Construction and electrophoretic migration of single-stranded DNA knots and catenanes

Bucka, Alexander; Stasiak, Andrzej

doi:10.1093/nar/30.6.e24

Cited by 29 publications

(31 citation statements)

References 13 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…2A). Each oligonucleotide contained a 12-bp complementary region that was flanked by flexible poly(dT) linkers to allow the formation of a mixture of singly linked and doubly linked single-stranded catenanes (30). Consistent with the properties of a closed circular singlestranded DNA catenane, the final product exhibited slower mobility than the monomer circles on a denaturing polyacrylamide gel (Fig.…”

Section: Expression and Purification Of Recombinant Htopo Iii␣-be-mentioning

confidence: 82%

See 1 more Smart Citation

Human Topoisomerase IIIα Is a Single-stranded DNA Decatenase That Is Stimulated by BLM and RMI1

Yang

Bachrati

et al. 2010

Journal of Biological Chemistry

View full text Add to dashboard Cite

Human topoisomerase III␣ is a type IA DNA topoisomerase that functions with BLM and RMI1 to resolve DNA replication and recombination intermediates. BLM, human topoisomerase III␣, and RMI1 catalyze the dissolution of double Holliday junctions into noncrossover products via a strand-passage mechanism. We generated single-stranded catenanes that resemble the proposed dissolution intermediate recognized by human topoisomerase III␣. We demonstrate that human topoisomerase III␣ is a single-stranded DNA decatenase that is specifically stimulated by the BLM-RMI1 pair. In addition, RMI1 interacts with human topoisomerase III␣, and the interaction is required for the stimulatory effect of RMI1 on decatenase activity. Our data provide direct evidence that human topoisomerase III␣ functions as a decatenase with the assistance of BLM and RMI1 to facilitate the processing of homologous recombination intermediates without crossing over as a mechanism to preserve genome integrity.Topoisomerases are ubiquitous enzymes conserved from bacteria to humans. Their roles in modulating DNA topology in replication, transcription, and other cellular processes (1, 2) make them indispensable for cell viability. There are four subfamilies of topoisomerases as follows: IA, IB, IIA, and IIB. Type IA topoisomerases change DNA topological states in discrete steps of one via an enzyme-bridging mechanism (1, 2). The catalytic tyrosine residue initiates a transesterification reaction in a single-stranded region to generate a transient DNA break, allowing for the passage of the intact strand through the break. After religation of the broken strand by a reversal of the reaction, the enzyme is free to engage in another round of catalysis (1, 2). Members of the type IA topoisomerase family include Escherichia coli topoisomerase I (EcTop1) and III (EcTop3), yeast topoisomerase III (Top3), and two isoforms of topoisomerase III, ␣ (Topo 2 III␣) and ␤ (Topo III␤), in higher eukaryotes. These enzymes exhibit high sequence similarity in the N-terminal catalytic core domain, whereas the C-terminal tails are variable (1). In addition to the ability to relax negatively supercoiled DNA, EcTop1 is capable of catalyzing knotting, unknotting, and interlinking of DNA substrates that contain exposed single-stranded regions (1). Because single-stranded DNA gaps are a common feature found at DNA replication forks, replication termination sites, and replication and repair sites, it is believed that the main function of type IA topoisomerases is to unlink DNA catenanes.Type IA topoisomerases function in concert with RecQ helicases to control recombination events (3). RecQ helicases are a highly conserved family of DNA helicases that are required for the maintenance of genome integrity (4). Human topoisomerase III␣ (hTopo III␣) physically interacts with BLM, one of the five RecQ helicases in humans (5, 6). Biallelic mutations of BLM give rise to a clinically defined cancer predisposition disorder, Bloom syndrome (BS) (7). BS cells display signs of genome instability, fea...

show abstract

Section: Expression and Purification Of Recombinant Htopo Iii␣-be-mentioning

confidence: 82%

“…Generation of Single-stranded Catenanes-The single strand catenane substrate was constructed as described previously (30), with several modifications. Briefly, oligos C1 and C2 were annealed in the presence of oligo B1 to form the catenane.…”

Section: Methodsmentioning

confidence: 99%

Human Topoisomerase IIIα Is a Single-stranded DNA Decatenase That Is Stimulated by BLM and RMI1

Yang

Bachrati

et al. 2010

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…Therefore, other ways will have to be designed in order to prepare hemicatenanes of distinct DNA molecules, perhaps using the procedure suggested recently by Bucka & Stasiak for making knotted DNA circles. 48 Since the DNA hemicatenane and the four-way junction both consist in the junction of two doublestranded DNA molecules, they could be expected to share some degree of structural similarity. In particular, our finding that the DNA-intercalating residue of the HMGB1 domain A (Phe38), rather than those of the domain B, is involved in highaffinity binding to hcDNA is in accord with previous reports on the dominant role of domain A in the structure-specific binding of HMGB1 protein to four-way-junctions, DNA minicircles, or bent (cisplatin-modified) DNA.…”

Section: Discussionmentioning

confidence: 99%

Determinants of Specific Binding of HMGB1 Protein to Hemicatenated DNA Loops

Jaouen

Koning

Gaillard

et al. 2005

Journal of Molecular Biology

View full text Add to dashboard Cite

Protein HMGB1 has long been known as one of the most abundant non-histone proteins in the nucleus of mammalian cells, and has regained interest recently for its function as an extracellular cytokine. As a DNA-binding protein, HMGB1 facilitates DNA-protein interactions by increasing the flexibility of the double helix, and binds specifically to distorted DNA structures. We have previously observed that HMGB1 binds with extremely high affinity to a novel DNA structure, hemicatenated DNA loops (hcDNA), in which double-stranded DNA fragments containing a tract of poly(CA).poly(TG) form a loop maintained at its base by a hemicatenane. Here, we show that the single HMGB1 domains A and B, the HMG-box domain of sex determination factor SRY, as well as the prokaryotic HMGB1-like protein HU, specifically interact with hcDNA (Kd approximately 0.5 nM). However, the affinity of full-length HMGB1 for hcDNA is three orders of magnitude higher (Kd<0.5 pM) and requires the simultaneous presence of both HMG-box domains A and B plus the acidic C-terminal tail on the molecule. Interestingly, the high affinity of the full-length protein for hcDNA does not decrease in the presence of magnesium. Experiments including a comparison of HMGB1 binding to hcDNA and to minicircles containing the CA/TG sequence, binding studies with HMGB1 mutated at intercalating amino acid residues (involved in recognition of distorted DNA structures), and exonuclease III footprinting, strongly suggest that the hemicatenane, not the DNA loop, is the main determinant of the affinity of HMGB1 for hcDNA. Experiments with supercoiled CA/TG-minicircles did not reveal any involvement of left-handed Z-DNA in HMGB1 binding. Our results point to a tight structural fit between HMGB1 and DNA hemicatenanes under physiological conditions, and suggest that one of the nuclear functions of HMGB1 could be linked to the possible presence of hemicatenanes in the cell.

show abstract

“…[373] Mehr als sechs Milliarden Primknoten sind in der Mathematik bekannt. [301d, 374] Die Zahl derer, [303] die durch chemische Synthese erzeugt wurden, steht nun bei drei.…”

Section: Addendum (August 2011)unclassified

Strategien und Taktiken für die metallgesteuerte Synthese von Rotaxanen, Knoten, Catenanen und Verschlingungen höherer Ordnung

et al. 2011

View full text Add to dashboard Cite

Mehr als ein Vierteljahrhundert nach der ersten Metalltemplatsynthese eines [2]Catenans in Straßburg existiert nun eine Fülle an Strategien zum Aufbau mechanisch verbundener und verflochtener Strukturen auf molekularer Ebene. Catenane, Rotaxane, Knoten und Borromäische Ringe sind alle erfolgreich über Methoden zugänglich, in denen Metallionen eine Schlüsselrolle spielen. Ursprünglich wurden Metallionen ausschließlich aufgrund ihrer Koordinationschemie verwendet, indem sie entweder die einzelnen Bausteine auf eine Weise anordneten, die durch anschließende Reaktionen die Erzeugung der verschlungenen Produkte ermöglichte, oder indem sie selbst als wesentlicher Bestandteil der Ringe oder als “Stopper” dienten. Vor kurzem wurde die Rolle des Metalls auch auf die Katalyse ausgedehnt: Die Metallionen ordnen die Bausteine nicht nur zu einer verflochtenen oder eingefädelten Struktur an, sondern fördern auch aktiv die Strukturbildung durch kovalenten Einfangen. Dieser Aufsatz fasst die Strategien zur Bildung mechanisch verbundener Molekülstrukturen mit Metallionen zusammen und diskutiert die Taktiken, die zum Aufbau von Überkreuzungen, zur Maximierung der Ausbeuten verschlungener und nichtverschlungener Produkte und zur Bildung eingefädelter oder verflochtener Intermediate durch kovalenten Einfang zur Verfügung stehen.

show abstract

Construction and electrophoretic migration of single-stranded DNA knots and catenanes

Cited by 29 publications

References 13 publications

Human Topoisomerase IIIα Is a Single-stranded DNA Decatenase That Is Stimulated by BLM and RMI1

Human Topoisomerase IIIα Is a Single-stranded DNA Decatenase That Is Stimulated by BLM and RMI1

Determinants of Specific Binding of HMGB1 Protein to Hemicatenated DNA Loops

Strategien und Taktiken für die metallgesteuerte Synthese von Rotaxanen, Knoten, Catenanen und Verschlingungen höherer Ordnung

Contact Info

Product

Resources

About