File Name: dna repair and mutagenesis .zip
DNA repair diseases: what do they tell us about cancer and aging? Send correspondence to. The discovery of DNA repair defects in human syndromes, initially in xeroderma pigmentosum XP but later in many others, led to striking observations on the association of molecular defects and patients' clinical phenotypes. For example, patients with syndromes resulting from defective nucleotide excision repair NER or translesion synthesis TLS present high levels of skin cancer in areas exposed to sunlight.
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But it has since been recognized that DNA is subject to continuous damage and the cell has an arsenal of ways of responding to such injury.
Although mutations or deficiencies in repair can have catastrophic consequences, causing a range of human diseases, mutations are nonetheless fundamental to life and evolution.
I later came to realise that DNA is so precious that probably many distinct repair mechanisms would exist. This retrospective reflection by Francis Crick, penned two decades after he and James Watson reported the structure of DNA, hints at the early perception of DNA as a highly stable macromolecular entity.
This prevailing view at the time significantly delayed serious consideration of biochemical processes such as mutation and repair. It became apparent that DNA in all living organisms continually incurs a myriad of types of damage, and that cells have devised ingenious mechanisms for tolerating and repairing the damage. Failure of these mechanisms can lead to serious disease consequences, as well illustrated in the human hereditary diseases xeroderma pigmentosum XP , hereditary non-polyposis colon cancer HNPCC and some forms of breast cancer.
XP is characterized by about a 10,fold increased risk of skin cancer associated with sunlight exposure; individuals with HNPCC manifest an increased hereditary predisposition to colon and other cancer. The early work on DNA damage and repair in the s was stimulated by a small but prominent group of physicists 3.
Their partnership was stimulated by the work of Hermann Muller, a geneticist working on the fruitfly Drosophila who first demonstrated that external agents, such as ionizing radiation, can cause mutations in living organisms 6.
In retrospect, it was inevitable that the deployment of physical and later chemical tools, such as ionizing and ultraviolet UV radiation, to study genes would in due course lead to questions as to how these agents damaged DNA 3.
And, once it was recognized that these interactions promoted deleterious effects on the structure and function of genes, to questions concerning how cells cope with damaged DNA. Hints of the ability of living cells to recover from the lethal effect of UV radiation emerged as early as the mids 8.
They were both using UV radiation as an experimental tool, but observed anomalous survival rates when cells or bacteriophage bacteria-infecting viruses were inadvertently exposed to long-wavelength light, either as sunlight or fluorescent light in their respective laboratories 9 , Their efforts to explain these confounding observations led to the discovery of the phenomenon now known as photoreactivation, whereby the DNA damage incurred by exposure to UV light is repaired by a light-dependent enzyme reaction 11 Fig.
DNA exposed to ultraviolet UV radiation results in covalent dimerization of adjacent pyrimidines, typically thymine residues thymine dimers , illustrated here as a purple triangle. Curiously, even with the elucidation of the structure of DNA only four years away, neither Dulbecco nor Watson — who was a graduate student in Luria's laboratory when Dulbecco stumbled on photoreactivation, and had himself examined the effects of ionizing radiation for his doctoral thesis 2 — thought about DNA repair.
Tautomerism is the property of a compound that allows it to exist in two interconvertible chemical states; in the case of DNA bases, as either keto or enol forms. Watson and Crick had initially overlooked the complications of tautomerism and were trying unsuccessfully to construct their DNA model with the rare enol form of bases.
It was only after Jerry Donohue, a former graduate student of Linus Pauling, pointed out to Watson that he should be using the more common keto form that the problem of how bases could stably pair was solved But no consideration was then given to the fact that the chemical lability of DNA implicit in tautomerism might have wider implications for the stability of genes.
Indeed, the field gave little thought to the precise nature of DNA damage and its possible biological consequences. One must recall, however, that even at the time the DNA double helix was unveiled, its 'pathology' and the biological consequences thereof were far less compelling problems than deciphering the genetic code or understanding the essential features of DNA replication.
Even mutagenesis — put to extensive use as a tool for determining the function of genes and their polypeptide products, and for defining the genetic code — was not widely considered in mechanistic terms until much later This is despite the fact that the repair phenomenon of photoreactivation was known before the discovery of the structure of DNA. However, it was not intuitively obvious that a double-stranded molecule should be required for DNA replication. In principle, a single-stranded chain could just as easily do.
But the significance of the duplex DNA structure soon became apparent. It was shown that DNA replicates in a semi-conservative fashion, whereby each strand of the double helix pairs with a new strand generated by replication.
This enables errors introduced during DNA replication to be corrected by a mechanism known as excision repair, which relies on the redundancy inherent in having two complementary strands of the genetic code.
If the nucleotides on one strand are damaged, they can be excised and the intact opposite strand used as a template to direct repair synthesis of DNA 15 Fig. DNA damage illustrated as a black triangle results in either repair or tolerance. Mispaired bases, usually generated by mistakes during DNA replication, are excised as single nucleotides during mismatch repair.
A damaged base is excised as a single free base base excision repair or as an oligonucleotide fragment nucleotide excision repair. Such fragments are generated by incisions flanking either side of the damaged base. Nucleotide excision repair can also transpire in some organisms by a distinct biochemical mechanism involving only a single incision next to a site of damage unimodal incision.
The elucidation of the DNA structure provided the essential foundation for defining the different types of mutations arising from both spontaneous and environmental DNA damage that affect all living cells Once again, the insights of physicists featured prominently 3 , including among others, Richard Setlow who identified thymine dimers as stable and naturally occurring DNA lesions arising in cells exposed to sunlight UV radiation.
Such lesions comprise a covalent joining of two adjacent thymine residues in the same DNA chain. They generate considerable distortion of the normal structure of DNA and seriously impede DNA transactions such as replication and transcription.
The repair of these lesions could be monitored experimentally, and promoted the discovery by Setlow 16 and others 2 of excision repair in bacteria and higher organisms As the profusion of alterations in DNA became more widely recognized, scientists came to appreciate that the identification of any new type of naturally occurring base damage would, if one searched diligently enough, almost certainly lead to the discovery of one or more mechanisms for its repair or tolerance 2 , Such has indeed been the case.
DNA repair now embraces not only the direct reversal of some types of damage such as the enzymatic photoreactivation of thymine dimers , but also multiple distinct mechanisms for excising damaged bases, termed nucleotide excision repair NER , base excision repair BER and mismatch repair MMR 11 Fig 2.
The principle of all three mechanisms of repair involves splicing out the damaged region and inserting new bases to fill the gap, followed by ligation of the pieces. The process of NER is biochemically complicated, involving as many as 30 distinct proteins in human cells that function as a large complex called the nucleotide excision repairosome. This 'repair machine' facilitates the excision of damaged nucleotides by generating bimodal incisions in the flanking regions and removing a fragment about 30 nucleotides in length 11 Fig.
Damaged bases that are not recognized by the NER machinery are corrected by BER, whereby the bases are excised from the genome as free bases by a different set of repair enzymes. In MMR, incorrect bases incorporated as a result of mistakes during DNA replication are excised as single nucleotides by yet a third group of repair proteins Fig.
Both NER and BER transpire by somewhat different mechanisms depending on whether the DNA damage is located in regions of the genome that are undergoing active gene expression transcription-coupled repair or are transcriptionally silent global genome repair 11 , In addition to the various modes of excision repair that evolved to cope with damaged bases or mistakes during replication, cells frequently suffer breakage of one or both chains of the DNA duplex Naturally occurring reactive oxygen molecules and ionizing radiation are prevalent sources of such damage Strand breaks must be repaired in order to maintain genomic integrity.
In particular, double-strand breaks DSBs sever the chromosomes and are lethal unless repaired Several mechanisms for the repair of DSBs have been elucidated Fig. One of these involves swapping equivalent regions of DNA between homologous chromosomes — a process called recombination This type of exchange occurs naturally during meiosis, the special type of cell division that generates the germ cells sperm and ova.
It can also be used to repair a damaged site on a DNA strand by using information located on the undamaged homologous chromosome. This process requires an extensive region of sequence homology between the damaged and template strands. Multiple proteins are required for DSB repair by recombination and deficiencies in this repair mechanism can cause cancer.
For example, mutation of at least one of these repair proteins called BRCA1 causes hereditary breast cancer. An alternative mechanism for the repair of DSBs, called non-homologous end joining, also requires a multi-protein complex, and essentially joins broken chromosome ends in a manner that does not depend on sequence homology and may not be error free Fig.
Double-strand breaks can result from exposure to ionizing radiation, oxidative damage and the spontaneous cleavage of the sugar-phosphate backbone of the DNA molecule. Their repair can be effected by either rejoining the broken ends left or by homologous recombination with a sister DNA molecule right.
Both processes involve different multi-protein complexes. Although insights into DNA repair have progressed at an impressive pace, especially in the past decade, an understanding of the mechanisms of mutagenesis — a phenomenon that, as mentioned earlier, was demonstrated experimentally before discovery of the structure of DNA — has lagged.
A breakthrough came from the experimental demonstration that some mutations arise as a consequence of a cell's efforts to tolerate damage. One such damage-tolerance mechanism, called translesion DNA synthesis, involves the replication machinery bypassing sites of base damage, allowing normal DNA replication and gene expression to proceed downstream of the unrepaired damage 20 Fig.
It involves specialized low-fidelity 'sloppy' DNA polymerases that are able to bypass DNA lesions that typically stall the high-fidelity polymerases required for DNA replication. To overcome the block, these 'sloppy copiers' add nucleotides to the replicating strand opposing the DNA lesion, thus allowing replication to continue, but nevertheless introducing mutations into the newly synthesized sequence Once the lesion has been completely bypassed, the replication machinery resumes DNA replication.
As a result of this process, mutations to the DNA sequence are now incorporated into one strand. Recent years have witnessed the recognition that biological responsiveness to genetic insult embraces more than the repair and tolerance of DNA damage. The exposure of cells to many DNA-damaging agents results in the transcriptional upregulation of a large number of genes, the precise function s of many of which remains to be established.
Additionally, cells have evolved complex signalling pathways to arrest the progression of the cell cycle in the presence of DNA damage, thereby providing increased time for repair and tolerance mechanisms to operate 21 Fig. Finally, when the burden of genomic insult is simply too large to be effectively met by the various responses discussed, cells are able to initiate programmed cell death apoptosis , thereby eliminating themselves from a population that otherwise might suffer serious pathological consequences The 'somatic mutation hypothesis' of cancer embraces the notion that neoplastic transformation arises from mutations that alter the function of specific genes now called oncogenes and tumour-suppressor genes that are critical for cell division.
This theory has its roots in correlations between chromosomal abnormalities and cancer first observed by the developmental biologist Theodore Boveri 23 , who at the beginning of the twentieth century reported abnormal numbers of chromosomes aneuploidy in cancerous somatic cells. The discovery of the structure of DNA progressed our understanding of tumorigenesis at several levels.
The genetic basis of many cancers is now known to arise from abnormal recombination events, such as chromosomal translocations, where a region of one chromosome is juxtaposed to another chromosome. Watson himself developed an early and ardent interest in cancer biology when he recognized that the experimentally tractable genomes of oncogenic viruses could provide important insights into the pathogenesis of cancer.
Mutagenesis is now documented as a fundamental cornerstone of the molecular basis of all forms of cancer Arguably the most definitive validation of the somatic mutation hypothesis derives from the discovery that defective responses to DNA damage and the accumulation of mutations underlies two distinct types of hereditary cancer; skin cancer associated with defective NER and colorectal cancer associated with defective MMR In both instances, credit belongs to scholars of DNA repair.
In the late s, James Cleaver providentially noted an article in the San Francisco Chronicle that reported the extreme proneness to skin cancer in individuals with XP, a rare sun-sensitive hereditary disease 2. Cleaver was then searching for mammalian cell lines that were defective in excision repair, and his intuitive notion that XP individuals might be sunlight-sensitive and prone to cancer because they were genetically defective in excision repair proved to be correct The subsequent elucidation of the genes defective in XP patients 26 , and their role in NER of damaged bases in human cells 11 , 27 , 28 , represents a triumph of modern genetics and its application to molecular biology.
The additional discovery that the process of NER in eukaryotes requires elements of the basic transcription apparatus 11 has yielded insights into the complex relationships between deficient DNA repair, defective transcription and hereditary human diseases A fascinating denouement to the skin-cancer predisposition in XP patients derives from the recent solution of the 'XP variant problem'.
A significant fraction of XP individuals who are clinically indistinguishable from those defective in NER were found to be proficient in this repair process Thus, cancer predisposition in XP essentially derives from an excessive mutational burden in skin cells associated with exposure to sunlight.
This led to the formal demonstration of defective MMR in this human hereditary disease and formed another persuasive validation of the somatic mutation theory of cancer 32 , 33 , The study of biological responsiveness to DNA damage embraces DNA repair, mutagenesis, damage tolerance, cell-cycle checkpoint control, programmed cell death, and other cellular responses to genomic insult.
As these pathways become better understood, parallel technological gains in gene therapy and therapeutic intervention by rational drug design will offer new strategies for blocking the unwanted consequences of DNA damage, especially cancer.
Once production of your article has started, you can track the status of your article via Track Your Accepted Article. Help expand a public dataset of research that support the SDGs. The journal publishes original observations on genetic, cellular, biochemical, structural and molecular aspects of DNA repair, mutagenesis, cell cycle regulation, apoptosis and other biological The journal publishes original observations on genetic, cellular, biochemical, structural and molecular aspects of DNA repair, mutagenesis, cell cycle regulation, apoptosis and other biological responses in cells exposed to genomic insult, as well as their relationship to human disease. DNA Repair publishes full-length research articles, brief reports on research, and reviews. The journal welcomes articles describing databases, methods and new technologies supporting research on DNA repair and responses to DNA damage.
The conference discusses through plenary sessions the overall standpoint of DNA repair. The papers presented and other important documents, such as short summaries by the workshop session conveners, comprise this book. The compilation describes the opposing views, those that agree and dispute about certain topic areas. This book, divided into 15 parts, is arranged according to the proceedings in the conference. The plenary sessions are grouped with the related workshop and poster manuscripts. The first two parts generally tackle repair in terms of its identification and quantification, as well as the models, systems, and perspectives it utilizes. This reference material looks into the replicative bypass mechanisms in mammalian cells, viral probes, and hereditary repair defects.
The BER pathway is widely used to repair DNA damage in cells, but it can also introduce unwanted mutations and is sometimes hijacked by other pathways. DNA can be damaged in many ways—bases can, for example, be oxidized, alkylated or deaminated—so cells need a way to repair DNA damage. This process involves three basic steps: first, enzymes called nucleases break the DNA strand that is damaged on either side of the lesion so that the section containing the lesion can be removed; second, DNA polymerases make a new stretch of DNA to replace the section that has been removed, using the undamaged strand as a template; third, DNA ligases join this new stretch to the existing DNA. Moreover, DNA is normally tightly packaged inside the nucleus to protect it from damage: however, the BER pathway involves regions of DNA being unpackaged, and this provides other enzymes and repair pathways with access to the DNA, which can lead to lesions and mutations. The overall result is that DNA repair can sometimes lead to more rather than less damage and, in some cases, this damage can ultimately kill the cell Fu et al. Large-scale DNA sequencing has revealed a complex pattern of lesions and mutations that includes mutational hotspots and mutations that are linked to specific sequences of bases. Finally, some seemingly random mutations occur with high frequency.
As one of the most extensively studied DNA repair processes in both prokaryotes and eukaryotes, nucleotide excision appears to be not only universally present.
Metrics details. DNA is subject to constant chemical modification and damage, which eventually results in variable mutation rates throughout the genome.
The consequences of DNA damage have been the subject of numerous studies in the last few decades. Replication of damaged DNA may result in an increased rate of mutations in the progeny, which may impart deleterious consequence on the organism. Various types of cancers have been linked to DNA damages and it is believed that the initiation of carcinogenesis may result from misreplication of the damaged DNA. DNA repair systems maintain the integrity of the genome by removing the damaged base, sugar, or phosphate from the DNA. In humans, specific DNA repair deficiencies have been associated with elevated risks of diseases, notably cancer, which underscores the importance of DNA repair. DNA damage is also known to induce lesion bypass polymerases which are error-prone on undamaged DNA and may bypass lesions in error-free or error-prone manners.
The genomic integrity of every organism is constantly challenged by endogenous and exogenous DNA-damaging factors. Mutagenic agents cause reduced stability of plant genome and have a deleterious effect on development, and in the case of crop species lead to yield reduction. It is crucial for all organisms, including plants, to develop efficient mechanisms for maintenance of the genome integrity. DNA repair processes have been characterized in bacterial, fungal, and mammalian model systems. The description of these processes in plants, in contrast, was initiated relatively recently and has been focused largely on the model plant Arabidopsis thaliana. Consequently, our knowledge about DNA repair in plant genomes - particularly in the genomes of crop plants - is by far more limited. However, the relatively small size of the Arabidopsis genome, its rapid life cycle and availability of various transformation methods make this species an attractive model for the study of eukaryotic DNA repair mechanisms and mutagenesis.
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Танкадо использовал ТРАНСТЕКСТ, чтобы запустить вирус в главный банк данных.
Это был Стратмор. Лицо его снизу подсвечивалось маленьким предметом, который он извлек из кармана. Сьюзан обмякла, испытав огромное облегчение, и почувствовала, что вновь нормально дышит: до этого она от ужаса задержала дыхание. Предмет в руке Стратмора излучал зеленоватый свет.
Он явно не верил своим ушам. - Dov'ela plata. Где деньги. Беккер достал из кармана пять ассигнаций по десять тысяч песет и протянул мотоциклисту.
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Пожалуйста, ваше удостоверение. Сьюзан протянула карточку и приготовилась ждать обычные полминуты. Офицер пропустил удостоверение через подключенный к компьютеру сканер, потом наконец взглянул на .
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Сначала используемые пароли были довольно короткими, что давало возможность компьютерам АНБ их угадывать. Если искомый пароль содержал десять знаков, то компьютер программировался так, чтобы перебирать все комбинации от 0000000000 до 9999999999, и рано или поздно находил нужное сочетание цифр. Этот метод проб и ошибок был известен как применение грубой силы.
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