Table of Contents
Overview
Importance of DNA Replication
DNA replication is a fundamental process essential for cell growth and division in all living organisms. The initiation of this process occurs at specific sites known as origins of replication (ORIs), which are regulated by a set of proteins that play critical roles in the biochemical mechanisms underlying replication.[30.1] Understanding ORIs is vital for comprehending the cell-division cycle and the regulation of gene expression, as these sites dictate the onset of DNA replication.[30.1] The accurate identification of replication origins (ORIs) is essential for a thorough investigation into human cell growth and cancer therapy.[33.1] To address this need, we proposed a computational approach called Ori-FinderH, which efficiently and precisely predicts human ORIs of various lengths by integrating the Z-curve method with deep learning techniques.[33.1] This innovative method enhances the prediction accuracy by utilizing valid mathematical descriptors, which include incorporating dinucleotide position-specific propensity into the general pseudo nucleotide composition.[33.1] Moreover, the fidelity of DNA replication is closely linked to cancer development. Normal cells maintain genomic integrity by replicating their DNA with remarkable accuracy, thereby avoiding deleterious mutations that could lead to cancer.[43.1] Research indicates that a certain number of mutations, estimated to be six or seven driver mutations, are necessary for a normal human cell to progress to advanced cancer stages.[44.1] This highlights the importance of replication fidelity and the mechanisms cells employ to correct errors during replication, as replication errors can contribute to carcinogenesis.[43.1]Mechanisms of DNA Replication
DNA replication is a highly regulated and intricate process that ensures the accurate duplication of genetic material in all living organisms. The fundamental mechanism of DNA replication is known as semiconservative replication, where each strand of the original DNA molecule serves as a template for the synthesis of a new complementary strand, resulting in two identical DNA molecules from a single original molecule.[3.1] The process begins with the unwinding of the double helix structure of DNA, which creates two Y-shaped structures called replication forks, forming a replication bubble.[2.1] This unwinding is facilitated by various enzymes, including helicases, which separate the two strands of DNA. DNA polymerase III plays a crucial role at the replication fork, synthesizing new DNA strands by adding nucleotides in the 5' to 3' direction.[4.1] During the DNA replication process, an entirely new strand of DNA is synthesized using the original template strand, with complementary bases being matched. DNA polymerase III moves along the leading strand towards the replication fork, adding nucleotides from the 5’ end to the 3’ end, which allows for continuous synthesis.[4.1] In contrast, the lagging strand is synthesized discontinuously in short segments known as Okazaki fragments. This process requires the addition of RNA primers to the newly exposed bases on the lagging strand before DNA polymerase III can attach and synthesize the new DNA strand in the correct 5’ to 3’ direction.[6.1] The antiparallel nature of DNA strands further complicates replication, as one strand runs in the 5’ to 3’ direction while the other runs in the opposite 3’ to 5’ direction.[5.1] The synthesis of the lagging strand involves multiple steps: RNA primers are laid down, and DNA polymerase III synthesizes the new DNA in fragments, which are later joined together by the enzyme DNA ligase.[6.1] This meticulous orchestration of events ensures that each daughter cell receives an accurate copy of the genetic material during cell division, highlighting the critical importance of DNA replication in biological inheritance and cellular function.[3.1]History
Key Discoveries in DNA Replication
The history of DNA replication is marked by several key discoveries that have shaped our understanding of the molecular mechanisms involved. One of the foundational insights came from Watson and Crick, who proposed the double helical structure of DNA in 1953. This discovery suggested a mechanism for DNA replication, where the two strands could separate, allowing each strand to serve as a template for the synthesis of a new complementary strand.[53.1] In 2001, Frederic Lawrence Holmes published a comprehensive account of the debates surrounding DNA replication in his book, "Meselson, Stahl, and the Replication of DNA: A History of 'The Most Beautiful Experiment in Biology.'" This work chronicles the pivotal 1950s experiments that confirmed the semi-conservative nature of DNA replication, as originally proposed by Watson and Crick.[49.1] The semi-conservative model posits that each new DNA molecule consists of one parental strand and one newly synthesized strand, a concept that was crucial in understanding how genetic information is accurately passed on during cell division.[54.1] Over the past three decades, our understanding of eukaryotic DNA replication has significantly advanced, revealing the complexity of this essential biological process. DNA replication is a semiconservative mechanism in which each parental strand serves as a template for the synthesis of new complementary daughter strands, ensuring accurate duplication of genetic material prior to cell division.[54.1] The process initiates at discrete sites known as replication origins, where various proteins, including DNA polymerases and DNA primases, are recruited to facilitate the unwinding of the DNA helix and the synthesis of new strands.[52.1] The central enzyme, DNA polymerase, catalyzes the joining of deoxyribonucleoside triphosphates (dNTPs) to form the growing DNA chain, operating in a 3’ to 5’ direction to synthesize DNA in a 5’ to 3’ orientation.[54.1] For the leading strand, a special primer is required only at the start of replication; once a replication fork is established, DNA polymerase continuously adds nucleotides.[64.1] In contrast, the lagging strand is synthesized in short segments due to its antiparallel orientation, necessitating additional proteins such as DNA ligase and topoisomerases to manage the complexities of the replication fork and ensure fidelity during DNA synthesis.[64.1] This comprehensive understanding of DNA replication mechanisms has evolved through the contributions of numerous researchers, emphasizing the importance of timely and accurate DNA duplication in maintaining genetic integrity across generations.[52.1] The discovery of the mechanisms of DNA replication has not only advanced molecular biology but has also underscored the importance of understanding replication errors. Such errors can lead to mutations, which may contribute to genetic diseases and cancer.[62.1] For instance, sickle cell disease is a genetic disorder resulting from a single nucleotide change in the DNA sequence, illustrating the profound impact of replication fidelity on health.[59.1]Recent Advancements
Current Research Trends
Recent advancements in molecular biology have underscored the significance of DNA replication, which is the biological process of producing two identical replicas of DNA from one original DNA molecule. This process is fundamental to all living organisms, serving as a crucial component of biological inheritance. DNA replication is essential for cell division during growth and the repair of damaged tissues, ensuring that each new cell receives its own copy of the DNA. Each strand of the original DNA molecule acts as a template for the production of its counterpart, a mechanism known as semiconservative replication.[1.1] Understanding these processes is vital for ongoing research in genomics, particularly as it relates to cancer prognosis and treatment.Innovations in DNA Replication Techniques
Recent advancements in DNA replication techniques have significantly enhanced our understanding of the mechanisms underlying this fundamental biological process. One notable innovation is the development of methodologies such as HydEn-seq, PU-seq, ribose-seq, and emRiboSeq, which provide insights into polymerase activity and strand synthesis, thereby aiding in the comprehension of DNA replication dynamics.[99.1] Additionally, the introduction of DNA combing has allowed researchers to obtain large quantities of data regarding the state of DNA during replication, particularly in the S phase, enabling the extraction of various parameters such as fork velocity and origin initiation rate.[105.1] Moreover, advanced computational methods have emerged as powerful tools for modeling elements of DNA replication and repair processes. These techniques facilitate the reconstruction of the DNA replication process in vitro, offering comprehensive insights into the dynamic and real-time molecular mechanisms involved.[108.1] Recent efforts to utilize computer simulations in DNA metabolism have gained popularity, although they have yet to become mainstream within the community.[107.1] The integration of these innovative techniques not only enhances the understanding of DNA replication but also contributes to the development of targeted therapies for genetic disorders. For instance, the application of genetic therapies using viral vectors for treating inborn metabolic disorders is gaining traction, reflecting the maturation of technology in this field.[101.1] Furthermore, the rapid development of small molecule inhibitors targeting enzymes involved in DNA damage response and repair has emerged as a successful strategy for targeted cancer therapeutics.[102.1]Mechanisms Of Dna Replication
Enzymes Involved in DNA Replication
DNA replication is a complex process that involves several key enzymes, each playing a crucial role in ensuring the accuracy and efficiency of the replication process. The primary enzyme responsible for synthesizing new DNA strands is DNA polymerase, specifically DNA Polymerase III in prokaryotes, which catalyzes the addition of deoxyribonucleotides to form the growing DNA chain.[164.1] This enzyme operates by reading the nucleotides on the template strand and adding complementary nucleotides to the new strand, thereby facilitating the elongation phase of DNA replication.[164.1] Helicase plays an indispensable role in the DNA replication process by unwinding double-stranded DNA, which creates the necessary single-stranded templates essential for replication.[161.1] This unwinding is critical because DNA polymerases, the enzymes responsible for synthesizing new DNA strands, cannot initiate synthesis on their own; they require a primer to begin the process.[161.1] The efficiency of replication progression depends on the coordination of helicase and DNA polymerase, which work together to perform duplex unwinding and nascent-strand DNA synthesis.[146.1] The coupling between helicase and DNA polymerase significantly increases the speed of DNA unwinding and synthesis, with studies showing that when T7 gp4 helicase is coupled to T7 DNA polymerase, the two motors can move through double-stranded DNA at speeds of approximately 120 base pairs per second, which is about ten times faster than helicase alone.[148.1] This coordination is vital for ensuring that the synthesis of the leading and lagging strands occurs efficiently and accurately during DNA replication.[161.1] DNA replication is a fundamental genetic process essential for cell growth and division, utilizing a semi-conservative method that results in a double-stranded DNA molecule composed of one parental strand and one newly synthesized daughter strand.[163.1] The process begins with DNA primase, which synthesizes short RNA primers to initiate replication once the DNA strands are separated.[164.1] The primary enzyme responsible for synthesizing the new DNA strand is DNA polymerase III, which reads the nucleotides on the template strand and adds them sequentially to form the new strand.[164.1] During the replication of the lagging strand, DNA polymerase III synthesizes DNA in fragments known as Okazaki fragments, which can leave gaps between them.[164.1] To address these gaps, DNA ligase is employed to join the Okazaki fragments, ensuring that the newly synthesized DNA is continuous.[164.1] Additionally, topoisomerases play a crucial role in relieving the torsional strain that occurs during replication. DNA topoisomerase I relaxes the DNA helix by creating a nick in one of the DNA strands, while DNA topoisomerase II alleviates strain by forming supercoils through nicks in both strands of DNA.[163.1] Together, these enzymes coordinate to facilitate the accurate and efficient replication of DNA, which is vital for the transmission of genetic information. DNA replication is a fundamental biological process in which a cell duplicates its DNA, resulting in two identical daughter molecules, thereby facilitating the transmission of genetic information across generations.[137.1] This intricate process is catalyzed by various enzymes and proteins that play essential roles in the initiation, elongation, and termination of replication, each contributing unique functions to the overall mechanism.[137.1] Key enzymes involved in DNA replication include helicases, DNA topoisomerase, primase, DNA polymerase, and ligase.[138.1] Among these, DNA polymerases are particularly significant as they utilize deoxyribonucleotides to synthesize new DNA strands by assembling nucleotides.[138.1] The fidelity of DNA replication is largely enhanced by the activities of DNA polymerase, which helps select the correct base for insertion into the newly synthesized DNA, thereby discriminating between matched and mismatched bases.[139.1] This high degree of fidelity is crucial for preserving genetic integrity, as errors during replication can lead to mutations and other genetic disorders.[139.1] Overall, the coordinated actions of these enzymes ensure that DNA replication occurs accurately, which is vital for biological inheritance in all living organisms.[137.1]Steps of DNA Replication Process
DNA replication is a complex process that involves several key steps to ensure accurate duplication of genetic material. The process can be divided into three main stages: initiation, elongation, and termination. DNA replication is a crucial biological process that allows a cell to duplicate its DNA, ensuring the transmission of genetic information to subsequent generations of cells. This process consists of three main steps: strand separation, priming, and the synthesis of new DNA strands.[144.1] The first step involves the opening of the DNA helix, which is essential for providing a template for replication. Enzymes, including DNA helicases, play a vital role in this phase by unwinding the double helix and creating single-stranded DNA templates.[143.1] As the helix unwinds, RNA primers are added to the newly exposed bases on the lagging strand, facilitating DNA synthesis in fragments while still proceeding in the 5′ to 3′ direction.[142.1] In contrast, the leading strand requires a special primer only at the start of replication; once a replication fork is established, DNA polymerase can continuously add nucleotides to the growing chain.[143.1] This intricate coordination of enzymatic activity underscores the sophistication of cellular machinery in maintaining genetic integrity.[167.1] During the DNA replication process, an entirely new strand of DNA is synthesized using the original template strand, with complementary bases being matched accordingly. DNA polymerase III plays a crucial role in this process by moving down the leading strand toward the replication fork, adding nucleotides in the 5' to 3' direction.[139.1] This enzyme synthesizes the new strand by reading the nucleotides on the template strand and adding one nucleotide after another.[140.1] In contrast, the lagging strand is synthesized in a discontinuous manner, resulting in the formation of Okazaki fragments. For each Okazaki fragment, a primer must be added before DNA polymerase III can initiate the synthesis of the corresponding DNA segment.[167.1] This mechanism illustrates the complexity and efficiency of DNA replication, as the cellular machinery must coordinate the synthesis of both strands while overcoming directional challenges.[167.1] The process of DNA replication is crucial for cell division, ensuring that each daughter cell receives an accurate genetic blueprint necessary for proper cellular function. This replication is initiated at specific regions of the genome known as origins, where the assembly of the DNA replication machinery, or replisome, begins during the G1 phase of the cell cycle. The hexameric Mcm2-7 complex (MCM) is loaded at these origins by the origin recognition complex (ORC), Cdc6, and Cdt1, facilitating the dynamic and simultaneous nature of bidirectional replication, which significantly enhances the efficiency and accuracy of the process.[152.1] During replication, DNA Polymerase III synthesizes new strands by reading the nucleotides on the template strand and adding complementary nucleotides one at a time. The leading strand is synthesized continuously, while the lagging strand is produced in short segments known as Okazaki fragments, which are later joined together by DNA ligase to form a continuous strand.[167.1] This intricate mechanism underscores the sophistication of cellular machinery in maintaining genetic integrity and highlights the importance of complementary base pairing in DNA synthesis.[151.1]Applications Of Dna Replication
Implications in Medicine and Biotechnology
DNA replication technologies play a crucial role in both medicine and biotechnology, with one of the most prominent applications being the polymerase chain reaction (PCR). PCR is recognized as the best known and one of the earliest DNA polymerase-based biotechnology applications, having served as a foundational tool for amplifying and detecting specific DNA sequences since its development over 30 years ago.[189.1] This technique relies on DNA polymerases, which possess an intrinsic capability to replicate DNA strands with astoundingly high fidelity. As a result, a multitude of biotechnological techniques utilized in basic research and clinical diagnostics depend on these enzymes, underscoring their fundamental importance to modern molecular biology.[190.1] In the realm of personalized medicine, advancements in DNA replication technologies are paving the way for revolutionary approaches to disease treatment, prediction, and prevention. Personalized sequencing is a critical step in this evolution, allowing for the identification of germline mutations that can inform treatment strategies.[192.1] Furthermore, the ability to detect somatic mutations, which are specific to certain cell populations, is becoming increasingly important in tailoring therapies to individual patients.[191.1] Gene therapy represents another significant application of DNA replication technologies. This approach involves genetically modifying cells to produce therapeutic effects, such as correcting genes associated with diseases.[193.1] The development of CRISPR-Cas systems has further enhanced the capabilities of gene editing, enabling precise corrections of genetic mutations responsible for hereditary diseases.[199.1] These advancements are crucial for the treatment of conditions like sickle cell disease, where researchers are actively working on next-generation therapies to improve accessibility and safety.[193.1] Moreover, the integration of DNA replication technologies into diagnostic tools is revolutionizing patient care. Techniques such as rolling circle amplification (RCA) enable robust isothermal amplification of nucleic acid templates, which, when combined with CRISPR-Cas technologies, lead to innovative diagnostic strategies with remarkable specificity and sensitivity.[202.1] Additionally, DNA nanotechnology is being explored for developing advanced materials for biosensing and disease diagnostics, showcasing the versatility of DNA replication applications in medicine.[201.1]Challenges And Future Directions
Issues in DNA Replication
During the replication of genetic material, cells encounter various challenges that can lead to replication stress, characterized by slowing or stalling of replication fork progression.[238.1] This stress can arise from multiple sources, including nucleotide depletion due to insufficient dNTP pools, which significantly slows down the replication process.[231.1] Additionally, replication barriers such as telomeres, highly repetitive sequences, DNA lesions, and secondary DNA structures further complicate DNA duplication.[238.1] Environmental factors, including metabolites, drugs, and radiation, can also disrupt the faithful copying of the genome, contributing to replication stress.[237.1] These challenges underscore the complexity of DNA replication and the necessity for robust cellular mechanisms to address replication stress, as deficiencies in these processes can lead to genomic instability, a hallmark of cancer.[230.1] The replication process of DNA is significantly challenged by the presence of non-B DNA secondary structures, such as G-quadruplexes, H-DNA, and Z-DNA, which can form at specific repetitive sequences within the genome. These structures complicate the progression of DNA replication forks.[233.1] Replication stress is a complex phenomenon that arises from the generation of aberrant replication fork structures, which has serious implications for genome stability, cell survival, and human disease.[234.1] When cells bypass critical genome surveillance mechanisms, it can lead to genomic instability, a factor that is closely associated with tumor initiation and progression.[235.1] Understanding the normal regulatory mechanisms of DNA replication and how these processes are altered in disease is crucial for identifying vulnerabilities in cancer cells and addressing the implications of replication stress on genetic stability. Replication stress is a significant concern in the context of genomic stability and cell survival, as it is characterized by slowing or stalling in replication fork progression. This stress can arise from various sources, including telomeres, repetitive sequences, DNA lesions, and collisions between replication and transcription complexes, which are considered replication barriers.[238.1] Disruptions in DNA replication can lead to the faithful propagation of genetic and epigenetic information being compromised, ultimately altering developmental programs and contributing to genome instability, which drives tumor initiation and progression when cells bypass genome surveillance mechanisms.[235.1] Additionally, environmental factors such as ultraviolet (UV) radiation can induce DNA damage, resulting in replication errors that may have lasting effects on genetic integrity and contribute to disease development.[236.1] Understanding these mechanisms is crucial for identifying potential therapeutic targets in cancer treatment and developing strategies to mitigate the effects of replication stress on genomic integrity.Future Research Opportunities
Advancements in machine learning are poised to enhance our understanding of DNA replication challenges, particularly in eukaryotic systems. Recent developments have led to the creation of machine learning methods that can identify DNA replication origins by analyzing DNA structure properties, which may significantly contribute to genomic studies.[259.1] One such tool, MnM, has been developed to efficiently disentangle single-cell replication timing (scRT) profiles from heterogeneous samples. This tool utilizes single-cell copy number data to accurately perform missing value imputation, identify cell replication states, and detect genomic heterogeneity, which has been largely overlooked in previous studies.[261.1] The MnM tool employs a combination of deep learning, UMAP, DBSCAN, and KNN algorithms to uncover replication states and subpopulations from single-cell whole-genome copy number data, thereby addressing the complexities of genomic heterogeneity.[261.1] In addition to supervised learning approaches that classify S-phase patterns in embryonic stem cells, unsupervised methods are being developed to detect aberrant S-phase cells on a larger scale.[262.1] These advancements indicate a shift towards more sophisticated analytical techniques that can handle the intricacies of DNA replication dynamics in various cellular contexts. Moreover, the integration of replication stress regulators with radiation therapy represents a promising therapeutic strategy in cancer treatment. This approach capitalizes on the high replication stress characteristic of tumors, potentially providing a selective means of eliminating cancer cells.[264.1] Current research is focused on understanding the role of replication stress in tumor progression and exploring ways to enhance tumor response to therapies.[265.1] The activation of pathways such as ATM and ATR in response to replication stress is critical, as it leads to cell cycle arrest and DNA repair pathway activation, which are essential for maintaining genomic stability.[267.1]References
[1] DNA replication - Wikipedia — In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part of biological inheritance. This is essential for cell division during growth and repair of damaged tissues, while it also ensures that each of the new cells receives its own copy of the DNA. Each strand of the original DNA molecule then serves as a template for the production of its counterpart, a process referred to as semiconservative replication.
[2] DNA Replication - Definition, Process, Steps, & Labeled Diagram — Home / Life Science / DNA Replication DNA Replication DNA replication is the process through which a cell’s DNA forms two exact copies of itself. It is what DNA replication does. Role of DNA Polymerase in DNA Replication When and Where does DNA Replication Occur How is DNA Replicated DNA Replication When the DNA unwinds, two Y-shaped structures called replication forks are formed, together making up the replication bubble. Two molecules of DNA polymerase III at the replication fork carry out replication. The strand that runs 5′ to 3′ in the direction of the replication fork is easily replicated continuously as the DNA polymerase moves in the same direction as the replication fork. What is DNA replication?
[3] Origins of DNA replication - PMC - PubMed Central (PMC) — Abstract. In all kingdoms of life, DNA is used to encode hereditary information. Propagation of the genetic material between generations requires timely and accurate duplication of DNA by semiconservative replication prior to cell division to ensure each daughter cell receives the full complement of chromosomes.DNA synthesis of daughter strands starts at discrete sites, termed replication
[4] DNA Replication - The Definitive Guide - Biology Dictionary — During the replication process, an entirely new strand of DNA is created by using the original template strand and matching the complimentary bases. DNA polymerase III moves down the leading strand towards the replication fork, adding bases to the new strand from the 5’ end to the 3’ end. By creating these multiple segments, DNA polymerase III is able to synthesize a small portion of the new DNA strand away from the replication fork in the correct 5′-3′ direction. However, in the lagging strand, a primer must be added in front of the Okazaki fragment being synthesized before DNA polymerase III can attach and synthesize the new DNA strand opposite of the replication fork.
[5] Biochemistry, DNA Replication - StatPearls - NCBI Bookshelf — Each strand runs antiparallel, meaning in opposite directions, one from the 5’ => 3’, the other 3’ => 5’ (This numbering comes from the carbon atoms in the sugar, which are labeled 1’ => 5’; the phosphate and hydroxyl group are attached to the 5’ and 3’ carbons respectively, creating the directionality of the nucleotide and, therefore, the DNA strand). The DNA polymerase runs in the 3’ => 5’ direction (therefore creating DNA in the 5’ => 3’ orientation), but only one DNA template strand, known as the leading strand, is in the proper orientation. For the lagging strand, which is 5’ => 3’, the new strand is synthesized in segments and discontinuously because the DNA polymerase can only read in the 3’ => 5’ direction. DNA polymerase alpha (in eukaryotes) is a complex that has the DNA primase which creates the RNA primer, and then the polymerase alpha itself elongates around 20 nucleotides and passes off to DNA polymerase epsilon or delta. This book is distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
[6] DNA Replication - Stages of Replication - TeachMePhyiology — In this article, we shall discuss the structure of DNA, the steps involved in DNA replication (initiation, elongation and termination) and the clinical consequences that can occur when this process goes wrong. Instead, as the helix unwinds, RNA primers are added to the newly exposed bases on the lagging strand and DNA synthesis occurs in fragments, but still in the 5′ to 3′ direction as before. In this article, we shall discuss the structure of DNA, the steps involved in DNA replication (initiation, elongation and termination) and the clinical consequences that can occur when this process goes wrong. Instead, as the helix unwinds, RNA primers are added to the newly exposed bases on the lagging strand and DNA synthesis occurs in fragments, but still in the 5' to 3' direction as before.
[30] computational platform to identify origins of replication sites in ... — Abstract The locations of the initiation of genomic DNA replication are defined as origins of replication sites (ORIs), which regulate the onset of DNA replication and play significant roles in the DNA replication process. The study of ORIs is essential for understanding the cell-division cycle and gene expression regulation.
[33] Unveiling human origins of replication using deep learning: accurate ... — Accurate identification of replication origins (ORIs) is crucial for a comprehensive investigation into the progression of human cell growth and cancer therapy. Here, we proposed a computational approach Ori-FinderH, which can efficiently and precisely predict the human ORIs of various lengths by combining the Z-curve method with deep learning
[43] DNA replication fidelity and cancer - ScienceDirect — Cancer is fueled by mutations and driven by adaptive selection. Normal cells avoid deleterious mutations by replicating their genomes with extraordinary accuracy. Here we review the pathways governing DNA replication fidelity and discuss evidence implicating replication errors (point mutation instability or PIN) in carcinogenesis.
[44] Links between DNA Replication, Stem Cells and Cancer - PMC — Estimates for the number of mutations required for a normal human cell to progress to an advanced cancer, based on the relationship between age and incidence, suggest that six or seven driver mutations are required. ... Sabatino R.D., Myers T.W., Tan C.K., Downey K.M., So A.G., Bambara R.A., Kunkel T.A. Fidelity of mammalian DNA replication and
[49] Meselson, Stahl, and the Replication of DNA: A History of "The Most ... — In 2001, Yale University Press published Frederic Lawrence Holmes' book, Meselson, Stahl, and the Replication of DNA: A History of "The Most Beautiful Experiment in Biology" (Replication of DNA), which chronicles the 1950s debate about how DNA replicates. That experiment verified that DNA replicates semi-conservatively as originally proposed by Watson and Crick.
[52] Origins of DNA replication | PLOS Genetics — In all kingdoms of life, DNA is used to encode hereditary information. Propagation of the genetic material between generations requires timely and accurate duplication of DNA by semiconservative replication prior to cell division to ensure each daughter cell receives the full complement of chromosomes. DNA synthesis of daughter strands starts at discrete sites, termed replication origins, and
[53] 14.3A: Basics of DNA Replication - Biology LibreTexts — Basics of DNA Replication Watson and Crick's discovery that DNA was a two-stranded double helix provided a hint as to how DNA is replicated. During cell division, each DNA molecule has to be perfectly copied to ensure identical DNA molecules to move to each of the two daughter cells. The double-stranded structure of DNA suggested that the two strands might separate during replication with
[54] DNA Replication - The Cell - NCBI Bookshelf — Search term DNA Replication As discussed in Chapter 3, DNA replication is a semiconservative process in which each parental strand serves as a template for the synthesis of a new complementary daughter strand. The central enzyme involved is DNA polymerase, which catalyzes the joining of deoxyribonucleoside 5′-triphosphates (dNTPs) to form the growing DNA chain. However, DNA replication is much more complex than a single enzymatic reaction. Other proteins are involved, and proofreading mechanisms are required to ensure that the accuracy of replication is compatible with the low frequency of errors that is needed for cell reproduction.
[59] Genetics, DNA Damage and Repair - StatPearls - NCBI Bookshelf — For example, sickle cell disease is a genetic disorder that results because of a difference in a single nucleotide in the DNA of a carrier when compared to the DNA of a non-carrier. This difference occurs in the gene that codes for one of the subunits of hemoglobin, the protein that carries oxygen through the bloodstream.
[62] DNA Replication Errors: Causes and Consequences — However, errors in this process can lead to significant biological consequences, affecting genetic stability and potentially leading to mutations and diseases. Understanding DNA replication errors is crucial in genetics and medicine, aiding in the comprehension of how these errors contribute to genetic diversity and disease development.
[64] DNA Replication Mechanisms - Molecular Biology of the Cell - NCBI Bookshelf — For the leading strand, a special primer is needed only at the start of replication: once a replication fork is established, the DNA polymerase is continuously presented with a base-paired chain end on which to add new nucleotides. Additional replication proteins are needed to help in opening the double helix and thus provide the appropriate single-stranded DNA template for the DNA polymerase to copy. These include (1) DNA polymerase and DNA primase to catalyze nucleoside triphosphate polymerization; (2) DNA helicases and single-strand DNA-binding (SSB) proteins to help in opening up the DNA helix so that it can be copied; (3) DNA ligase and an enzyme that degrades RNA primers to seal together the discontinuously synthesized lagging-strand DNA fragments; and (4) DNA topoisomerases to help to relieve helical winding and DNA tangling problems.
[99] Unraveling the complexity of asymmetric DNA replication: Advancements ... — These methodologies, such as HydEn-seq, PU-seq, ribose-seq, and emRiboSeq, offer insights into polymerase activity and strand synthesis, aiding in understanding DNA replication dynamics. Recent advancements include novel conditional mutants for ribonucleotide excision repair, enzymatic cleavage alternatives, and unified pipelines for data analysis.
[101] A primer to gene therapy: Progress, prospects, and problems — Specifically, the application of genetic therapies using viral vectors for the treatment of inborn metabolic disorders is growing and clinical applications are starting to appear. While the field has matured from the technology perspective and has yielded efficacious products, it is the perception of many stakeholders that from the regulatory
[102] Rare Genetic Diseases with Defects in DNA Repair: Opportunities and ... — Additionally, the rapid development of small molecule inhibitors against enzymes that participate in DNA damage response and repair has been a successful strategy for targeted cancer therapeutics. Here, we discuss the recent advances in our understanding of how many rare disease genes participate in promoting genome stability.
[105] Computational methods to study kinetics of DNA replication — New technologies such as DNA combing have led to the availability of large quantities of data that describe the state of DNA while undergoing replication in S phase. In this chapter, we describe methods used to extract various parameters of replication--fork velocity, origin initiation rate, fork density, numbers of potential and utilized
[107] Molecular Mechanisms of DNA Replication and Repair Machinery: Insights ... — In this review, we describe recent efforts to model elements of DNA replication and repair processes using computer simulations, an approach that has gained immense popularity in many areas of molecular biophysics but has yet to become mainstream in the DNA metabolism community. .Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K. .Brooks BR, Brooks CL, MacKerell AD Jr., Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M.
[108] Concise Overview of Methodologies Employed in the Study of Bacterial ... — These tools are a powerful asset for the study of DNA replication, offering comprehensive insights into the dynamic, real-time processes and molecular mechanisms involved in this process. These techniques allow for the following: Reconstruction of the DNA replication process in vitro (TIRF).
[137] DNA Replication Steps and Process - ThoughtCo — Learn about our Editorial Process Updated on May 02, 2024 DNA replication is the process in which a cell makes an identical copy of its DNA. It is vital for cell growth, repair, and reproduction in organisms as it helps with the transmission of genetic information. The process that copies DNA is called replication. Enzymes are vital to DNA replication since they catalyze very important steps in the process.
[138] DNA Replication - Definition, Process, Steps, & Labeled Diagram — Home / Life Science / DNA Replication DNA Replication DNA replication is the process through which a cell’s DNA forms two exact copies of itself. It is what DNA replication does. Role of DNA Polymerase in DNA Replication When and Where does DNA Replication Occur How is DNA Replicated DNA Replication When the DNA unwinds, two Y-shaped structures called replication forks are formed, together making up the replication bubble. Two molecules of DNA polymerase III at the replication fork carry out replication. The strand that runs 5′ to 3′ in the direction of the replication fork is easily replicated continuously as the DNA polymerase moves in the same direction as the replication fork. What is DNA replication?
[139] DNA Replication - The Definitive Guide - Biology Dictionary — During the replication process, an entirely new strand of DNA is created by using the original template strand and matching the complimentary bases. DNA polymerase III moves down the leading strand towards the replication fork, adding bases to the new strand from the 5’ end to the 3’ end. By creating these multiple segments, DNA polymerase III is able to synthesize a small portion of the new DNA strand away from the replication fork in the correct 5′-3′ direction. However, in the lagging strand, a primer must be added in front of the Okazaki fragment being synthesized before DNA polymerase III can attach and synthesize the new DNA strand opposite of the replication fork.
[140] DNA Replication: Steps, Process, Diagram And Simple Explanation — The enzyme DNA Polymerase III makes the new strand by reading the nucleotides on the template strand and specifically adding one nucleotide after the other. DNA Primase – Once the strands are separated and ready, replication can be initiated. DNA Polymerase III – This enzyme makes the new strand by reading the nucleotides on the template strand and specifically adding one nucleotide after the other. However, for the strand being synthesized in the other direction, which is known as the ‘lagging’ strand, the polymerase has to synthesize one fragment of DNA. DNA ligase – When Polymerase III is adding nucleotides to the lagging strand and creating Okazaki fragments, it at times leaves a gap or two between the fragments.
[142] DNA Replication - Stages of Replication - TeachMePhyiology — In this article, we shall discuss the structure of DNA, the steps involved in DNA replication (initiation, elongation and termination) and the clinical consequences that can occur when this process goes wrong. Instead, as the helix unwinds, RNA primers are added to the newly exposed bases on the lagging strand and DNA synthesis occurs in fragments, but still in the 5′ to 3′ direction as before. In this article, we shall discuss the structure of DNA, the steps involved in DNA replication (initiation, elongation and termination) and the clinical consequences that can occur when this process goes wrong. Instead, as the helix unwinds, RNA primers are added to the newly exposed bases on the lagging strand and DNA synthesis occurs in fragments, but still in the 5' to 3' direction as before.
[143] DNA Replication Mechanisms - Molecular Biology of the Cell - NCBI Bookshelf — For the leading strand, a special primer is needed only at the start of replication: once a replication fork is established, the DNA polymerase is continuously presented with a base-paired chain end on which to add new nucleotides. Additional replication proteins are needed to help in opening the double helix and thus provide the appropriate single-stranded DNA template for the DNA polymerase to copy. These include (1) DNA polymerase and DNA primase to catalyze nucleoside triphosphate polymerization; (2) DNA helicases and single-strand DNA-binding (SSB) proteins to help in opening up the DNA helix so that it can be copied; (3) DNA ligase and an enzyme that degrades RNA primers to seal together the discontinuously synthesized lagging-strand DNA fragments; and (4) DNA topoisomerases to help to relieve helical winding and DNA tangling problems.
[144] What is DNA Replication? - Steps, Enzymes, Mechanism, Applications — DNA Replication Overview. DNA replication is the process by which a cell duplicates its DNA to ensure genetic information is transmitted to the next generation of cells. It involves three main steps: strand separation, priming, and the synthesis of new DNA strands. Below is a detailed breakdown of the process. Step 1: Opening the DNA Helix
[146] DNA Polymerase-Parental DNA Interaction Is Essential for Helicase ... — The efficiency of replication progression depends on the coordination of the helicase and polymerase to perform duplex unwinding and nascent-strand DNA synthesis. The helicase is an essential component for most replisomes and has been proposed to be the driving motor in the unwinding of duplex parental DNA.
[148] Dynamic coupling between the motors of DNA replication: hexameric ... — The coupling between helicase and DNA polymerase increases the speed of DNA unwinding-synthesis (Figure 3b). When T7 gp4 is coupled to T7 DNA polymerase, the two motors together move through dsDNA with speeds of ~120 bp/s, which is ~10 times faster than the speed of the helicase alone **. Similar observations have been made in other replication
[151] Bidirectional Replication - Biology Simple — The dynamic and simultaneous nature of bidirectional replication contributes to the overall efficiency and accuracy of DNA replication. ... During cell division, DNA needs to be replicated with utmost precision so that each daughter cell carries the exact genetic blueprint required for the cell's proper functioning. ... DNA replication is
[152] Mechanism of Bidirectional Leading-Strand Synthesis ... - Cell Press — Bidirectional DNA replication is initiated from specific regions of the genome, termed origins. In eukaryotes, assembly of the DNA replication machinery (replisome) begins in the G1 phase of the cell cycle when the ATP-dependent motor component of the replicative helicase, the hexameric Mcm2-7 complex (MCM), is loaded at origins by the origin recognition complex (ORC), Cdc6 and Cdt1 (Bell
[161] Key Enzymes and Steps in DNA Replication - BiologyInsights — Helicase plays an indispensable role in the DNA replication process, as it unwinds the double-stranded DNA, creating the necessary single-stranded templates that are essential for replication. These primers are necessary because DNA polymerases, the enzymes responsible for synthesizing new DNA strands, cannot initiate synthesis on their own. DNA polymerase is the workhorse of the DNA replication process, responsible for synthesizing new DNA strands by adding nucleotides to the growing chain. Since DNA polymerase can only add nucleotides in the 5’ to 3’ direction, the lagging strand is synthesized discontinuously, moving away from the replication fork. The coordination between the synthesis of the leading and lagging strands ensures that the DNA replication process is both efficient and accurate.
[163] Prokaryotic DNA Replication- Enzymes, Steps and Significance — Prokaryotic DNA Replication- Enzymes, Steps and Significance Prokaryotic DNA Replication- Enzymes, Steps and Significance DNA replication uses a semi-conservative method that results in a double-stranded DNA with one parental strand and a new daughter strand. Enzymes of DNA Replication Steps of DNA Replication Enzymes of DNA Replication DNA topoisomerase I: Relaxes the DNA helix during replication through creation of a nick in one of the DNA strands. DNA topoisomerase II: Relieves the strain on the DNA helix during replication by forming supercoils in the helix through the creation of nicks in both strands of DNA. Steps of DNA Replication DNA replication is a fundamental genetic process that is essential for cell growth and division.
[164] How Does DNA Replication Occur? What Are The Enzymes Involved? — The enzyme DNA Polymerase III makes the new strand by reading the nucleotides on the template strand and specifically adding one nucleotide after the other. DNA Primase – Once the strands are separated and ready, replication can be initiated. DNA Polymerase III – This enzyme makes the new strand by reading the nucleotides on the template strand and specifically adding one nucleotide after the other. However, for the strand being synthesized in the other direction, which is known as the ‘lagging’ strand, the polymerase has to synthesize one fragment of DNA. DNA ligase – When Polymerase III is adding nucleotides to the lagging strand and creating Okazaki fragments, it at times leaves a gap or two between the fragments.
[167] Understanding DNA Synthesis: Leading vs. Lagging Strands — Published Time: 2024-10-07T23:13:21+00:00 Understanding DNA Synthesis: Leading vs. Lagging Strands - BiologyInsights Botany and Plant Sciences Environmental Science Marine Biology Understanding DNA Synthesis: Leading vs. Published Oct 7, 2024 The process of leading strand synthesis is a marvel of biological efficiency and precision. Complementary base pairing plays a significant role in this synthesis. This careful coordination underscores the sophistication of cellular machinery in maintaining genetic integrity. The formation of Okazaki fragments is a fascinating aspect of DNA replication, illustrating the cellular innovation in overcoming directional challenges. These primers are indispensable because they provide the necessary starting point for DNA polymerase to begin nucleotide addition. Oct 7, 2024 Oct 26, 2024 Copyright © BiologyInsights All Rights Reserved.
[189] DNA polymerases in biotechnology - PMC - PubMed Central (PMC) — The best known and one of the earliest DNA polymerase-based biotechnology applications is PCR. Since its development over 30 years ago, PCR has been a foundational tool for amplifying and detecting specific ... Zahn K. E. (2014). Structural insights into eukaryotic DNA replication. Front. Microbiol. 5:444. 10.3389/fmicb.2014.00444
[190] DNA polymerases and biotechnological applications - PubMed — A multitude of biotechnological techniques used in basic research as well as in clinical diagnostics on an everyday basis depend on DNA polymerases and their intrinsic capability to replicate DNA strands with astoundingly high fidelity. Applications with fundamental importance to modern molecular bi …
[191] Personalized medicine: the future is here - PMC — For years, personalized medicine and DNA analysis in clinical work have been based on germline mutation detection. However, much less is known about somatic (acquired) mutations. Germline mutations could be present in all somatic cells, while somatic mutations are more or less specific for a post-zygotic cell population.
[192] Personalized sequencing and the future of medicine: discovery ... — Future perspective. Personalized sequencing represents a major step toward a revolutionary future of disease treatment, prediction and prevention in the practice of medicine. Acknowledgments. The authors thank the members of the Snyder laboratory and our collaborators in the study of applications for genome sequencing in personalized medicine
[193] How Designer DNA Is Changing Medicine - Scientific American — Some strategies, such as gene therapy, have been available for some time, including the ability to genetically modify cells in order to produce a therapeutic effect—that is, to add a corrected gene into the genome in order to try to treat disease. Matthew Porteus, a gene-editing pioneer, founder of CRISPR Therapeutics and professor of pediatrics at Stanford School of Medicine, says researchers currently employ two primary gene-editing strategies in their attempt to cure sickle cell patients. Says Doudna, “A true cure means a treatment for everyone who needs it, which is why we’re hard at work on the next generation of therapies to bring down the cost and make it more accessible.”And, as gene editing is not perfect, “The long-term safety of all the genetic modification therapies will have to be studied carefully,” says Porteus.
[199] Recent Advances in Genome-Engineering Strategies - PMC — Due to the simplicity of class II CRISPR-Cas systems, in which a single Cas protein is sufficient to mediate the target’s binding and incision, they are easier to exploit for research purposes and have already been established as an efficient and powerful tool for genome editing approaches, both in prokaryotic and eukaryotic cells. More specifically, the development of diverse methods grounded on CRISPR-Cas systems laid the groundwork for the study of the genetic information in multiple levels since these technologies enabled us to mediate KO in vital genes, alter the epigenomic profile of the DNA, and correct the sequence of mutated genes that are responsible for hereditary diseases.
[201] Integrating DNA logic computation and Self-Replication on nanospheres ... — DNA nanotechnology offers unprecedented opportunities for developing advanced functional materials for biosensing and disease diagnostics. Herein, we present an innovative DNA-based localized amplification strategy that integrated logic computation and self-replication. The system implemented a Boolean AND gate based on miR-21 and miR-122.
[202] Recent progress in molecular diagnostics: The synergy of rolling circle ... — RCA, known for its robust isothermal amplification capabilities, enables the exponential replication of circular nucleic acid templates. The integration of RCA with CRISPR-Cas technologies has paved the way for innovative diagnostic strategies that boast remarkable specificity and sensitivity in the detection of nucleic acid sequences.
[230] DNA Replication Stress and the Human Genome: Hurdles ... - IntechOpen — During replication of the genetic material, cells often face hurdles that challenge DNA replication machinery, leading to replication stress. Multiple complex signalling pathways have evolved to counteract and overcome such challenges. However, DNA repair defects caused by inefficient functioning of the DNA damage response pathways (DDR) drive genomic instability, one of the hallmarks of cancer.
[231] Stalled Replication Fork: Mechanisms, Consequences, and Recovery — Replication stress challenges DNA duplication, often leading to fork stalling. Nucleotide depletion, caused by insufficient dNTP pools, slows replication. Hydroxyurea, a ribonucleotide reductase inhibitor, induces replication stress by reducing nucleotide availability. Tightly packed chromatin and highly repetitive sequences, such as common
[233] DNA replication stress: Causes, resolution and disease — The canonical DNA structure is the right-handed double helix B form of DNA. However, it can adopt several other non-B DNA structures including: cruciforms, hairpins, H DNA, Z DNA and G4. These secondary conformations form in the genome at specific DNA repetitive sequences and present a challenge for progression of DNA replication forks.
[234] Causes and consequences of replication stress - Nature — Replication stress is a complex phenomenon that has serious implications for genome stability, cell survival and human disease. Generation of aberrant replication fork structures containing single
[235] Understanding DNA replication and replication stress as avenues to ... — The research articles in the Collection further showcase how disruptions to DNA replication impact the faithful propagation of genetic and epigenetic information, alter developmental programs, and fuel genome instability, driving tumor initiation and progression when cells bypass genome surveillance mechanisms. By understanding the normal regulatory mechanisms of DNA replication and how these processes are altered in cancer cells, researchers can identify critical vulnerabilities—pathways and components necessary for stress adaptation and unchecked proliferation. Although our Call for papers is formally closed, we remain very interested in publishing papers on the normal mechanisms of DNA replication, how these are perturbed in disease and work that explores how cancer cells can be specifically targeted through their stress adaptation and alterations of regulatory mechanisms.
[236] DNA Replication Errors: Causes and Consequences — DNA Replication Errors: Causes and Consequences - BiologyInsights DNA Replication Errors: Causes and Consequences Explore the subtle intricacies of DNA replication errors, their origins, and their effects on genetic diversity and health. Understanding DNA replication errors is crucial in genetics and medicine, aiding in the comprehension of how these errors contribute to genetic diversity and disease development. Ultraviolet (UV) radiation can induce DNA damage, leading to replication errors. DNA replication errors manifest in various forms, each with distinct implications for genetic integrity. These errors often occur during replication when DNA polymerase slips on repetitive sequences, leading to nucleotide omission. DNA replication errors, while often corrected by repair mechanisms, can have lasting effects that contribute to genetic variation and disease.
[237] Replication stress as a driver of cellular senescence and aging - Nature — Replication stress can be caused by an endogenous or environmental condition that disrupts the faithful copying of the genome (Table 1) 1.In addition to metabolites, drugs, and radiation that can
[238] DNA replication stress: Causes, resolution and disease — Replication stress is defined as slowing or stalling in replication fork progression. It arises from many different sources, which are considered as replication barriers such as telomeres, repetitive sequences, DNA lesions and misincorporation of ribonucleotides, secondary DNA structures, DNA-RNA hybrids, dormant replication origins, collisions between replication and transcription complexes
[259] Recent Advances on the Machine Learning Methods in Identifying DNA ... — Keywords: eukaryotic DNA replication, origins of replication, machine learning method, DNA structure properties, webserver. Citation: Dao F-Y, Lv H, Wang F and Ding H (2018) Recent Advances on the Machine Learning Methods in Identifying DNA Replication Origins in Eukaryotic Genomics. Front. Genet. 9:613. doi: 10.3389/fgene.2018.00613
[261] Unravelling single-cell DNA replication timing dynamics using machine ... — We use single-cell copy number data to accurately perform missing value imputation, identify cell replication states, and detect genomic heterogeneity. Our tool, MnM, is designed to accurately establish single-cell replication states and identify genomic subpopulations based on the DNA copy numbers of a mixture of heterogenous cells issued from a single sample. A schematic representation of MnM main steps (Fig. 1) illustrates that the combination of deep learning, UMAP, DBSCAN and KNN algorithms allows uncovering replication states and subpopulations from single-cell whole-genome copy number calling data (detailed in the following sections). The R script to discover qualitative barcodes from single cells through the expectation-maximisation algorithm, the Python script to split subpopulation and replicate copy number files, the related code scRT files and scCNV matrices from the data can be found at the MnM GitHub depository.
[262] Supervised and unsupervised deep learning-based approaches for studying ... — We first apply supervised machine learning, successfully classifying S-phase patterns in wild-type mouse embryonic stem cells (mESCs), while additionally identifying altered replication dynamics in Rif1-deficient mESCs. Given the constraints imposed by a classification-based approach, we then develop an unsupervised method for large-scale detection of aberrant S-phase cells. We analysed the images using an unsupervised approach analogous to the one described above for Rif1 mutant mESCs. After training the BYOL model on images of non-induced U2OS cells (‘0 h’ timepoint), we proceeded to visualise the image embeddings for the entire dataset, consisting of 26,137 S-phase nuclei across the five timepoints (Supplementary Fig. 8b).
[264] Exploiting DNA Replication Stress for Cancer Treatment — American Association for Cancer Research. Cancer Res (2019) 79 (8): 1730-1739. ... exploiting replication stress for cancer treatment seems to be a promising strategy as it provides a selective means of eliminating tumors, and with continuous advances in our knowledge of the replication stress response and lessons learned from current
[265] Replication Stress: A Review of Novel Targets to Enhance ... — Current research trends have highlighted the potential of combining replication stress regulators with radiation therapy to capitalize on the high replication stress of tumors. Here, we review the current body of evidence regarding the role of replication stress in tumor progression and discuss potential means of enhancing tumor
[267] Targeting replication stress in cancer therapy - PMC — Activation of ataxia telangiectasia mutated (ATM) and Rad3-related (ATR) pathway because of replication stress or double-strand breaks results in cell cycle arrest, activation of DNA repair pathways, fork stabilization, inhibition of origin firing, decrease in deoxynucleotide (dNTP) degradation and increase in dNTP synthesis. Sources of replication stress in cancer cells include loss of G1/S checkpoint (for example, owing to deleterious TP53 mutations), premature entry into S phase (due to RB1 loss, CCNE1 amplification or FBXW7 loss), oncogenic drive (oncogene-related replication stress such as that due to KRAS activating mutations or MYC amplification) and DNA repair deficiencies (such as HRR or NER pathway deficiency)9.