A Strand of Dna is a Polymer of

Dna Strand

Okazaki Fragment

L.J.
Reha-Krantz
, in


Brenner’s Encyclopedia of Genetics (2nd Edition), 2013

DNA Replication Is Semiconservative


DNA strands
are polymers or bondage of deoxynucleoside monophosphates that are linked together past phosphodiester bonds (


Effigy 1
(a)). The DNA strands take the opposite orientation: one strand is in the 5′ to three′ direction with respect to the carbon atoms on the sugar (deoxyribose) and the complementary strand is in the 3′ to 5′ direction (
Figure 1
(a)). The 2 DNA strands are separated during Deoxyribonucleic acid replication and each parental strand serves as a template for the synthesis of a new girl strand (
Figure 1
(b)). After replication, there will exist two double-stranded DNAs; each volition have 1 parental Dna strand and one newly synthesized DNA strand. Because the original double-stranded Dna is not conserved but one parental strand is found in each new duplex Dna, replication is said to be semiconservative. This ‘rule’ of DNA replication was demonstrated by Meselson and Stahl in 1958.


Figure 1.
Dna construction: (a) the chemic construction of double-stranded DNA and (b) semiconservative Deoxyribonucleic acid replication.



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Replication Fork

L.J.
Reha-Krantz
,
50.
Zhang
, in


Brenner’s Encyclopedia of Genetics (Second Edition), 2013

DNA Replication Forks Are Sites of Ongoing Dna Replication


DNA strands
are polymers or chains of deoxynucleoside monophosphates (dNMPs) that are linked together by phosphodiester bonds (


Effigy ane
(a)). The chromosomes of many organisms are equanimous of ii Deoxyribonucleic acid strands: ane strand is oriented in the 5′–iii′ direction with respect to the carbon atoms on the sugar (deoxyribose) and the complimentary strand is in the opposite 3′–5′ management. The two Deoxyribonucleic acid strands are held together past hydrogen (H) bonds formed between the bases adenine and thymine to form the AT base pair and betwixt the bases guanine and cytosine to form the GC base pair. Watson and Crick published the double helical structure of Dna in 1953 (
Figure i
(b)).


Figure ane.
Deoxyribonucleic acid structure: (a) the chemic structure of double-stranded DNA, (b) semi-conservative Dna replication, and (c) Deoxyribonucleic acid replication is in the v′–3′ direction.



Watson and Crick stated that “It has not escaped our notice that the specific pairing nosotros take postulated immediately suggests a possible copying mechanism for the genetic material.” As predicted, the two Dna strands are separated during Dna replication and each parental strand serves as a template for the synthesis of a new, complimentary girl strand (
Figure one
(b)). DNA polymerases synthesize the daughter strands using the four building blocks of Dna – the deoxynucleoside triphosphates (deoxynucleoside adenosine triphosphate (dATP), deoxynucleoside cytosine triphosphate (dCTP), deoxynucleoside guanine triphosphate (dGTP), and deoxynucleoside thymine triphosphate (dTTP)). An A (adenine) in the template strand directs the incorporation of the T nucleotide (dTMP), T (thymine) templates the incorporation of A (damp), G (guanine) templates the incorporation of C (dCMP), and C (cytosine) templates the incorporation of G (dGMP). Later replication, there are two double-stranded DNAs; each with one parental Deoxyribonucleic acid strand and one newly synthesized DNA strand (
Figure one
(c)). Because the original double-stranded DNA is non conserved, but one parental strand is found in each new duplex DNA, replication is said to be semi-conservative. This rule of Deoxyribonucleic acid replication was demonstrated by Meselson and Stahl in 1958.

Some other rule of DNA replication is that DNA polymerases replicate DNA in the 5′–three′ direction (
Figure 1
(a)), which ways that Deoxyribonucleic acid polymerases at a replication fork must move in opposite directions with respect to their template strands (
Effigy 1
(c)); however, replication of both girl strands is coupled. To explain this topological problem, R. Okazaki proposed and demonstrated that one Deoxyribonucleic acid strand at the replication fork is synthesized continuously while the second strand is synthesized discontinuously in short fragments (
Figure 2
(a)). The continuously synthesized Deoxyribonucleic acid strand is called the ‘leading strand’ and the discontinuously synthesized strand is called the ‘lagging strand’. The short, lagging strand fragments are chosen ‘Okazaki fragments’.


Figure ii.
Both daughter Dna strands are replicated at the same fourth dimension and in the 5′–3′ management, but leading strand replication is continuous and lagging strand replication is discontinuous (a). The trombone model for lagging strand replication (b).



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Recombination: DNA-Strand Transferases

W.D.
Wright
,
West.-D.
Heyer
, in


Encyclopedia of Biological Chemistry (Second Edition), 2013

Mediators for Presynaptic Filament Germination

Dna-strand transferases are impeded from nucleating filaments when ssDNA-bounden proteins saturate ssDNA. Recombination mediators were divers biochemically as proteins that allow filament formation of Deoxyribonucleic acid-strand transferases on ssDNA coated by the cognate ssDNA-binding protein. The prototypical recombination mediator is UvsY protein from bacteriophage T4, which overcomes the block to ssDNA binding imposed by Gp32 SSB protein to allow UvsX filament formation. RecFOR provides this function in
E. coli
for RecA protein. In eukaryotes, the situation is more circuitous.
Due south.
cerevisiae
Rad52, the ortholog of UvsY and RecO proteins, mediates Rad51 filament formation
in vitro, but human protein does not. Instead, in eukaryotes containing the BRCA2 protein, the mediator part is occupied by this protein, which was identified as a central tumor suppressor protein for chest and ovarian cancers.

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The Genetic Information (I)

Antonio
Blanco
,
Gustavo
Blanco
, in


Medical Biochemistry, 2017

Dna Replication is Semiconservative

Each
Deoxyribonucleic acid strand
of a progenitor cell serves every bit a template for the synthesis of a new complementary polynucleotide chain that is identical to that of the original cell. This process is known equally

DNA replication. The DNA received by each daughter cell contains one Deoxyribonucleic acid strand that is newly synthesized at replication, and another strand that is directly received from the parental Dna. For this reason, the replication process is referred to as semiconservative (Fig. 21.one). Deoxyribonucleic acid replication takes place before mitosis, during a express flow of the cell cycle, called S phase.


Effigy 21.i.
Dna replication.

Chains synthesized de novo are shown in
white.



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Deoxyribonucleic acid Damage Responses in Atherosclerosis

Kenichi
Shimada
, …
Moshe
Arditi
, in


Biological DNA Sensor, 2014

Dna Strand Breaks


Dna strand
breaks are produced in intermediate events of natural reactions such equally the process of 5(D)J recombination during lymphocyte development, which is a kind of programmed double-strand intermission

[37,38]. On the other hand, DNA strand breaks can be caused by oxidative Dna damage or by ionizing radiation (e.g. X-rays and gamma rays) as well equally drugs similar bleomycin
[39,forty]. These breaks in the Dna backbone tin can sometimes cause serious genomic instability, carcinogenesis, and cell death. Lacking single-strand break repair often results in neurological diseases rather than carcinogenesis or progeria
[41]. Since ROS are 1 of the major causes of the single-strand breaks, and the loftier level of oxygen consumption in the nervous system makes information technology more than susceptible to defects in single-strand interruption repair, it makes sense that single-strand breaks may contribute to neurological disorders
[42].

Unrepaired double stranded Dna breaks lead to genomic rearrangements, a common and serious trouble for all cells and organisms. These double stranded breaks are associated in patients with some progeroid syndromes such as Werner syndrome, clutter telangiectasia, and Fanconi’s anemia
[43,44].

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Modes of Activeness of Antibacterial Agents

David G.
Allison
,
Peter A.
Lambert
, in


Molecular Medical Microbiology (2d Edition), 2015

DNA Replication

The separated
DNA strands
are kept apart during replication by a specialized protein (Albert’south protein) and, with the separated strands every bit templates, a series of enzymes produce new strands of Deoxyribonucleic acid. An RNA polymerase then forms short primers of RNA on each strand at specific initiator sites, and DNA polymerase Iii synthesizes and joins short Dna strands onto the RNA primers. Dna polymerase I, which possesses nucleotidase activeness, then removes the primers and replaces them with DNA strands. Finally a DNA ligase joins the Deoxyribonucleic acid strands together to produce two daughter chromosomes. The entire process is closely surveyed and regulated past proofreading stages to ensure that each nucleotide is incorporated co-ordinate to the sequence specified in the template. And then far, no therapeutic antimicrobials are available that specifically target the DNA polymerases.

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General Principles

R.J.
Preston
,
J.A.
Ross
, in


Comprehensive Toxicology, 2010

i.16.3.8

Strand Breakage


Dna strand
breaks represent an of import blazon of DNA damage induced by some chemicals and past ionizing radiation. The chemotherapeutic agent bleomycin is an efficient inducer of both single-strand breaks (SSB) and double-strand breaks (DSB). Bleomycin intercalates into the Dna helix and abstracts a hydrogen from C4′ of deoxyribose, inducing a radical capable of leading to either a strand break or an abasic site. These strand breaks are not straight repairable by Deoxyribonucleic acid ligase, rather, several Dna bases must exist removed and the sequence resynthesized before the break can be ligated. Many chemicals that induce reactive oxygen species take been shown also to induce SSB. DSB are produced well-nigh exclusively by the radiomimetic enediyne C-1027, which is extremely cytotoxic (

Kennedy
et al.
2007
). Both SSB and DSB induction can atomic number 82 to the formation of chromosomal alterations.

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Microbiology of Atypical Environments

Hirak Ranjan
Dash
,
Surajit
Das
, in


Methods in Microbiology, 2018

3.2.2.1

DGGE/temperature gradient gel electrophoresis (TGGE)


DNA strands
of the same length and different sequences can be separated by the techniques of DGGE and/or TGGE. In this technique, the whole Deoxyribonucleic acid is extracted from the atypical ecology samples followed by amplification of 16S/18S rRNA gene by PCR and separation of the amplified sequences on a linear gradient of DNA denaturants or temperature (

Strathdee & Free, 2013). Thus, the separation of DNA fragments is based on the differential mobility of the partially single-stranded Deoxyribonucleic acid molecules in an acrylamide gel containing urea and formamide as denaturants (Mühling, Woolven-Allen, Murrell, & Joint, 2008). Additionally, TGGE too employs the aforementioned principle, where a gradient of temperature replaces the chemical denaturants in the polyacrylamide gel (Viglasky, 2013). In both the techniques, a GC clench of 30–fifty nucleotides long is attached to the 5′ stop of the amplicon which is essential to prevent complete dissociation of the Deoxyribonucleic acid fragment with increase in denaturant concentration or temperature gradients.

Applications of DGGE and TGGE are quite common to diverseness studies in atypical environments. Stabilization of saline nitrogen waste product water by highly diverse denitrifying bacteria has been well established past DGGE of PCR amplified 16S rRNA gene fragments where a taxonomic affiliation of the dominant microbial species has been established every bit γ-Proteobacteria (Yoshie et al., 2001). DGGE analysis besides revealed the occurrence of Archaea in mangrove trees such as
Rhizophora mangle
and
Laguncularia racemosa
in complex atypical environmental atmospheric condition (Pires et al., 2012). Application of the DGGE technique further revealed the occurrence of around 15 different prokaryotic taxa belonging to genera
Alcanivorax,
Pseudoxanthomonas,
Bosea,
Halomonas
and
Marinobacter
in oil contaminated desert soil, sea water and hypersaline coastal soil (Al-Mailem, Kansour, & Radwan, 2017).

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Noncoding RNAs in Genome Integrity

I.
Kovalchuk
, in


Genome Stability, 2016

v.4.1

Regulation of Sensors


DNA strand
breaks are sensed past several groups of proteins, such as the Mre11–Rad50–Nbs1 (MRN) complex, Ku70/80, and 53BP1. Proteins like ATM and γH2AX (the phosphorylated grade of H2AX protein) also play an essential part in the initial harm recognition and signaling because H2AX is one of the first immediate targets of ATM phosphorylation. The repair choice is influenced by this initial bounden (see

Affiliate 14). Therefore, the regulation of the abundance of 1 or several components of these sensors may significantly influence Deoxyribonucleic acid-repair choice and outcomes.

Two component proteins involved in sensing strand breaks, Nbs1 and Ku80, may likely exist regulated past miRNAs as they both contain the long 3′-UTRs with a high number of miRNA binding sites that can serve every bit a potential target for translation inhibition. Indeed, a 2015 work showed that Ku80 expression could indeed be affected past hsa–miR–526b in nonsmall-jail cell lung carcinoma (NSCLC)
[21]. Hsa–miR–526b was institute to be downregulated and Ku80 upregulated in the NSCLC cells compared to healthy tissues. No experimental information be for Nbs1, but an association study demonstrated that NBS1 likewise as Mre11 were likely to be regulated by miRNA; a instance–control study revealed the association between the presence of SNPs in binding of several miRNAs at the 3′-UTR of these genes with an increased risk of breast cancer development
[22]. Like information for Nbs1 were observed in case-control studies involving colorectal cancer
[23].

The expression of ATM is also regulated by miRNA at the posttranslational level; in neuroblastoma and HeLa cells, miR-421 downregulates ATM activity by modulating cell-cycle checkpoints and irresolute jail cell sensitivity to IR
[24]. Similarly, miR-100
[25], miR-101
[26], and miR-18a
[27]
are also probable to regulate ATM because all of them were shown to target the 3′-UTR of ATM and downregulate it. Details of miRNA impact on diverse steps of DSB repair are shown in
Fig. 25.1C
[15].

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Mycotoxins

Carina
Ladeira
, in


Environmental Mycology in Public Health, 2016

Formamidopyrimidine DNA Glycosylase

Measuring
DNA strand
breaks gives limited information. Breaks may represent the direct effect of some damaging agent, just generally they are speedily rejoined. They may in fact be apurinic/apyrimidinic (AP) sites baseless sugars, which are alkali labile and therefore appear as breaks. Or they may be intermediates in cellular repair considering both nucleotide and base excision–repair processes cutting out damage and replace it with sound nucleotides.


62,66

AP sites are alkali labile, and so in principle they are expected to appear amongst the strand breaks, detected in the standard alkaline metal comet analysis. However, it has non been assuredly demonstrated that all AP sites are converted under these conditions.
56,64

To make the assay more specific and sensitive, an actress step was introduced of digesting the nucleoids with an enzyme that recognizes a particular kind of damage and creates a break. FPG detects the major purine oxidation product viii-OHG as well equally other altered purines.
55,60,63,65

This enzyme was named for its ability to recognize imidazole-ring–opened purines, or formamidopyrimidines: namely, eight-oxo-Thou, 2,six-diamino-four-hydroxy-five-formadopyrimidine and iv,half dozen-diamino-5-formamidopyrimidine, which occur during the spontaneous breakdown of damaged purines; however, a major substrate in cellular DNA is 8-OHG.
56,59,61,66

A mammalian analogue of FPG, OGG1, has been applied in the Comet assay; withal, studies performed comparing FPG and OGG1 revealed the ineffectiveness of OGG1.
56

For that reason, FPG continues to be the enzyme of choice for oxidized purines.

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A Strand of Dna is a Polymer of

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