Application of a skein relation to difference topology experiments

2019 ◽  
Vol 28 (13) ◽  
pp. 1940016 ◽  
Author(s):  
Candice Price ◽  
Isabel Darcy
Keyword(s):  
Inverted Repeat ◽  
Direct Repeat ◽  
Circular Dna ◽  
Novel Technique ◽  
Pass Through ◽  
Dna Substrate ◽  
Tangle Model ◽  
Smc Proteins ◽  
Skein Relation

Difference topology is a technique used to study any protein that can stably bind to DNA. This technique is used to determine the conformation of DNA bound by protein. Motivated by difference topology experiments, we use the skein relation tangle model as a novel technique to study experiments using topoisomerase to study SMC proteins, a family of proteins that stably bind to DNA. The oriented skein relation involves an oriented knot, [Formula: see text], with a distinguished positive crossing; a knot [Formula: see text], obtained by changing the distinguished positive crossing of [Formula: see text] to a negative crossing; a knot, [Formula: see text], resulting from the non-orientation persevering resolution of the distinguished crossing; and a link [Formula: see text], the orientation preserving resolution of the distinguished crossing. We refer to [Formula: see text] as the skein quadruple. Topoisomerases are proteins that break one segment of DNA allowing a DNA segment to pass through before resealing the break. Recombinases are proteins that cut two segments of DNA and recombine them in some manner. They can act on direct repeat or inverted repeat sites, resulting in a link or knot, respectively. Thus, the skein quadruple is now viewed as [Formula: see text] circular DNA substrate, [Formula: see text] product of topoisomerase action, [Formula: see text] product of recombinase action on directed repeat sites, and [Formula: see text] product of recombinase action of inverted repeat sites.

scholarly journals Minimal and Contributing Sequence Determinants of thecis-Acting Locus of Transfer (clt) of Streptomycete Plasmid pIJ101 Occur within an Intrinsically Curved Plasmid Region

2000 ◽  
Vol 182 (23) ◽  
pp. 6834-6841 ◽  
Author(s):  
Matthew J. Ducote ◽  
Shubha Prakash ◽  
Gregg S. Pettis
Keyword(s):  
Transfer Function ◽  
Inverted Repeat ◽  
Regulatory Gene ◽  
Direct Repeat ◽  
Higher Order ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Repeat Sequences ◽  
Inherent Feature ◽  
Close Proximity

ABSTRACT Efficient interbacterial transfer of streptomycete plasmid pIJ101 requires the pIJ101 tra gene, as well as acis-acting plasmid function known as clt. Here we show that the minimal pIJ101 clt locus consists of a sequence no greater than 54 bp in size that includes essential inverted-repeat and direct-repeat sequences and is located in close proximity to the 3′ end of the korB regulatory gene. Evidence that sequences extending beyond the minimal locus and into thekorB open reading frame influence clt transfer function and demonstration that clt-korB sequences are intrinsically curved raise the possibility that higher-order structuring of DNA and protein within this plasmid region may be an inherent feature of efficient pIJ101 transfer.

The topology of plasmid-monomerizing Xer site-specific recombination

2013 ◽  
Vol 41 (2) ◽  
pp. 589-594 ◽  
Author(s):  
Sean D. Colloms
Keyword(s):  
Dna Sequences ◽  
Direct Repeat ◽  
Accessory Proteins ◽  
Site Specific ◽  
Circular Dna ◽  
Site Specific Recombination ◽  
Daughter Cells ◽  
The Core ◽  
Bacterial Plasmid ◽  
Negative Supercoils

Xer site-specific recombination at cer and psi converts bacterial plasmid multimers into monomers so that they can be efficiently segregated to both daughter cells at cell division. Recombination is catalysed by the XerC and XerD recombinases acting at ~30 bp core sites, and is regulated by the action of accessory proteins bound to accessory DNA sequences adjacent to the core sites. Recombination normally occurs only between sites in direct repeat in a negatively supercoiled circular DNA molecule, and yields two circular products linked together in a right-handed four-node catenane with antiparallel sites. These and other topological results are explained by a model in which the accessory DNA sequences are interwrapped around the accessory proteins, trapping three negative supercoils so that strand exchange by the XerC and XerD yields the observed four-node catenane.

A DNA endonuclease isolated from yeast nuclear extract

1978 ◽  
Vol 56 (3) ◽  
pp. 181-189 ◽  
Author(s):  
Douglas W. Bryant ◽  
Robert H. Haynes
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Molecular Weight ◽  
Dna Repair ◽  
Nuclear Extract ◽  
Dna Duplexes ◽  
Replicative Form ◽  
Yeast Saccharomyces Cerevisiae ◽  
Dna Endonuclease ◽  
Circular Dna ◽  
Dna Substrate

We have isolated and partially purified a DNA endonuclease from nuclei of the yeast Saccharomyces cerevisiae. Although purified on the basis of its ability to degrade denatured DNA, the enzyme can also attack native DNA. Denatured oligonucleotide products of the enzyme are sensitive to venom phosphodiesterase (EC 3.1.4.1) but not to bovine spleen phosphodiesterase (EC 3.1.4.18). The enzyme has an estimated molecular weight of 6.6–7.5 × 104, more than twice as large as the endonucleases involved in DNA repair in Escherichia coli.When analyzed on glycerol gradients, the endonuclease sedimented as a single activity against both denatured DNA and closed circular DNA duplexes. The enzyme showed a 10-fold preference for denatured over native T7 DNA substrate, and appears to produce random nicks in a supercoiled replicative form of [Formula: see text] DNA (RFI) with no discernable preference for the unpaired bases in the supercoiled duplex. The endonuclease appears to be distinct from the yeast endonucleases previously described.

Insertional polymorphism in introns 4 and 10 of the maize ß-glucosidase gene glu1

Genome ◽  
1998 ◽  
Vol 41 (4) ◽  
pp. 597-604 ◽  
Author(s):  
Asim Esen ◽  
Hema Bandaranayake
Keyword(s):  
Inverted Repeat ◽  
Insertion Sequence ◽  
Sequence Data ◽  
Direct Repeat ◽  
Repeat Sequence ◽  
Inverted Repeat Sequence ◽  
Repeat Elements ◽  
New Family ◽  
Polymorphic Gene ◽  
Insertional Polymorphism

The major ß-glucosidase isozyme Glu1 is encoded by a highly polymorphic gene (glu1) in maize. The glu1 gene comprises 12 exons and 11 introns. Two of these introns, introns 4 and 10, show insertional polymorphism: those in allele glu1-1 (represented by inbred line OH7B) are longer than those in other inbred genotypes and in two teosintes (Zea mexicana and Zea parviglumis) surveyed. Sequence data revealed that an increase in the length of intron 4 from 150 to 477 bp in OH7B is due to a short (11 bp) tandem duplication and a large insertion sequence of 313 bp plus a 4-bp (5 ATAG 3) direct repeat. The 313-bp insertion sequence (referred to as mzsTn-1) has all the features of a transposon, having a 25-bp well-conserved (3/25 mismatches) inverted repeat sequence at its termini flanked by a 4-bp direct repeat. The increase in length from 1041 to 1302 bp in intron 10 of OH7B is due to a 259-bp insertion sequence (referred to as mzsTn-2) plus a 2-bp (5 TA 3) direct repeat. The mzsTn-2 element also possesses all the hallmarks of a transposon: a 34-bp well-conserved (3/34 mismatches) inverted repeat sequence at its termini flanked by a 2-bp direct repeat. The mzsTn-1 element belongs to a new family of inverted repeat elements, while mzsTn-2 belongs to the Stowaway family of inverted repeat elements. Analysis of PCR products from amplifications off genomic-DNA templates, using primers derived from the inverted repeat termini, and Southern blotting data suggest that both small transposons are members of a multigene family. The occurrence of two different small transposons in introns of the same glu1 allele in inbred OH7B and their absence in other genotypes suggest that they have moved into this glu1 allele recently through mediation of their autonomous counterparts that are active in OH7B or in its ancestry.Key words: ß-glucosidase, maize, intron, small transposon, polymorphism.

scholarly journals Plasmid recombination in a rad52 mutant of Saccharomyces cerevisiae.

Genetics ◽  
1992 ◽  
Vol 131 (2) ◽  
pp. 261-276 ◽  
Author(s):  
K J Dornfeld ◽  
D M Livingston
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Inverted Repeat ◽  
Wild Type Strain ◽  
Direct Repeat ◽  
Cell Types ◽  
Wild Type ◽  
Plasmid Recombination ◽  
Intramolecular Recombination ◽  
In The Wild ◽  
Repeat Events

Abstract Using plasmids capable of undergoing intramolecular recombination, we have compared the rates and the molecular outcomes of recombination events in a wild-type and a rad52 strain of Saccharomyces cerevisiae. The plasmids contain his3 heteroalleles oriented in either an inverted or a direct repeat. Inverted repeat plasmids recombine approximately 20-fold less frequently in the mutant than in the wild-type strain. Most events from both cell types have continuous coconversion tracts extending along one of the homologous segments. Reciprocal exchange occurs in fewer than 30% of events. Direct repeat plasmids recombine at rates comparable to those of inverted repeat plasmids in wild-type cells. Direct repeat conversion tracts are similar to inverted repeat conversion tracts in their continuity and length. Inverted and direct repeat plasmid recombination differ in two respects. First, rad52 does not affect the rate of direct repeat recombination as drastically as the rate of inverted repeat recombination. Second, direct repeat plasmids undergo crossing over more frequently than inverted repeat plasmids. In addition, crossovers constitute a larger fraction of mutant than wild-type direct repeat events. Many crossover events from both cell types are unusual in that the crossover HIS3 allele is within a plasmid containing the parental his3 heteroalleles.

scholarly journals Staphylococcal Cassette Chromosome mec-Like Element in Macrococcus caseolyticus

2010 ◽  
Vol 54 (4) ◽  
pp. 1469-1475 ◽  
Author(s):  
Sae Tsubakishita ◽  
Kyoko Kuwahara-Arai ◽  
Tadashi Baba ◽  
Keiichi Hiramatsu
Keyword(s):  
Mobile Element ◽  
Direct Repeat ◽  
Multidrug Resistant ◽  
Gene Complex ◽  
Potential Mechanism ◽  
Commensal Bacterium ◽  
Circular Dna ◽  
Repeat Sequences ◽  
Animal Skin ◽  
Staphylococcal Cassette Chromosome

ABSTRACT Macrococcus is a bacterial genus that is closely related to Staphylococcus, which typically is isolated from animal skin and products. The genome analysis of multidrug-resistant Macrococcus caseolyticus strain JCSC5402, isolated from chicken, previously led to the identification of plasmid pMCCL2, which carries a transposon containing an unusual form of the Macrococcus mec gene complex (mecAm -mecR1m -mecIm -blaZm ). In M. caseolyticus strain JCSC7096, this mec transposon containing the mec gene complex (designated Tn6045 in this study) was found integrated downstream of orfX on the chromosome. Tn6045 of JCSC7096 was bracketed by the direct repeat sequences (DR) specifically recognized by cassette chromosome recombinase (CCR). A non-mecA-containing staphylococcal cassette chromosome (SCC) element, designated SCC7096, was integrated next to the mec transposon and separated from the latter by a DR. Nested PCR experiments showed that the mec transposon not only was excised singly but also coexcised with SCC7096 from the chromosome at the DRs. The coexcised elements formed the extrachromosomal closed circular DNA of the SCCmec-like element. SCCmec is known to be the mobile element conveying methicillin (meticillin) resistance in staphylococci. However, its origin has been unknown. Our observation revealed a potential mechanism of the generation of a new SCCmec-like element in M. caseolyticus, a commensal bacterium of food animals.

scholarly journals Characterization of the Termini of Cytoplasmic Hepatitis B Virus Deproteinated Relaxed Circular DNA

2020 ◽  
Vol 95 (1) ◽  
Author(s):  
Dawei Cai ◽  
Ran Yan ◽  
Jerry Z. Xu ◽  
Hu Zhang ◽  
Sheng Shen ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Molecular Mechanisms ◽  
Direct Repeat ◽  
Hydroxyl Group ◽  
Viral Polymerase ◽  
Circular Dna ◽  
Phosphodiester Bond ◽  
Covalently Closed Circular Dna ◽  
B Virus

ABSTRACT The biosynthesis of hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) requires the removal of the covalently linked viral polymerase from the 5′ end of the minus strand [(−)strand] of viral relaxed circular DNA (rcDNA), which generates a deproteinated rcDNA (DP-rcDNA) intermediate. In the present study, we systematically characterized the four termini of cytoplasmic HBV DP-rcDNA by 5′/3′ rapid amplification of cDNA ends (RACE), 5′ radiolabeling, and exonuclease digestion, which revealed the following observations: (i) DP-rcDNA and rcDNA possess an identical 3′ end of (−)strand DNA; (ii) compared to rcDNA, DP-rcDNA has an extended but variable 3′ end of plus strand [(+)strand] DNA, most of which is in close proximity to direct repeat 2 (DR2); (iii) DP-rcDNA exhibits an RNA primer-free 5′ terminus of (+)strand DNA with either a phosphate or hydroxyl group; and (iv) the 5′ end of the DP-rcDNA (−)strand is unblocked at nucleotide G1828, bearing a phosphate moiety, indicating the complete removal of polymerase from rcDNA via unlinking the tyrosyl-DNA phosphodiester bond during rcDNA deproteination. However, knockout of cellular 5′ tyrosyl-DNA phosphodiesterase 2 (TDP2) did not markedly affect rcDNA deproteination or cccDNA formation. Thus, our work sheds new light on the molecular mechanisms of rcDNA deproteination and cccDNA biogenesis. IMPORTANCE The covalently closed circular DNA (cccDNA) is the persistent form of the hepatitis B virus (HBV) genome in viral infection and an undisputed antiviral target for an HBV cure. HBV cccDNA is converted from viral genomic relaxed circular DNA (rcDNA) through a complex process that involves removing the covalently bound viral polymerase from rcDNA, which produces a deproteinated-rcDNA (DP-rcDNA) intermediate for cccDNA formation. In this study, we characterized the four termini of cytoplasmic DP-rcDNA and compared them to its rcDNA precursor. While rcDNA and DP-rcDNA have an identical 3′ terminus of (−)strand DNA, the 3′ terminus of (+)strand DNA on DP-rcDNA is further elongated. Furthermore, the peculiarities on rcDNA 5′ termini, specifically the RNA primer on the (+)strand and the polymerase on the (−)strand, are absent from DP-rcDNA. Thus, our study provides new insights into a better understanding of HBV rcDNA deproteination and cccDNA biosynthesis.

scholarly journals Trace diagrams and biquandle brackets

2017 ◽  
Vol 28 (14) ◽  
pp. 1750104 ◽  
Author(s):  
S. Nelson ◽  
N. Oyamaguchi
Keyword(s):  
Spatial Graphs ◽  
Pass Through ◽  
Trace Diagrams ◽  
Stop Condition ◽  
Knots And Links ◽  
Skein Relation

We introduce a method of computing biquandle brackets of oriented knots and links using a type of decorated trivalent spatial graphs we call trace diagrams. We identify algebraic conditions on the biquandle bracket coefficients for moving strands over and under traces and identify a new stop condition for the recursive expansion. In the case of monochromatic crossings we show that biquandle brackets satisfy a Homflypt-style skein relation and we identify algebraic conditions on the biquandle bracket coefficients to allow pass-through trace moves.

Sign in / Sign up

Export Citation Format

Share Document