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.

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.

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.

DNA supercoiling and transcription: topological coupling of promoters

1996 ◽  
Vol 29 (3) ◽  
pp. 203-225 ◽  
Author(s):  
David M. J. Lilley ◽  
Dongrong Chen ◽  
Richard P. Bowater
Keyword(s):  
Fundamental Property ◽  
Dna Supercoiling ◽  
The Other ◽  
Linear Dna ◽  
Dna Molecule ◽  
Linking Number ◽  
Closed Circle ◽  
A Chain

DNA supercoiling is a consequence of the double-stranded nature of DNA. When a linear DNA molecule is ligated into a covalently closed circle, the two strands become intertwined like the links of a chain, and will remain so unless one of the strands is broken. The number of times one strand is linked with the other is described by a fundamental property of DNA supercoiling, the linking number (Lk).

scholarly journals Replication forms of the gene-sized DNA molecules of hypotrichous ciliates.

1983 ◽  
Vol 3 (9) ◽  
pp. 1562-1566 ◽  
Author(s):  
K G Murti ◽  
D M Prescott
Keyword(s):  
Electron Microscopy ◽  
S Phase ◽  
Origin Of Replication ◽  
Dna Molecules ◽  
Linear Dna ◽  
Dna Molecule ◽  
Independent Unit

Using a method for obtaining DNA from 10 to 40 macronuclei for electron microscopy, we analyzed the structure of gene-sized, linear DNA molecules from S-phase macronuclei of two hypotrichous ciliates, Euplotes eurystomus and Styx sp. Three types of putative replicating intermediates were observed: (i) molecules with a bubble close to one end, (ii) molecules with single forks, and (iii) molecules with two forks. We conclude that: (i) each macronuclear DNA molecule replicates as an independent unit, (ii) the molecules contain an origin of replication close to one or both ends, and (iii) the mode of replication is bidirectional.

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.

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

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.

scholarly journals Genome of the Opportunistic Pathogen Streptococcus sanguinis

2007 ◽  
Vol 189 (8) ◽  
pp. 3166-3175 ◽  
Author(s):  
Ping Xu ◽  
Joao M. Alves ◽  
Todd Kitten ◽  
Arunsri Brown ◽  
Zhenming Chen ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Opportunistic Pathogen ◽  
Surface Proteins ◽  
The Other ◽  
Vitamin B ◽  
Circular Dna ◽  
Streptococcus Sanguinis ◽  
Dna Molecule ◽  
Neutropenic Patients

ABSTRACT The genome of Streptococcus sanguinis is a circular DNA molecule consisting of 2,388,435 bp and is 177 to 590 kb larger than the other 21 streptococcal genomes that have been sequenced. The G+C content of the S. sanguinis genome is 43.4%, which is considerably higher than the G+C contents of other streptococci. The genome encodes 2,274 predicted proteins, 61 tRNAs, and four rRNA operons. A 70-kb region encoding pathways for vitamin B12 biosynthesis and degradation of ethanolamine and propanediol was apparently acquired by horizontal gene transfer. The gene complement suggests new hypotheses for the pathogenesis and virulence of S. sanguinis and differs from the gene complements of other pathogenic and nonpathogenic streptococci. In particular, S. sanguinis possesses a remarkable abundance of putative surface proteins, which may permit it to be a primary colonizer of the oral cavity and agent of streptococcal endocarditis and infection in neutropenic patients.

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