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Article ; Online: Replication Fork Barriers and Topological Barriers: Progression of DNA Replication Relies on DNA Topology Ahead of Forks.

Schvartzman, Jorge B / Hernández, Pablo / Krimer, Dora B

BioEssays : news and reviews in molecular, cellular and developmental biology

2020 Volume 42, Issue 5, Page(s) e1900204

Abstract: During replication, the topology of DNA changes continuously in response to well-known activities of DNA helicases, polymerases, and topoisomerases. However, replisomes do not always progress at a constant speed and can slow-down and even stall at ... ...

Abstract	During replication, the topology of DNA changes continuously in response to well-known activities of DNA helicases, polymerases, and topoisomerases. However, replisomes do not always progress at a constant speed and can slow-down and even stall at precise sites. The way these changes in the rate of replisome progression affect DNA topology is not yet well understood. The interplay of DNA topology and replication in several cases where progression of replication forks reacts differently to changes in DNA topology ahead is discussed here. It is proposed, there are at least two types of replication fork barriers: those that behave also as topological barriers and those that do not. Two-Dimensional (2D) agarose gel electrophoresis is the method of choice to distinguish between these two different types of replication fork barriers.
MeSH term(s)	DNA/genetics ; DNA Helicases/metabolism ; DNA Replication
Chemical Substances	DNA (9007-49-2) ; DNA Helicases (EC 3.6.4.-)
Language	English
Publishing date	2020-03-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.201900204
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Article: Replication Fork Barriers and Topological Barriers: Progression of DNA Replication Relies on DNA Topology Ahead of Forks

Schvartzman, Jorge B / Hernández, Pablo / Krimer, Dora B

BioEssays. 2020 May, v. 42, no. 5

2020

Abstract: During replication, the topology of DNA changes continuously in response to well‐known activities of DNA helicases, polymerases, and topoisomerases. However, replisomes do not always progress at a constant speed and can slow‐down and even stall at ... ...

Abstract	During replication, the topology of DNA changes continuously in response to well‐known activities of DNA helicases, polymerases, and topoisomerases. However, replisomes do not always progress at a constant speed and can slow‐down and even stall at precise sites. The way these changes in the rate of replisome progression affect DNA topology is not yet well understood. The interplay of DNA topology and replication in several cases where progression of replication forks reacts differently to changes in DNA topology ahead is discussed here. It is proposed, there are at least two types of replication fork barriers: those that behave also as topological barriers and those that do not. Two‐Dimensional (2D) agarose gel electrophoresis is the method of choice to distinguish between these two different types of replication fork barriers.
Keywords	DNA ; DNA helicases ; DNA replication ; agar gel electrophoresis ; topology
Language	English
Dates of publication	2020-05
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	NAL-AP-2-clean ; JOURNAL ARTICLE
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.201900204
Database	NAL-Catalogue (AGRICOLA)

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Article: Changes in the topology of DNA replication intermediates: Important discrepancies between in vitro and in vivo

Schvartzman, Jorge B / Martínez, Víctor / Hernández, Pablo / Krimer, Dora B / Fernández‐Nestosa, María‐José

BioEssays. 2021 May, v. 43, no. 5

2021

Abstract: The topology of DNA duplexes changes during replication and also after deproteinization in vitro. Here we describe these changes and then discuss for the first time how the distribution of superhelical stress affects the DNA topology of replication ... ...

Abstract	The topology of DNA duplexes changes during replication and also after deproteinization in vitro. Here we describe these changes and then discuss for the first time how the distribution of superhelical stress affects the DNA topology of replication intermediates, taking into account the progression of replication forks. The high processivity of Topo IV to relax the left‐handed (+) supercoiling that transiently accumulates ahead of the forks is not essential, since DNA gyrase and swiveling of the forks cooperate with Topo IV to accomplish this task in vivo. We conclude that despite Topo IV has a lower processivity to unlink the right‐handed (+) crossings of pre‐catenanes and fully replicated catenanes, this is indeed its main role in vivo. This would explain why in the absence of Topo IV replication goes‐on, but fully replicated sister duplexes remain heavily catenated.
Keywords	DNA ; DNA replication ; DNA topoisomerase (ATP-hydrolysing) ; catenanes ; topology
Language	English
Dates of publication	2021-05
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	NAL-AP-2-clean ; JOURNAL ARTICLE
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.202000309
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Changes in the topology of DNA replication intermediates: Important discrepancies between in vitro and in vivo.

Schvartzman, Jorge B / Martínez, Víctor / Hernández, Pablo / Krimer, Dora B / Fernández-Nestosa, María-José

BioEssays : news and reviews in molecular, cellular and developmental biology

2021 Volume 43, Issue 5, Page(s) e2000309

Abstract	The topology of DNA duplexes changes during replication and also after deproteinization in vitro. Here we describe these changes and then discuss for the first time how the distribution of superhelical stress affects the DNA topology of replication intermediates, taking into account the progression of replication forks. The high processivity of Topo IV to relax the left-handed (+) supercoiling that transiently accumulates ahead of the forks is not essential, since DNA gyrase and swiveling of the forks cooperate with Topo IV to accomplish this task in vivo. We conclude that despite Topo IV has a lower processivity to unlink the right-handed (+) crossings of pre-catenanes and fully replicated catenanes, this is indeed its main role in vivo. This would explain why in the absence of Topo IV replication goes-on, but fully replicated sister duplexes remain heavily catenated.
MeSH term(s)	DNA/genetics ; DNA Replication ; DNA Topoisomerase IV/genetics ; DNA Topoisomerase IV/metabolism ; Nucleic Acid Conformation
Chemical Substances	DNA (9007-49-2) ; DNA Topoisomerase IV (EC 5.99.1.-)
Language	English
Publishing date	2021-02-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.202000309
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Two-Dimensional Gel Electrophoresis to Study the Activity of Type IIA Topoisomerases on Plasmid Replication Intermediates.

Cebrián, Jorge / Martínez, Victor / Hernández, Pablo / Krimer, Dora B / Fernández-Nestosa, María-José / Schvartzman, Jorge B

Biology

2021 Volume 10, Issue 11

Abstract: DNA topoisomerases are the enzymes that regulate DNA topology in all living cells. Since the discovery and purification of ω (omega), when the first were topoisomerase identified, the function of many topoisomerases has been examined. However, their ... ...

Abstract	DNA topoisomerases are the enzymes that regulate DNA topology in all living cells. Since the discovery and purification of ω (omega), when the first were topoisomerase identified, the function of many topoisomerases has been examined. However, their ability to relax supercoiling and unlink the pre-catenanes of partially replicated molecules has received little attention. Here, we used two-dimensional agarose gel electrophoresis to test the function of three type II DNA topoisomerases in vitro: the prokaryotic DNA gyrase, topoisomerase IV and the human topoisomerase 2α. We examined the proficiency of these topoisomerases on a partially replicated bacterial plasmid: pBR-
Language	English
Publishing date	2021-11-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology10111195
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Two-Dimensional Gel Electrophoresis to Study the Activity of Type IIA Topoisomerases on Plasmid Replication Intermediates

Jorge Cebrián / Victor Martínez / Pablo Hernández / Dora B. Krimer / María-José Fernández-Nestosa / Jorge B. Schvartzman

Biology, Vol 10, Iss 1195, p

2021 Volume 1195

Abstract	DNA topoisomerases are the enzymes that regulate DNA topology in all living cells. Since the discovery and purification of ω (omega), when the first were topoisomerase identified, the function of many topoisomerases has been examined. However, their ability to relax supercoiling and unlink the pre-catenanes of partially replicated molecules has received little attention. Here, we used two-dimensional agarose gel electrophoresis to test the function of three type II DNA topoisomerases in vitro: the prokaryotic DNA gyrase, topoisomerase IV and the human topoisomerase 2α. We examined the proficiency of these topoisomerases on a partially replicated bacterial plasmid: pBR- TerE @AatII, with an unidirectional replicating fork, stalled when approximately half of the plasmid had been replicated in vivo. DNA was isolated from two strains of Escherichia coli : DH5αF’ and parE10. These experiments allowed us to assess, for the first time, the efficiency of the topoisomerases examined to resolve supercoiling and pre-catenanes in partially replicated molecules and fully replicated catenanes formed in vivo. The results obtained revealed the preferential functions and also some redundancy in the abilities of these DNA topoisomerases in vitro.
Keywords	DNA topology ; replication ; supercoiling ; pre-catenation ; two-dimensional agarose gel electrophoresis ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Two-Dimensional Gel Electrophoresis to Study the Activity of Type IIA Topoisomerases on Plasmid Replication Intermediates

Cebrián, Jorge / Martínez, Victor / Hernández, Pablo / Krimer, Dora B. / Fernández-Nestosa, María-José / Schvartzman, Jorge B.

Biology. 2021 Nov. 17, v. 10, no. 11

2021

Abstract	DNA topoisomerases are the enzymes that regulate DNA topology in all living cells. Since the discovery and purification of ω (omega), when the first were topoisomerase identified, the function of many topoisomerases has been examined. However, their ability to relax supercoiling and unlink the pre-catenanes of partially replicated molecules has received little attention. Here, we used two-dimensional agarose gel electrophoresis to test the function of three type II DNA topoisomerases in vitro: the prokaryotic DNA gyrase, topoisomerase IV and the human topoisomerase 2α. We examined the proficiency of these topoisomerases on a partially replicated bacterial plasmid: pBR-TerE@AatII, with an unidirectional replicating fork, stalled when approximately half of the plasmid had been replicated in vivo. DNA was isolated from two strains of Escherichia coli: DH5αF’ and parE10. These experiments allowed us to assess, for the first time, the efficiency of the topoisomerases examined to resolve supercoiling and pre-catenanes in partially replicated molecules and fully replicated catenanes formed in vivo. The results obtained revealed the preferential functions and also some redundancy in the abilities of these DNA topoisomerases in vitro.
Keywords	DNA topoisomerase (ATP-hydrolysing) ; Escherichia coli ; agar gel electrophoresis ; catenanes ; humans ; plasmids ; topology ; two-dimensional gel electrophoresis
Language	English
Dates of publication	2021-1117
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology10111195
Database	NAL-Catalogue (AGRICOLA)

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Article: CRISPR/Cas9-mediated deletion of the Wiskott-Aldrich syndrome locus causes actin cytoskeleton disorganization in murine erythroleukemia cells.

Fernández-Calleja, Vanessa / Fernández-Nestosa, María-José / Hernández, Pablo / Schvartzman, Jorge B / Krimer, Dora B

PeerJ

2019 Volume 7, Page(s) e6284

Abstract: Wiskott-Aldrich syndrome (WAS) is a recessive X-linked inmmunodeficiency caused by loss-of-function mutations in the gene encoding the WAS protein (WASp). WASp plays an important role in the polymerization of the actin cytoskeleton in hematopoietic cells ...

Abstract	Wiskott-Aldrich syndrome (WAS) is a recessive X-linked inmmunodeficiency caused by loss-of-function mutations in the gene encoding the WAS protein (WASp). WASp plays an important role in the polymerization of the actin cytoskeleton in hematopoietic cells through activation of the Arp2/3 complex. In a previous study, we found that actin cytoskeleton proteins, including WASp, were silenced in murine erythroleukemia cells defective in differentiation. Here, we designed a CRISPR/Cas9 strategy to delete a 9.5-kb genomic region encompassing the
Language	English
Publishing date	2019-01-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.6284
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Closing the DNA replication cycle: from simple circular molecules to supercoiled and knotted DNA catenanes.

Schvartzman, Jorge B / Hernández, Pablo / Krimer, Dora B / Dorier, Julien / Stasiak, Andrzej

Nucleic acids research

2019 Volume 47, Issue 14, Page(s) 7182–7198

Abstract: Due to helical structure of DNA, massive amounts of positive supercoils are constantly introduced ahead of each replication fork. Positive supercoiling inhibits progression of replication forks but various mechanisms evolved that permit very efficient ... ...

Abstract	Due to helical structure of DNA, massive amounts of positive supercoils are constantly introduced ahead of each replication fork. Positive supercoiling inhibits progression of replication forks but various mechanisms evolved that permit very efficient relaxation of that positive supercoiling. Some of these mechanisms lead to interesting topological situations where DNA supercoiling, catenation and knotting coexist and influence each other in DNA molecules being replicated. Here, we first review fundamental aspects of DNA supercoiling, catenation and knotting when these qualitatively different topological states do not coexist in the same circular DNA but also when they are present at the same time in replicating DNA molecules. We also review differences between eukaryotic and prokaryotic cellular strategies that permit relaxation of positive supercoiling arising ahead of the replication forks. We end our review by discussing very recent studies giving a long-sought answer to the question of how slow DNA topoisomerases capable of relaxing just a few positive supercoils per second can counteract the introduction of hundreds of positive supercoils per second ahead of advancing replication forks.
MeSH term(s)	DNA/chemistry ; DNA/genetics ; DNA Replication ; DNA, Catenated/chemistry ; DNA, Circular/chemistry ; DNA, Superhelical/chemistry ; Eukaryotic Cells/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Prokaryotic Cells/metabolism
Chemical Substances	DNA, Catenated ; DNA, Circular ; DNA, Superhelical ; DNA (9007-49-2)
Language	English
Publishing date	2019-07-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkz586
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Article ; Online: DNA Catenation Reveals the Dynamics of DNA Topology During Replication.

Castán, Alicia / Hernández, Pablo / Krimer, Dora B / Schvartzman, Jorge B

Methods in molecular biology (Clifton, N.J.)

2017 Volume 1703, Page(s) 75–86

Abstract: Two-dimensional agarose gel electrophoresis is the method of choice to identify and quantify all the topological forms DNA molecules can adopt in vivo. Here we describe the materials and protocols needed to analyze catenanes, the natural outcome of DNA ... ...

Abstract	Two-dimensional agarose gel electrophoresis is the method of choice to identify and quantify all the topological forms DNA molecules can adopt in vivo. Here we describe the materials and protocols needed to analyze catenanes, the natural outcome of DNA replication, in Saccharomyces cerevisiae. We describe the formation of pre-catenanes during replication and how inhibition of topoisomerase 2 leads to the accumulation of intertwined sister duplexes. This knowledge is essential to determine how replication forks blockage or pausing affects the dynamic of DNA topology during replication.
MeSH term(s)	DNA Replication/drug effects ; DNA Topoisomerases, Type II/metabolism ; DNA, Catenated/chemistry ; DNA, Catenated/genetics ; DNA, Fungal/chemistry ; DNA, Fungal/genetics ; Electrophoresis, Gel, Two-Dimensional ; Nucleic Acid Conformation ; Saccharomyces cerevisiae/genetics ; Topoisomerase II Inhibitors/pharmacology
Chemical Substances	DNA, Catenated ; DNA, Fungal ; Topoisomerase II Inhibitors ; DNA Topoisomerases, Type II (EC 5.99.1.3)
Language	English
Publishing date	2017-11-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-7459-7_5
Database	MEDical Literature Analysis and Retrieval System OnLINE

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