scholarly journals Elastic property of single double-stranded DNA molecules: Theoretical study and comparison with experiments

2000 ◽  
Vol 62 (1) ◽  
pp. 1045-1058 ◽  
Author(s):  
Haijun Zhou ◽  
Yang Zhang ◽  
Zhong-can Ou-Yang
Keyword(s):  
Elastic Property ◽  
Theoretical Study ◽  
Dna Molecules ◽  
Double Stranded Dna ◽  
Comparison With Experiments

A New Relation of Second Order Limit Language in Simple and Semi-Simple Splicing System

2014 ◽  
Vol 71 (5) ◽  
Author(s):  
Muhammad Azrin Ahmad ◽  
Nor Haniza Sarmin ◽  
Wan Heng Fong ◽  
Yuhani Yusof
Keyword(s):  
Formal Language ◽  
Theoretical Study ◽  
Second Order ◽  
Language Theory ◽  
Biological Traits ◽  
Dna Molecules ◽  
Double Stranded Dna ◽  
New Type ◽  
Limit Language ◽  
Dna Splicing

Splicing system, which is an abstraction of operations on DNA molecules, can be modelled mathematically under the framework of formal language theory and informational macromolecules. The recombinant behavior of the set of double-stranded DNA molecules under the influence of restriction enzyme and ligase further lead to the cut and paste phenomenon in splicing system. The theoretical study of splicing language has contributed to a new type of splicing language known as a second order limit language, which is an extension of limit language. Some types of splicing system can produce second order limit language. Y-G splicing system is chosen among other models to model the DNA splicing process as this model preserves the biological traits and presents the transparent behavior of the DNA splicing process. In this paper, the relation between second order limit language with simple splicing and semi-simple splicing system are presented.

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 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.

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
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