scholarly journals An algorithm and application to efficiently analyze DNA fiber data

2021 ◽  
Author(s):  
Teodor Kirilov ◽  
Anastas Gospodinov ◽  
Kiril Kirilov
Keyword(s):  
Dna Replication ◽  
Genetic Information ◽  
Control Mechanisms ◽  
Dna Molecules ◽  
Dna Molecule ◽  
Java Application ◽  
Replication Control ◽  
Standardized Measurement ◽  
Single Dna Molecule ◽  
Dna Size

The duplication of genetic information (DNA replication) is central to life. Numerous control mechanisms ensure the exact course of the process during each cell division. Disturbances of DNA replication have severe consequences for the affected cell, and current models link them to cancer development. One of the most accurate methods for studying DNA replication is labeling newly synthesized DNA molecules with halogenated nucleotides, followed by immunofluorescence and microscopy detection, known as DNA fiber labeling. The method allows the registration of the activity of single replication complexes by measuring the length of the "trace" left by each of them. The major difficulty of the method is the labor-intensive analysis, which requires measuring the lengths of a large number of labeled fragments. Recently, the interest in this kind of image analysis has grown rapidly. In this manuscript, we provide a detailed description of an algorithm and a lightweight Java application to automatically analyze single DNA molecule images we call "DNA size finder". DNA size finder significantly simplified the analysis of the experimental data while increasing reliability by the standardized measurement of a greater number of DNA molecules. It is freely available and does not require any paid platforms or services to be used. We hope that the application will facilitate both the study of DNA replication control and the effects of various compounds used in human activity on the process of DNA replication.

The Structure of DNA Taking Into Account the Higher Dimension of Its Components

2021 ◽  
pp. 730-747
Author(s):  
Gennadiy Vladimirovich Zhizhin
Keyword(s):  
Phosphoric Acid ◽  
Genetic Information ◽  
Higher Dimension ◽  
Dna Molecules ◽  
Dna Molecule ◽  
First Time ◽  
In Cells

The process of formation of spirals (right and left) in the DNA molecule is described for the first time. Representations of the higher dimensionality of the constituent DNA molecules (D-ribose and phosphoric acid ion), developed in the previous works of the author, are used. Images of a DNA molecule with elements of higher dimension are presented. The higher dimensionality of the constituent DNA molecules, which allows to describe mathematically the structure of DNA, requires reconsidering the issues of tight packing of DNA molecules in cells, viruses and bacteria, provided that the DNA chains necessary for the preservation and transfer of genetic information are complementary.

The control of histone gene expression

2012 ◽  
Vol 40 (4) ◽  
pp. 880-885 ◽  
Author(s):  
Alexander M.J. Rattray ◽  
Berndt Müller
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Dna Replication ◽  
Histone Gene ◽  
Transcriptional Level ◽  
Control Mechanisms ◽  
Histone Proteins ◽  
Histone Gene Expression ◽  
Replication Control

Histone proteins are essential for the packaging of DNA into chromosomes. Histone gene expression is cell-cycle-regulated and coupled to DNA replication. Control of histone gene expression occurs at the transcriptional and post-transcriptional level and ensures that a fine balance between histone abundance and DNA replication is maintained for the correct packaging of newly replicated DNA into chromosomes. In the present paper, we review histone gene expression, highlighting the control mechanisms and key molecules involved in this process.

Replication of Bacteriophage 186 DNA

1972 ◽  
Vol 30 ◽  
pp. 194-195
Author(s):  
Dhruba K. Chattoraj ◽  
Ross B. Inman
Keyword(s):  
Electron Microscopy ◽  
Dna Replication ◽  
Frame Of Reference ◽  
Dna Molecules ◽  
E Coli ◽  
Phage Dna ◽  
Partial Denaturation

Electron microscopy of replicating intermediates has been quite useful in understanding the mechanism of DNA replication in DNA molecules of bacteriophage, mitochondria and plasmids. The use of partial denaturation mapping has made the tool more powerful by providing a frame of reference by which the position of the replicating forks in bacteriophage DNA can be determined on the circular replicating molecules. This provided an easy means to find the origin and direction of replication in λ and P2 phage DNA molecules. DNA of temperate E. coli phage 186 was found to have an unique denaturation map and encouraged us to look into its mode of replication.

PrimPol (Primase/Polymerase), replicating enzyme – A mini review

2020 ◽  
Vol 2 (4) ◽  
pp. 89-92
Author(s):  
Muhammad Amir ◽  
Sabeera Afzal ◽  
Alia Ishaq
Keyword(s):  
Dna Replication ◽  
Dna Polymerase ◽  
Genetic Information ◽  
Nuclear Dna ◽  
De Novo ◽  
Dna Polymerases ◽  
Test Site ◽  
Mitochondrial Dna Replication ◽  
Dna Template ◽  
Preliminary Phase

Polymerases were revealed first in 1970s. Most important to the modest perception the enzyme responsible for nuclear DNA replication that was pol , for DNA repair pol and for mitochondrial DNA replication pol  DNA construction and renovation done by DNA polymerases, so directing both the constancy and discrepancy of genetic information. Replication of genome initiate with DNA template-dependent fusion of small primers of RNA. This preliminary phase in replication of DNA demarcated as de novo primer synthesis which is catalyzed by specified polymerases known as primases. Sixteen diverse DNA-synthesizing enzymes about human perspective are devoted to replication, reparation, mutilation lenience, and inconsistency of nuclear DNA. But in dissimilarity, merely one DNA polymerase has been called in mitochondria. It has been suggest that PrimPol is extremely acting the roles by re-priming DNA replication in mitochondria to permit an effective and appropriate way replication to be accomplished. Investigations from a numeral of test site have significantly amplified our appreciative of the role, recruitment and regulation of the enzyme during DNA replication. Though, we are simply just start to increase in value the versatile roles that play PrimPol in eukaryote.

scholarly journals Remodeler Catalyzed Nucleosome Repositioning: Influence of Structure and Stability

2020 ◽  
Vol 22 (1) ◽  
pp. 76
Author(s):  
Aaron Morgan ◽  
Sarah LeGresley ◽  
Christopher Fischer
Keyword(s):  
Free Energy ◽  
Dna Replication ◽  
Recent Work ◽  
Chromatin Remodeling ◽  
Chromatin Structure ◽  
Genetic Information ◽  
Molecular Machines ◽  
Mechanical Work ◽  
Eukaryotic Genome ◽  
Hydrolysis Of

The packaging of the eukaryotic genome into chromatin regulates the storage of genetic information, including the access of the cell’s DNA metabolism machinery. Indeed, since the processes of DNA replication, translation, and repair require access to the underlying DNA, several mechanisms, both active and passive, have evolved by which chromatin structure can be regulated and modified. One mechanism relies upon the function of chromatin remodeling enzymes which couple the free energy obtained from the binding and hydrolysis of ATP to the mechanical work of repositioning and rearranging nucleosomes. Here, we review recent work on the nucleosome mobilization activity of this essential family of molecular machines.

The elastic theory of a single DNA molecule

Pramana ◽  
2003 ◽  
Vol 61 (2) ◽  
pp. 353-360
Author(s):  
Haijun Zhou ◽  
Yang Zhang ◽  
Zhang-Can Ou-Yang
Keyword(s):  
Elastic Theory ◽  
Dna Molecule ◽  
Single Dna Molecule

Label-free plasmonic assisted optical trapping of single DNA molecule

2021 ◽  
Author(s):  
Lei Chen ◽  
Wei Liu ◽  
Dongyi Shen ◽  
Zhihao Zhou ◽  
Yuehan Liu ◽  
...  
Keyword(s):  
Optical Trapping ◽  
Label Free ◽  
Dna Molecule ◽  
Single Dna Molecule

Analysis of an origin of DNA amplification in Sciara coprophila by a novel three-dimensional gel method

1994 ◽  
Vol 14 (2) ◽  
pp. 1520-1529
Author(s):  
C Liang ◽  
S A Gerbi
Keyword(s):  
Three Dimensional ◽  
Dna Amplification ◽  
Gel Method ◽  
Dna Molecule ◽  
Cutting Out ◽  
Origin Region ◽  
2D Gel ◽  
Third Dimension ◽  
Single Dna Molecule ◽  
Replication Intermediates

The replication origin region for DNA amplification in Sciara coprophila DNA puff II/9A was analyzed with a novel three-dimensional (3D) gel method. Our 3D gel method involves running a neutral/neutral 2D gel and then cutting out vertical gel slices from the area containing replication intermediates, rotating these slices 90 degrees to form the third dimension, and running an alkaline gel for each of the slices. Therefore, replication intermediates are separated into forks and bubbles and then are resolved into parental and nascent strands. We used this technique to determine the size of forks and bubbles and to confirm the location of the major initiation region previously mapped by 2D gels to a 1-kb region. Furthermore, our 3D gel analyses suggest that only one initiation event in the origin region occurs on a single DNA molecule and that the fork arc in the composite fork-plus-bubble pattern in neutral/neutral 2D gels does not result from broken bubbles.

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