Comparison of linear and ring DNA macromolecules moderately and strongly confined in nanochannels

2013 ◽  
Vol 41 (2) ◽  
pp. 625-629 ◽  
Author(s):  
Zuzana Benková ◽  
Peter Cifra
Keyword(s):  
Present Article ◽  
Experimental Results ◽  
Chain Extension ◽  
Circular Dna ◽  
Linear Dna ◽  
Linear Chains ◽  
Strong Confinement

Understanding the mechanism of DNA extension in nanochannels is necessary for interpretation of experiments in nanofluidic channel devices that have been conducted recently with both linear and ring chains. The present article reviews the situation with linear chains and analyses the experimental results and simulations for channel-induced extension (linearization) of ring chains. Results for confined rings indicate a transition between moderate and strong confinement similar to that of linear chains. Owing to stronger self-avoidance in confined rings, the transition and chain extension is shifted relative to linear DNA. We suggest that a relationship similar to that used for the extension of linear chains may also be used for circular DNA.

The tra locus of streptomycete plasmid pIJ101 mediates efficient transfer of a circular but not a linear version of the same replicon

Microbiology ◽  
2010 ◽  
Vol 156 (9) ◽  
pp. 2723-2733 ◽  
Author(s):  
Jing Wang ◽  
Gregg S. Pettis
Keyword(s):  
Conjugal Transfer ◽  
Circular Dna ◽  
Linear Dna ◽  
Double Stranded Dna ◽  
Donor Cells ◽  
Linear Version ◽  
Necessary And Sufficient ◽  
Unique Mechanism ◽  
Original Configuration ◽  
Efficient Transfer

Conjugal transfer of circular plasmids in Streptomyces involves a unique mechanism employing few plasmid-encoded loci and the transfer of double-stranded DNA by an as yet uncharacterized intercellular route. Efficient transfer of the circular streptomycete plasmid pIJ101 requires only two plasmid loci: the pIJ101 tra gene, and as a cis-acting function known as clt. Here, we compared the ability of the pIJ101 transfer apparatus to promote conjugal transfer of circular versus linear versions of the same replicon. While the pIJ101 tra locus readily transferred the circular form of the replicon, the linear version was transferred orders of magnitude less efficiently and all plasmids isolated from the transconjugants were circular, regardless of their original configuration in the donor. Additionally, relatively rare circularization of linear plasmids was detectable in the donor cells, which is consistent with the notion that this event was a prerequisite for transfer by TraB(pIJ101). Linear versions of this same replicon did transfer efficiently, in that configuration, from strains containing the conjugative linear plasmid SLP2. Our data indicate that functions necessary and sufficient for transfer of circular DNA were insufficient for transfer of a related linear DNA molecule. The results here suggest that the conjugation mechanisms of linear versus circular DNA in Streptomyces spp. are inherently different and/or that efficient transfer of linear DNA requires additional components.

scholarly journals Topology-dependent anomalous dynamics of ring and linear DNA are sensitive to cytoskeleton crosslinking

2019 ◽  
Vol 5 (12) ◽  
pp. eaay5912 ◽  
Author(s):  
Devynn M. Wulstein ◽  
Kathryn E. Regan ◽  
Jonathan Garamella ◽  
Ryan J. McGorty ◽  
Rae M. Robertson-Anderson
Keyword(s):  
Transport Properties ◽  
Single Molecule ◽  
Intracellular Transport ◽  
Conformational Stability ◽  
Conformational Dynamics ◽  
Single Mode ◽  
Dna Molecules ◽  
Linear Dna ◽  
Linear Chains ◽  
Anomalous Dynamics

Cytoskeletal crowding plays a key role in the diffusion of DNA molecules through the cell, acting as a barrier to effective intracellular transport and conformational stability required for processes such as transfection, viral infection, and gene therapy. Here, we elucidate the transport properties and conformational dynamics of linear and ring DNA molecules diffusing through entangled and crosslinked composite networks of actin and microtubules. We couple single-molecule conformational tracking with differential dynamic microscopy to reveal that ring and linear DNA exhibit unexpectedly distinct transport properties that are influenced differently by cytoskeleton crosslinking. Ring DNA coils are swollen and undergo heterogeneous and biphasic subdiffusion that is hindered by crosslinking. Conversely, crosslinking actually facilitates the single-mode subdiffusion that compacted linear chains exhibit. Our collective results demonstrate that transient threading by cytoskeleton filaments plays a key role in the dynamics of ring DNA, whereas the mobility of the cytoskeleton dictates transport of linear DNA.

scholarly journals Symmetric-in-Plane Compression of Polyamide Pantographic Fabrics—Modelling, Experiments and Numerical Exploration

Symmetry ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 693 ◽  
Author(s):  
Chuong Anthony Tran ◽  
Maciej Gołaszewski ◽  
Emilio Barchiesi
Keyword(s):  
Experimental Data ◽  
Present Article ◽  
Lattice Structure ◽  
Experimental Results ◽  
Fiber Density ◽  
Numerical Exploration ◽  
Peculiar Behaviour ◽  
Plane Compression ◽  
Pantographic Fabrics

Symmetric in-plane compression of a pantographic lattice structure is modelled and simulated, and the results are compared to previously available experimental data. Said experimental results had shown a peculiar behaviour: depending on the fiber density, the deformed shape could present either one or two swellings under compression. The present article is a preliminary modelling attempt aiming at capturing that behaviour numerically.

scholarly journals Knot localization in proteins

2013 ◽  
Vol 41 (2) ◽  
pp. 538-541 ◽  
Author(s):  
Eric J. Rawdon ◽  
Kenneth C. Millett ◽  
Joanna I. Sułkowska ◽  
Andrzej Stasiak
Keyword(s):  
Present Article ◽  
Protein A ◽  
Biological Role ◽  
Complete Analysis ◽  
Precise Localization ◽  
Limited Information ◽  
Linear Chains ◽  
Different Types ◽  
The Matrix ◽  
Knotted Protein

The backbones of proteins form linear chains. In the case of some proteins, these chains can be characterized as forming linear open knots. The knot type of the full chain reveals only limited information about the entanglement of the chain since, for example, subchains of an unknotted protein can form knots and subchains of a knotted protein can form different types of knots than the entire protein. To understand fully the entanglement within the backbone of a given protein, a complete analysis of the knotting within all of the subchains of that protein is necessary. In the present article, we review efforts to characterize the full knotting complexity within individual proteins and present a matrix that conveys information about various aspects of protein knotting. For a given protein, this matrix identifies the precise localization of knotted regions and shows the knot types formed by all subchains. The pattern in the matrix can be considered as a knotting fingerprint of that protein. We observe that knotting fingerprints of distantly related knotted proteins are strongly conserved during evolution and discuss how some characteristic motifs in the knotting fingerprints are related to the structure of the knotted regions and their possible biological role.

Analysis of the mechanism of DNA recombination using tangles

1995 ◽  
Vol 28 (3) ◽  
pp. 253-313 ◽  
Author(s):  
De Witt Sumners ◽  
Claus Ernst ◽  
Sylvia J. Spengler ◽  
Nicholas R. Cozzarelli
Keyword(s):  
Dna Recombination ◽  
Dna Supercoiling ◽  
Topological Properties ◽  
Circular Dna ◽  
Linear Dna ◽  
Naturally Occurring

The DNA of all organisms has a complex and essential topology. The three topological properties of naturally occurring DNA are supercoiling, catenation, and knotting. Although these properties are denned rigorously only for closed circular DNA, even linear DNA in vivo can have topological properties because it is divided into topologically separate subdomains (Drlica 1987; Roberge & Gasser, 1992). The essentiality of topological properties is demonstrated by the lethal consequence of interfering with topoisomerases, the enzymes that regulate the level of DNA supercoiling and that unlink DNA during its replication (reviewed in Wang, 1991; Bjornsti, 1991; Drlica, 1992; Ullsperger et al. 1995).

Mapping unintegrated avian sarcoma virus DNA: Termini of linear DNA bear 300 nucleotides present once or twice in two species of circular DNA

Cell ◽  
1978 ◽  
Vol 15 (4) ◽  
pp. 1383-1395 ◽  
Author(s):  
Peter R. Shank ◽  
Stephen H. Hughes ◽  
Hsing-Jien Kung ◽  
John E. Majors ◽  
Nancy Quintrell ◽  
...  
Keyword(s):  
Avian Sarcoma Virus ◽  
Circular Dna ◽  
Linear Dna ◽  
Sarcoma Virus ◽  
Avian Sarcoma

Study of Airscrews for High Speed Aeroplanes

1940 ◽  
Vol 44 (352) ◽  
pp. 322-337
Author(s):  
Lucio Lazzarino
Keyword(s):  
Special Reference ◽  
Present Article ◽  
High Speed ◽  
Numerical Evaluation ◽  
Experimental Results ◽  
Aerodynamic Efficiency ◽  
Angular Velocities ◽  
Mach Numbers ◽  
High Mach

RésuméIt is demonstrated how, with increase in speed, the diameter of optimum efficiency and the maximum possible value of efficiency of an airscrew diminish. The efficiency of a system of two counter-revolving airscrews with different angular velocities is then determined, and the variation of efficiency with variation in the relation between the angular velocities of the two airscrews.With increase in the height and speed of flight, airscrew performance inevitably falls off, frequently in a marked degree; this being mainly due to the decrease in aerodynamic efficiency of the blade sections at high Mach numbers.The object of the present article is to analyse the influence exerted upon the performance of an airscrew by the various parameters that determine it, wit-h special reference to those connected with the speed and height of flight.A similar study has also been made of systems constituted of two counter-rotating airscrews, with a view to comparing them with isolated airscrews designed to absorb the same power under identical conditions.By the methods here described, an approximate numerical evaluation of the performance can be made, utilising the experimental results which are already to hand.

The lengths of fragments covering a fixed marker in randomly cut linear or circular DNA

1979 ◽  
Vol 16 (04) ◽  
pp. 721-731
Author(s):  
Samuel Litwin
Keyword(s):  
Fragment Length ◽  
Random Number ◽  
Length Distribution ◽  
Attachment Site ◽  
Jump Discontinuity ◽  
Circular Dna ◽  
Linear Dna ◽  
Dna Molecule ◽  
Recovery Pattern

A linear DNA molecule may be labelled at a fixed locus by a minute complementary radioactive molecule. A collection of identical molecules is to be so labelled and each one independently cut at a random number, N, of random places, X (N Poisson, X uniform). Fragments containing the label are to be collected and assayed by length. It is shown that the recovery pattern (fragment length distribution) contains a jump discontinuity at the fixed locus and may be used to determine the distance between the attachment site and the nearest end of the molecule. The recovery pattern under the hypothesis that the collection of molecules are circularly permuted, i.e. the labelled locus is uniformly distributed over the length of the molecule, does not contain such discontinuities. The case where the labelling molecule has a non-negligible extent is also treated.

scholarly journals Clog and Release, and Reverse Motions of DNA in a Nanopore

Polymers ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 84 ◽  
Author(s):  
Tomoya Kubota ◽  
Kento Lloyd ◽  
Naoto Sakashita ◽  
Seiya Minato ◽  
Kentaro Ishida ◽  
...  
Keyword(s):  
Finite Element Method ◽  
Finite Element ◽  
Fluorescence Microscopy ◽  
Numerical Simulations ◽  
Electric Fields ◽  
Reverse Direction ◽  
Dna Molecules ◽  
Circular Dna ◽  
Linear Dna ◽  
Streaming Flow

Motions of circular and linear DNA molecules of various lengths near a nanopore of 100 or 200 nm diameter were experimentally observed and investigated by fluorescence microscopy. The movement of DNA molecules through nanopores, known as translocation, is mainly driven by electric fields near and inside the pores. We found significant clogging of nanopores by DNA molecules, particularly by circular DNA and linear T4 DNA (165.65 kbp). Here, the probabilities of DNA clogging events, depending on the DNA length and shape—linear or circular—were determined. Furthermore, two distinct DNA motions were observed: clog and release by linear T4 DNA, and a reverse direction motion at the pore entrance by circular DNA, after which both molecules moved away from the pore. Finite element method-based numerical simulations were performed. The results indicated that DNA molecules with pores 100–200 nm in diameter were strongly influenced by opposing hydrodynamic streaming flow, which was further enhanced by bulky DNA configurations.

The lengths of fragments covering a fixed marker in randomly cut linear or circular DNA

1979 ◽  
Vol 16 (4) ◽  
pp. 721-731
Author(s):  
Samuel Litwin
Keyword(s):  
Fragment Length ◽  
Random Number ◽  
Length Distribution ◽  
Attachment Site ◽  
Jump Discontinuity ◽  
Circular Dna ◽  
Linear Dna ◽  
Dna Molecule ◽  
Recovery Pattern

A linear DNA molecule may be labelled at a fixed locus by a minute complementary radioactive molecule. A collection of identical molecules is to be so labelled and each one independently cut at a random number, N, of random places, X (N Poisson, X uniform). Fragments containing the label are to be collected and assayed by length. It is shown that the recovery pattern (fragment length distribution) contains a jump discontinuity at the fixed locus and may be used to determine the distance between the attachment site and the nearest end of the molecule.The recovery pattern under the hypothesis that the collection of molecules are circularly permuted, i.e. the labelled locus is uniformly distributed over the length of the molecule, does not contain such discontinuities. The case where the labelling molecule has a non-negligible extent is also treated.

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