scholarly journals Grid diagrams as tools to investigate knot spaces and topoisomerase-mediated simplification of DNA topology

2020 ◽  
Vol 6 (9) ◽  
pp. eaay1458 ◽  
Author(s):  
Agnese Barbensi ◽  
Daniele Celoria ◽  
Heather A. Harrington ◽  
Andrzej Stasiak ◽  
Dorothy Buck
Keyword(s):  
Dna Topology ◽  
Mathematical Formalism ◽  
Dna Molecules ◽  
Modeling Approach ◽  
Grid Diagrams ◽  
Double Stranded Dna ◽  
Open Question

Grid diagrams with their relatively simple mathematical formalism provide a convenient way to generate and model projections of various knots. It has been an open question whether these 2D diagrams can be used to model a complex 3D process such as the topoisomerase-mediated preferential unknotting of DNA molecules. We model here topoisomerase-mediated passages of double-stranded DNA segments through each other using the formalism of grid diagrams. We show that this grid diagram–based modeling approach captures the essence of the preferential unknotting mechanism, based on topoisomerase selectivity of hooked DNA juxtapositions as the sites of intersegmental passages. We show that the grid diagram–based approach provides an important, new, and computationally convenient framework for investigating entanglement in biopolymers.

Synchrony of Digestion of SV40 DNA by Exonuclease III Determined by EM

1975 ◽  
Vol 33 ◽  
pp. 674-675
Author(s):  
Ray Wu ◽  
G. Ruben ◽  
B. Siegel ◽  
P. Spielman ◽  
E. Jay
Keyword(s):  
Dark Field ◽  
Uranyl Acetate ◽  
Enzyme Digestion ◽  
Dna Molecules ◽  
Exonuclease Iii ◽  
Aluminum Films ◽  
Double Stranded Dna ◽  
Before And After ◽  
Exo Iii ◽  
Sv40 Dna

A method for determining long nucleotide sequences of double-stranded DNA is being developed. It involves (a) the synchronous digestion of the DNA from the 3' ends with EL coli exonuclease III (Exo III) followed by (b) resynthesis with labeled nucleotides and DNA polymerase. A crucial factor in the success of this method is the degree to which the enzyme digestion proceeds synchronously under proper conditions of incubation (step a). Dark field EM is used to obtain accurate measurements on the lengths and distribution of the DNA molecules before and after digestion with Exo III, while gel electrophoresis is used in parallel to obtain a mean length for these molecules. It is the measurements on a large enough sample of individual molecules by EM that provides the information on how synchronously the digestion proceeds. For length measurements, the DNA molecules were picked up on 20-30 Å thick carbon-aluminum films, using the aqueous Kleinschmidt technique and stained with 7.5 x 10-5M uranyl acetate in 90% ethanol for 3 minutes.

scholarly journals Static Watson-Crick Context-Free Grammars

2019 ◽  
Vol 15 (10) ◽  
pp. 65 ◽  
Author(s):  
Wan Heng Fong ◽  
Aqilahfarhana Abdul Rahman ◽  
Nor Haniza Sarmin ◽  
Sherzod Turaev
Keyword(s):  
Dna Computing ◽  
Biological Properties ◽  
Dna Molecules ◽  
Context Free Grammar ◽  
Double Stranded Dna ◽  
New Variant ◽  
Sticker System ◽  
Relationship Of ◽  
Context Free ◽  
Context Free Grammars

Sticker systems and Watson-Crick automata are two modellings of DNA molecules in DNA computing. A sticker system is a computational model which is coded with single and double-stranded DNA molecules; while Watson-Crick automata is the automata counterpart of sticker system which represents the biological properties of DNA. Both of these models use the feature of Watson-Crick complementarity in DNA computing. Previously, the grammar counterpart of the Watson-Crick automata have been introduced, known as Watson-Crick grammars which are classified into three classes: Watson-Crick regular grammars, Watson-Crick linear grammars and Watson-Crick context-free grammars. In this research, a new variant of Watson-Crick grammar called a static Watson-Crick context-free grammar, which is a grammar counterpart of sticker systems that generates the double-stranded strings and uses rule as in context-free grammar, is introduced. The static Watson-Crick context-free grammar differs from a dynamic Watson-Crick context-free grammar in generating double-stranded strings, as well as for regular and linear grammars. The main result of the paper is to determine the generative powers of static Watson-Crick context-free grammars. Besides, the relationship of the families of languages generated by Chomsky grammars, sticker systems and Watson-Crick grammars are presented in terms of their hierarchy.

scholarly journals TrwC-Mediated Site-Specific Recombination Is Controlled by Host Factors Altering Local DNA Topology

2007 ◽  
Vol 189 (24) ◽  
pp. 9037-9043 ◽  
Author(s):  
Carolina Elvira César ◽  
Matxalen Llosa
Keyword(s):  
Promoter Sequence ◽  
Dna Topology ◽  
Integration Host Factor ◽  
Host Factors ◽  
Elongation Complex ◽  
Site Specific ◽  
Double Stranded Dna ◽  
Transcript Elongation ◽  
A Site

ABSTRACT R388 conjugative relaxase TrwC acts as a site-specific recombinase, promoting recombination between two cognate oriTs on double-stranded DNA substrates. The relaxosome component TrwA is also required for efficient recombination. In this work we present data on the in vivo control of this reaction by host proteins that affect local DNA topology. In the absence of TrwA, binding of integration host factor (IHF) to the oriT keeps the recombination levels low, probably by keeping the relaxosome complex, formed at recombination locus 1, in a “closed” conformation. In an IHF-deficient (IHF−) background, the formation of a transcript elongation complex at this locus still hampers recombination. A mutation abating the promoter sequence at locus 1, or repression of transcription by exposure to rifampin, lifts the inhibition imposed on recombination in an IHF− background. We also observe an increase in conjugation efficiency under these conditions. Relieving the inhibition imposed by these host factors allows efficient levels of recombination between short oriT loci in the absence of TrwA. The presence of TrwA counteracts these inhibitory effects. TrwA would then activate both recombination and conjugation by switching the conformation of the relaxosome to an “open” form that exposes single-stranded DNA at the nic site, promoting the initial TrwC nicking reaction.

scholarly journals Response of Xenopus Cds1 in Cell-free Extracts to DNA Templates with Double-stranded Ends

2000 ◽  
Vol 11 (5) ◽  
pp. 1535-1546 ◽  
Author(s):  
Zijian Guo ◽  
William G. Dunphy
Keyword(s):  
Cell Cycle ◽  
Dna Replication ◽  
Dna Molecules ◽  
Dna Templates ◽  
Cell Cycle Delay ◽  
Checkpoint Kinases ◽  
Double Stranded Dna ◽  
Egg Extracts ◽  
Dna Ends ◽  
Damaged Dna

Although homologues of the yeast checkpoint kinases Cds1 and Chk1 have been identified in various systems, the respective roles of these kinases in the responses to damaged and/or unreplicated DNA in vertebrates have not been delineated precisely. Likewise, it is largely unknown how damaged DNA and unreplicated DNA trigger the pathways that contain these effector kinases. We report that XenopusCds1 (Xcds1) is phosphorylated and activated by the presence of some simple DNA molecules with double-stranded ends in cell-freeXenopus egg extracts. Xcds1 is not affected by aphidicolin, an agent that induces DNA replication blocks. In contrast,Xenopus Chk1 (Xchk1) responds to DNA replication blocks but not to the presence of double-stranded DNA ends. Immunodepletion of Xcds1 (and/or Xchk1) from egg extracts did not attenuate the cell cycle delay induced by double-stranded DNA ends. These results imply that the cell cycle delay triggered by double-stranded DNA ends either does not involve Xcds1 or uses a factor(s) that can act redundantly with Xcds1.

Selective recognition of G-quadruplexes by a dimeric carbocyanine dye

RSC Advances ◽  
2016 ◽  
Vol 6 (90) ◽  
pp. 87400-87404 ◽  
Author(s):  
P. Chilka ◽  
P. R. Patlolla ◽  
B. Datta
Keyword(s):  
Selective Recognition ◽  
Dna Molecules ◽  
Double Stranded Dna ◽  
Mixed Sequence ◽  
Carbocyanine Dye ◽  
G Quadruplex

A novel dimeric carbocyanine dye is found to recognise G-quadruplex structures selectively compared to mixed sequence or double-stranded DNA molecules.

scholarly journals Mechanisms of intermolecular homologous recombination in plants as studied with single- and double-stranded DNA molecules

1992 ◽  
Vol 20 (11) ◽  
pp. 2785-2794 ◽  
Author(s):  
Marcel J.A. de Groot ◽  
Remko Offringa ◽  
Mirjam P. Does ◽  
Paul J.J. Hooykaas ◽  
Peter J.M. van den Elzen
Keyword(s):  
Homologous Recombination ◽  
Dna Molecules ◽  
Double Stranded Dna

scholarly journals About Spatial Organization of Double-Stranded DNA Molecules in Cholesteric Liquid-Crystalline Phase

2016 ◽  
Vol 16 (1) ◽  
pp. 71-82
Author(s):  
Yu. M. Yevdokimov ◽  
S. G. Skuridin ◽  
V. I. Salyanov ◽  
L. A. Dadinova ◽  
O. N. Kompanets ◽  
...  
Keyword(s):  
Crystalline Phase ◽  
Liquid Crystalline ◽  
Spatial Organization ◽  
Liquid Crystalline Phase ◽  
Dna Molecules ◽  
Double Stranded Dna ◽  
Cholesteric Liquid Crystalline
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