluate the impact of tetrahydropyrimidine derivatives (THPs) on protein-DNA interaction and on restriction-modification systems, we have examined their effect on the cleavage of plasmid DNA by 10 type II restriction endonucleases. THP(A) completely arrested the cleavage of plasmid and bacteriophage lambda DNA by EcoRI endonuclease at 0.4 mM and the oligonucleotide (d(CGCGAATTCGCG))2 at about 4.0 mM. THP(B) was 10-fold less effective than THP(A), whereas for betaine and proline, a notable inhibition was observed only at 100 mM. Similar effects of THP(A) were observed for all tested restriction endonucleases, except for SmaI and PvuII, which were inhibited only partially at 50 mM THP(A). No effect of THP(A) on the activity of DNase I, RNase A, and Taq DNA polymerase was noticed. Gel-shift assays showed that THP(A) inhibited the EcoRI-(d(CGCGAATTCGCG))2 complex formation, whereas facilitated diffusion of EcoRI along the DNA was not affected. Methylation of the carboxy group significantly decreased the activity of THPs, suggesting that their zwitterionic character is essential for the inhibition effect. Possible mechanisms of inhibition, the role of THPs in the modulation of the protein-DNA interaction, and the in vivo relevance of the observed phenomena are discussed.
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Affiliation(s)
- G Malin
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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Lloyd RS. The initiation of DNA base excision repair of dipyrimidine photoproducts. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1999; 62:155-75. [PMID: 9932454 DOI: 10.1016/s0079-6603(08)60507-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
One of the major DNA repair pathways is base excision repair, in which DNA bases that have been damaged by endogenous or exogenous agents are removed by the action of a class of enzymes known as DNA glycosylases. One subset of the known DNA glycosylases has an associated abasic lyase activity that generates a phosphodiester bond scission. The base excision pathway is completed by the sequential action of abasic endonucleases, DNA polymerases, and DNA ligases. Base excision repair of ultraviolet (UV) light-induced dipyrimidine photoproducts has been described in a variety of prokaryotic and eukaryotic organisms and phages. These enzymes vary significantly in their exact substrate specificity and in the catalytic mechanism by which repair is initiated. The prototype enzyme within this class of UV-specific DNA glycosylases is T4 endonuclease V. Endonuclease V holds the distinction of being the first glycosylase (1) to have its structure solved by X-ray diffraction of the enzyme alone as well as in complex with pyrimidine dimer-containing DNA, (2) to have its key catalytic active site residues identified, and (3) to have its mechanism of target DNA site location determined and the biological relevance of this process established. Thus, the study of endonuclease V has been critical in gaining a better understanding of the mechanisms of all DNA glycosylases.
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Affiliation(s)
- R S Lloyd
- Sealy Center for Molecular Science, University of Texas Medical Branch at Galveston, Texas 77555, USA
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Horton JR, Bonventre J, Cheng X. How is modification of the DNA substrate recognized by the PvuII restriction endonuclease? Biol Chem 1998; 379:451-8. [PMID: 9628337 DOI: 10.1515/bchm.1998.379.4-5.451] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In restriction-modification systems, cleavage of substrate sites in cellular DNA by the restriction endonuclease is prevented by the action of a cognate methyltransferase that acts on the same substrate sites. The PvuII restriction endonuclease (R.PvuII) has been structurally characterized in a complex with substrate DNA (Cheng et al., 1994) and as an apoenzyme (Athanasiadis et al., 1994). We report here a structure, determined to 1.9 A resolution by crystallography, of a complex between R.PvuII and iodinated DNA. The presence of an iodine at the 5-carbon of the methylatable cytosine results in the following changes in the protein: His84 moved away from the modified base; this movement was amplified in His85 and disrupts an intersubunit hydrogen bond; and the base modification disturbs the distribution of water molecules that associate with these histidine residues and the area of the scissile bond. Considering these observations, hypotheses are given as to why a similar oligonucleotide, where a methyl group resides on the 5-carbon of the methylatable cytosine, is slowly cleaved by R.PvuII (Rice et al., 1995).
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Affiliation(s)
- J R Horton
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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Jeltsch A, Friedrich T, Roth M. Kinetics of methylation and binding of DNA by the EcoRV adenine-N6 methyltransferase. J Mol Biol 1998; 275:747-58. [PMID: 9480766 DOI: 10.1006/jmbi.1997.1492] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The EcoRV DNA methyltransferase (M.EcoRV) specifically methylates the first adenine within its recognition sequence GATATC. Methylation rates of DNA by this enzyme are strongly influenced by the length of oligonucleotide substrates employed. If substrates >20 bp compared to a 12mer substrate, the kcat/Km increases 100-fold, although the enzyme does not contact more than 12 base-pairs on the DNA. Single-turnover rates are higher than kcat values. M.EcoRV binding to DNA is fast but dissociation from the DNA is slow, demonstrating that the multiple-turnover rate is limited by the rate of product release. The kinetics of DNA binding by M.EcoRV are not in accordance with the thermodynamics binding constant, suggesting that the M.EcoRV-DNA complex is involved in a slow conformational change. The salt dependence of DNA binding is different for non-specific substrates (d ln(KAss)/d ln(cNaCl) = - 2, indicative of electrostatic interactions) and specific substrates (d ln(KAss)/d ln(cNaCl) = + 1, indicative of hydrophobic interactions). This result demonstrates that the M.EcoRV-DNA complex has a different conformation in both binding modes. M.EcoRV does not discriminate between hemimethylated and unmethylated substrates. Using the 20mer we have analyzed the temperature and pH dependence of the single-turnover rate constant of M.EcoRV-DNA methylation by M.EcoRV has an activation energy of 40 kJ/mol and its rate increases with increasing pH. The pH dependence reveals the presence of an ionizable residue with a pKa of 7.9, which must be unprotonated for catalysis. The rates of DNA methylation remain unchanged if an abasic site is introduced instead of the thymidine residue that is base-paired to the target adenine, demonstrating that flipping out the target adenine cannot contribute to the rate-limiting step of the enzymatic reaction.
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Affiliation(s)
- A Jeltsch
- Institut für Biochemie, Fachbereich Biologie, Justus-Liebig Universität, Heinrich-Buff Ring 58, Giessen, 35392, Germany
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Engler LE, Welch KK, Jen-Jacobson L. Specific binding by EcoRV endonuclease to its DNA recognition site GATATC. J Mol Biol 1997; 269:82-101. [PMID: 9193002 DOI: 10.1006/jmbi.1997.1027] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Restriction endonuclease EcoRV has been reported to be unable to distinguish its specific DNA site, GATATC, from non-specific DNA sites in the absence of the catalytic cofactor Mg2+, and thus to exercise sequence specificity solely in the catalytic step. In contrast, we show here that under appropriate conditions of pH and salt concentration, specific complexes with oligonucleotides containing the GATATC site can be detected by either filter-binding or gel-retardation. Equilibrium binding constants (K(A)) are easily measured by both direct equilibrium and equilibrium-competition methods. The preference for "specific" over "non-specific" binding at pH 7 in the absence of divalent cations is about 1000-fold (per mole of oligonucleotide) or 12,000-fold (per mole of binding sites). Ethylation-interference footprinting shows that the "specific" complex includes strong contacts to the phosphate groups GpApTpApTC. Specific DNA binding is strongly pH-dependent, decreasing about 15-fold for each increase of one pH unit above pH 6, but non-specific binding is not; thus, binding specificity decreases with increasing pH. Gel retardation and filter-binding at pH < or = 7 yield essentially identical values of K(A) for specific-site binding, but at pH > 7 gel retardation significantly underestimates K(A). Specific-site binding is stimulated about 700-fold by Ca2+ (not a cofactor for cleavage), but with non-cleavable 3'-phosphorothiolate and 4'-thiodeoxyribose derivatives whose response to Ca2+ is similar to that of the parent oligonucleotide, Mg2+ stimulates binding only fourfold and twofold, respectively. Thus, binding specificity is not dramatically enhanced by Mg2+. Taking into account discrimination in binding and in the first-order rate constant for phosphodiester bond scission, the overall discrimination exercised against the incorrect site GTTATC is about 10(7)-fold. EcoRV endonuclease is thus not a "new paradigm" for site-specific interaction without binding specificity, but like other type II restriction endonucleases achieves sequence specificity by discriminating both in DNA binding and in catalysis.
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Affiliation(s)
- L E Engler
- Department of Biological Sciences, University of Pittsburgh, PA 15260, USA
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Pingoud A, Jeltsch A. Recognition and cleavage of DNA by type-II restriction endonucleases. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 246:1-22. [PMID: 9210460 DOI: 10.1111/j.1432-1033.1997.t01-6-00001.x] [Citation(s) in RCA: 260] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Restriction endonucleases are enzymes which recognize short DNA sequences and cleave the DNA in both strands. Depending on the enzymological properties different types are distinguished. Type II restriction endonucleases are homodimers which recognize short palindromic sequences 4-8 bp in length and, in the presence of Mg2+, cleave the DNA within or next to the recognition site. They are capable of non-specific binding to DNA and make use of linear diffusion to locate their target site. Binding and recognition of the specific site involves contacts to the bases of the recognition sequence and the phosphodiester backbone over approximately 10-12 bp. In general, recognition is highly redundant which explains the extreme specificity of these enzymes. Specific binding is accompanied by conformational changes over both the protein and the DNA. This mutual induced fit leads to the activation of the catalytic centers. The precise mechanism of cleavage has not yet been established for any restriction endonuclease. Currently two models are discussed: the substrate-assisted catalysis mechanism and the two-metal-ion mechanism. Structural similarities identified between EcoRI, EcoRV, BamHI, PvuII and Cfr10I suggest that many type II restriction endonucleases are not only functionally but also evolutionarily related.
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Affiliation(s)
- A Pingoud
- Institut für Biochemie, Fachbereich Biologie, Justus-Liebig-Universität, Giessen, Germany
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Latham KA, Rajendran S, Carmical JR, Lee JC, Lloyd RS. T4 endonuclease V exists in solution as a monomer and binds to target sites as a monomer. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1292:324-34. [PMID: 8597580 DOI: 10.1016/0167-4838(95)00224-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Endonuclease V, a N-glycosylase/lyase from T4 bacteriophage that initiates the repair of cyclobutane pyrimidine dimers in DNA, has been reported to form a monomer-dimer equilibrium in solution [Nickell and Lloyd (1991) Biochemistry 30, 8638], although the enzyme has only been crystallized in the absence of substrate as a monomer [Morikawa et al. (1992) Science 256, 523]. In this study, analytical gel filtration and sedimentation equilibrium techniques were used to rigorously characterize the association state of the enzyme in solution. In contrast to the previous report, at 100 mM KCl endonuclease V was found to exist predominantly as a monomer in solution by both of these techniques; no evidence for dimerization was seen. To characterize the oligomeric state of the enzyme at its target sites on DNA, the enzyme was bound to oligonucleotides containing a single site specific pyrimidine dimer or tetrahydrofuran residue. These complexes were analyzed by nondenaturing gel electrophoresis at various acrylamide concentrations in order to determine the molecular weights of the enzyme-DNA complexes. The results from these experiments demonstrate that endonuclease V binds to cyclobutane pyrimidine dimer and tetrahydrofuran site containing DNA as a monomer.
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Affiliation(s)
- K A Latham
- Sealy Center for Molecular Science, University of Texas Medical Branch, Galveston 77555-1071, USA
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Berkhout B, van Wamel J. Accurate scanning of the BssHII endonuclease in search for its DNA cleavage site. J Biol Chem 1996; 271:1837-40. [PMID: 8567625 DOI: 10.1074/jbc.271.4.1837] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A facilitated diffusion mechanism has been proposed to account for the kinetic efficiency with which restriction endonucleases are able to locate DNA recognition sites. Such a mechanism involves the initial formation of a nonspecific complex upon collision of the protein with the DNA, with the subsequent diffusion of the protein along the DNA helix until either a recognition site is located or the protein dissociates into solution. Protein translocation may be facilitated by either sliding along the DNA, hopping to nearby sites, or intersegment transfer over larger distances. Previous analyses of the manner in which restriction enzymes cleave DNA substrates did rule out the latter mechanism. To discriminate between protein sliding or scanning and protein hopping, we designed a unique DNA template with three overlapping, mutually exclusive recognition sites for the BssHII endonuclease. Analysis of the cleavage pattern demonstrated efficient usage of both external sites, whereas the centrally located site was not efficiently cleaved. These results confirm that linear diffusion of the BssHII enzyme occurs by scanning along the DNA. Furthermore, the scanning enzyme was found to stop and cleave at the first site encountered. Thus, a sliding restriction endonuclease recognizes cleavage sites with high fidelity, without skipping of potential sites.
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Affiliation(s)
- B Berkhout
- University of Amsterdam, Department of Virology, The Netherlands
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