Okazaki Fragment

L.J. Reha-Krantz , in Brenner's Encyclopedia of Genetics (Second Edition), 2013

DNA Replication Is Semiconservative

DNA strands are polymers or chains of deoxynucleoside monophosphates that are linked together by phosphodiester bonds ( Figure 1 (a)). The DNA strands have the opposite orientation: one strand is in the 5′ to 3′ 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 two DNA strands are separated during DNA replication and each parental strand serves as a template for the synthesis of a new daughter strand ( Figure 1 (b)). After replication, there will be two double-stranded DNAs; each will have one 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 structure: (a) the chemical structure of double-stranded DNA and (b) semiconservative DNA replication.

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Recombination | Recombination DNA-Strand Transferases

William Wright , ... Hani Zaher , in Encyclopedia of Biological Chemistry (Third Edition), 2021

Homology Search and DNA-Strand Invasion by DNA-Strand Transferases

DNA-strand transferases catalyze homologous pairing between single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA, or duplex DNA), followed by the exchange of one strand of the dsDNA with the incoming ssDNA. The product of the DNA-strand exchange process is heteroduplex DNA, in which two single strands of DNA that were formerly from distinct DNA molecules form duplex DNA, displacing the original complimentary duplex strand in the region where strand exchange has occurred. This DNA-strand invasion reaction is fundamentally different from DNA-strand annealing, where two ssDNA regions come together to form duplex DNA, because it requires DNA-strand displacement and the original base pairs to be broken. The DNA substrates required for recombination are typically the 3′-overhanging ssDNA from a processed DNA double-strand break (DSB) or ssDNA gaps formed during replication fork stalling (Fig. 1) or other processes. The fundamental goal of a recombination reaction is a template switch to provide a 3′-OH primer a suitable template for DNA synthesis. This synthesis allows the cell to reference and recover sequence from an intact copy of a genetic locus when the other has been damaged (Ehmsen and Heyer, 2008; Heyer et al., 2010).

Fig. 1

Fig. 1. Involvement of DNA-strand transferases in DSB and gap repair by homologous recombination. (a) Double-strand break repair by synthesis-dependent strand annealing (SDSA). After DSB formation, nucleolytic DNA end-processing creates 3′-ended ssDNA that becomes the substrate for DNA strand transferase filament formation (spheres; not to scale or form). Homology search leads to the formation of a paranemic joint, which transitions to a plectonemic joint (D-loop) after strand intertwining. Upon dissociation of the DNA strand transferase from the heteroduplex product, the invading strand 3′ end is extended by DNA polymerase. SDSA is one pathway of DSB repair, and alternative pathways differ only in the steps after DNA synthesis (see suggested readings). In SDSA, the extended invading ssDNA retracts from the D-loop and anneals to the complementary strand of the other DSB end. Synthesis to fill in the remaining gaps and sealing of the nicks by ligation results in a fully restored chromosome. (b) Gap repair by homologous recombination. Recombination from a gap on the lagging strand can displace the newly synthesized leading strand for use as a template for DNA synthesis past a blocking DNA lesion (black box). Notice that the initial joint molecule that forms is an obligatory paraneme because there is no free DNA end to allow strand intertwining.

 Reproduced with permission from Yu, X., Jacobs, S.A., Westt, S.C., Ogawa, T., 2001. Domain structure and dynamics in the helical filaments formed by RecA and Rad51 on DNA. Proceedings of the National Academy of Sciences of the United States of America 98 (15), 8419–8424. Copyright (2001) National Academy of Sciences, U.S.A.

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Replication Fork

L.J. Reha-Krantz , L. 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 ( Figure 1 (a)). The chromosomes of many organisms are composed of two DNA strands: one strand is oriented in the 5′–3′ direction with respect to the carbon atoms on the sugar (deoxyribose) and the complimentary strand is in the opposite 3′–5′ direction. The two DNA strands are held together by hydrogen (H) bonds formed between the bases adenine and thymine to form the AT base pair and between the bases guanine and cytosine to form the GC base pair. Watson and Crick published the double helical structure of DNA in 1953 ( Figure 1 (b)).

Figure 1. DNA structure: (a) the chemical structure of double-stranded DNA, (b) semi-conservative DNA replication, and (c) DNA replication is in the 5′–3′ direction.

Watson and Crick stated that "It has not escaped our notice that the specific pairing we have 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 daughter strand ( Figure 1 (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). After replication, there are two double-stranded DNAs; each with one parental DNA strand and one newly synthesized DNA strand ( Figure 1 (c)). 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 semi-conservative. This rule of DNA replication was demonstrated by Meselson and Stahl in 1958.

Another rule of DNA replication is that DNA polymerases replicate DNA in the 5′–3′ direction ( Figure 1 (a)), which means that DNA polymerases at a replication fork must move in opposite directions with respect to their template strands ( Figure 1 (c)); however, replication of both daughter strands is coupled. To explain this topological problem, R. Okazaki proposed and demonstrated that one DNA strand at the replication fork is synthesized continuously while the second strand is synthesized discontinuously in short fragments ( Figure 2 (a)). The continuously synthesized DNA strand is called the 'leading strand' and the discontinuously synthesized strand is called the 'lagging strand'. The short, lagging strand fragments are called 'Okazaki fragments'.

Figure 2. Both daughter DNA strands are replicated at the same time and in the 5′–3′ direction, 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 , W.-D. Heyer , in Encyclopedia of Biological Chemistry (Second Edition), 2013

Mediators for Presynaptic Filament Formation

DNA-strand transferases are impeded from nucleating filaments when ssDNA-binding proteins saturate ssDNA. Recombination mediators were defined biochemically as proteins that allow filament formation of DNA-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 complex. S. 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 function is occupied by this protein, which was identified as a central tumor suppressor protein for breast and ovarian cancers.

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Base excision repair and nucleotide excision repair

Tadahide Izumi , Isabel Mellon , in Genome Stability (Second Edition), 2021

Poly(ADP-ribose) polymerases 1 (PARP1)

When DNA strand breaks, particularly SSBs, are generated, the earliest reaction occurring in the cells is binding of PARP1 to the damaged DNA. Although PARP1 does not directly participate in the repair reactions, unlike XRCC1, PARP1 possesses an enzymatic activity that polymerizes ADP-ribosyl groups to Lys, Asp, and Glu amino acid residues of many proteins [70] This poly(ADP-ribosyl)ation (PARylation) activity is triggered by DNA strand breaks (SSBs and DSBs to some extent) [71]. A number of proteins have been identified as targets of this posttranslational modification. Importantly, the major acceptor protein is PARP1 itself, and thus, PARP1 is auto-PARylated upon the formation of DNA strand breaks [72].

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The Genetic Information (I)

Antonio Blanco , Gustavo Blanco , in Medical Biochemistry, 2017

DNA Replication is Semiconservative

Each DNA strand of a progenitor cell serves as a template for the synthesis of a new complementary polynucleotide chain that is identical to that of the original cell. This process is known as DNA replication. The DNA received by each daughter cell contains one DNA 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. 21.1). DNA replication takes place before mitosis, during a limited period of the cell cycle, called S phase.

Figure 21.1. DNA replication.

Chains synthesized de novo are shown in white.

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DNA 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 as the process of V(D)J recombination during lymphocyte development, which is a kind of programmed double-strand break [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 as drugs like bleomycin [39,40]. These breaks in the DNA backbone can sometimes cause serious genomic instability, carcinogenesis, and cell death. Defective single-strand break repair often results in neurological diseases rather than carcinogenesis or progeria [41]. Since ROS are one of the major causes of the single-strand breaks, and the high level of oxygen consumption in the nervous system makes it more susceptible to defects in single-strand break 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 problem for all cells and organisms. These double stranded breaks are associated in patients with some progeroid syndromes such as Werner syndrome, ataxia telangiectasia, and Fanconi's anemia [43,44].

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Modes of Action of Antibacterial Agents

David G. Allison , Peter A. Lambert , in Molecular Medical Microbiology (Second Edition), 2015

DNA Replication

The separated DNA strands are kept apart during replication by a specialized protein (Albert's protein) and, with the separated strands as templates, a series of enzymes produce new strands of DNA. 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 activity, then removes the primers and replaces them with DNA strands. Finally a DNA ligase joins the DNA strands together to produce two daughter chromosomes. The entire process is closely surveyed and regulated by proofreading stages to ensure that each nucleotide is incorporated according to the sequence specified in the template. So 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

1.16.3.8 Strand Breakage

DNA strand breaks represent an important type of DNA damage induced by some chemicals and by 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 directly repairable by DNA ligase, rather, several DNA bases must be removed and the sequence resynthesized before the break can be ligated. Many chemicals that induce reactive oxygen species have been shown also to induce SSB. DSB are produced almost exclusively by the radiomimetic enediyne C-1027, which is extremely cytotoxic ( Kennedy et al. 2007). Both SSB and DSB induction can lead to the formation of chromosomal alterations.

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Fluorimetric Analysis of DNA-strand Breakage and Repair Kinetics. Application to Radiotoxicology

O. RIGAUD , H. MAGDELENAT , in New Trends in Genetic Risk Assessment, 1989

Detection of DNA Strand Breaks

DNA strand breaks were measured using the alkaline unwinding procedure, FADU, which was originally described by Birnboïm and Jevcak (1981) and modified by Thierry et al. (1985). Briefly irradiated or control cells were analysed immediately after irradiation or after varying periods of incubation at 37°C to allow DNA damage repair. The steps of the FADU procedure are shown in Fig. 6.1. Cells resuspended in an isotonic solution were distributed in 12 tubes and lysed in urea. Each set of four tubes was treated as follows: P tubes – a mild alkali treatment for 30 min at 0°C plus 60 min at 15°C allowed the partial unwinding of the DNA to occur; B tubes – after addition of the alkali solution and sonication of the cell lysate, the tubes were kept for 30 min at 20°C to ensure a total DNA unwinding. A neutralizing solution was then added to the P and B tubes. T tubes – the alkali buffer and the neutralizing solution were added simultaneously in order to prevent DNA unwinding. After a rapid sonication to homogenize, ethidium bromide (a fluorescent dye specific for short duplex DNA) was added to all tubes. Relative fluorescence intensities were read at room temperature in a spectrofluorimeter operating at 520 nm (excitation) and 590 nm (emission). The fraction of DNA that remains double-stranded after the alkali treatment was calculated as D = 100 × (P–B):(T–B). It has been shown empirically that the logarithm of the "fraction double-stranded" (F) was a linear function of dose (Rydberg, 1975). Results were expressed in units of Qd: Qd = 100 [log (% D control) – log (% D irradiated)] which gave an estimation of DNA-strand breaks induced after γ-irradiation. Empirically the dose–response curve was found to be linear in the dose range (0–7 Gy). The relationship Qd = k dose + b has been established. A mean value of k determined in previous experiments was about 12, the term b being negligible. From these experimental results (McWilliams et al., 1983; Thierry et al., 1985), it can be estimated that one Qd unit represents about 100 breaks per cell, so that one Gray of 137Cs produces 1200 breaks/cell. This assay, as in other methods involving alkaline conditions, does not discriminate between single- or double-strand breaks and alkali-labile sites. It can be assumed that three to eight double-strand breaks for 100 strand breaks detected occur after ionizing radiation (van der Schans, 1983). In repair experiments, percentage of residual DNA damage was expressed as %Dt = Qdt/Qd0 where subscript t represents the repair period of t min.

Fig. 6.1. Experimental schema of the FADU assay.

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