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100-397: Nuclear DNA is a nucleic acid , a polymeric biomolecule or biopolymer , found in the nucleus of eukaryotic cells. Its structure is a double helix , with two strands wound around each other, a structure first described by Francis Crick and James D. Watson (1953) using data collected by Rosalind Franklin . Each strand is a long polymer chain of repeating nucleotides . Each nucleotide

200-644: A Rossmann-like topology. This structure is also found in the catalytic domains of topoisomerase Ia, topoisomerase II, the OLD-family nucleases and DNA repair proteins related to the RecR protein. The primase used by archaea and eukaryotes, in contrast, contains a highly derived version of the RNA recognition motif (RRM). This primase is structurally similar to many viral RNA-dependent RNA polymerases, reverse transcriptases, cyclic nucleotide generating cyclases and DNA polymerases of

300-413: A cell , DNA replication begins at specific locations, or origins of replication , in the genome which contains the genetic material of an organism. Unwinding of DNA at the origin and synthesis of new strands, accommodated by an enzyme known as helicase , results in replication forks growing bi-directionally from the origin. A number of proteins are associated with the replication fork to help in

400-416: A purine or pyrimidine nucleobase (sometimes termed nitrogenous base or simply base ), a pentose sugar , and a phosphate group which makes the molecule acidic. The substructure consisting of a nucleobase plus sugar is termed a nucleoside . Nucleic acid types differ in the structure of the sugar in their nucleotides–DNA contains 2'- deoxyribose while RNA contains ribose (where the only difference

500-534: A case. Techniques used include polymerase chain reaction (PCR), which allows one to utilize very small amounts of DNA by making copies of targeted regions on the molecule, also known as short tandem repeats (STRs). Like mitosis , meiosis is a form of eukaryotic cell division . Meiosis gives rise to four unique daughter cells, each of which has half the number of chromosomes as the parent cell. Because meiosis creates cells that are destined to become gametes (or reproductive cells), this reduction in chromosome number

600-428: A cell goes through an interphase period in which it grows, replicates its chromosomes, and checks all of its systems to ensure that it is ready to divide. Like mitosis, meiosis also has distinct stages called prophase , metaphase , anaphase , and telophase . A key difference, however, is that during meiosis, each of these phases occurs twice — once during the first round of division, called meiosis I, and again during

700-480: A diverse set of DNA repair processes that remove nuclear DNA damages. These repair processes include base excision repair , nucleotide excision repair , homologous recombinational repair, non-homologous end joining and microhomology-mediated end joining . Such repair processes are essential for maintaining nuclear DNA stability. Failure of repair activity to keep up with the occurrence of damages has various negative consequences. Nuclear DNA damages, as well as

800-566: A new strand of DNA by extending the 3′ end of an existing nucleotide chain, adding new nucleotides matched to the template strand, one at a time, via the creation of phosphodiester bonds . The energy for this process of DNA polymerization comes from hydrolysis of the high-energy phosphate (phosphoanhydride) bonds between the three phosphates attached to each unincorporated base . Free bases with their attached phosphate groups are called nucleotides ; in particular, bases with three attached phosphate groups are called nucleoside triphosphates . When

900-421: A newly synthesized partner strand. DNA polymerases are a family of enzymes that carry out all forms of DNA replication. DNA polymerases in general cannot initiate synthesis of new strands but can only extend an existing DNA or RNA strand paired with a template strand. To begin synthesis, a short fragment of RNA, called a primer , must be created and paired with the template DNA strand. DNA polymerase adds

1000-428: A nucleotide is being added to a growing DNA strand, the formation of a phosphodiester bond between the proximal phosphate of the nucleotide to the growing chain is accompanied by hydrolysis of a high-energy phosphate bond with release of the two distal phosphate groups as a pyrophosphate . Enzymatic hydrolysis of the resulting pyrophosphate into inorganic phosphate consumes a second high-energy phosphate bond and renders

1100-456: A rate-limiting regulator of origin activity. Together, the G1/S-Cdks and/or S-Cdks and Cdc7 collaborate to directly activate the replication origins, leading to initiation of DNA synthesis. In early S phase, S-Cdk and Cdc7 activation lead to the assembly of the preinitiation complex, a massive protein complex formed at the origin. Formation of the preinitiation complex displaces Cdc6 and Cdt1 from

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1200-444: A recent report suggests that budding yeast ORC dimerizes in a cell cycle dependent manner to control licensing. In turn, the process of ORC dimerization is mediated by a cell cycle-dependent Noc3p dimerization cycle in vivo, and this role of Noc3p is separable from its role in ribosome biogenesis. An essential Noc3p dimerization cycle mediates ORC double-hexamer formation in replication licensing ORC and Noc3p are continuously bound to

1300-526: A regular double helix, and can adopt highly complex three-dimensional structures that are based on short stretches of intramolecular base-paired sequences including both Watson-Crick and noncanonical base pairs, and a wide range of complex tertiary interactions. Nucleic acid molecules are usually unbranched and may occur as linear and circular molecules. For example, bacterial chromosomes, plasmids , mitochondrial DNA , and chloroplast DNA are usually circular double-stranded DNA molecules, while chromosomes of

1400-456: A role in activating replication origins depending on species and cell type. Control of these Cdks vary depending on cell type and stage of development. This regulation is best understood in budding yeast , where the S cyclins Clb5 and Clb6 are primarily responsible for DNA replication. Clb5,6-Cdk1 complexes directly trigger the activation of replication origins and are therefore required throughout S phase to directly activate each origin. In

1500-524: A series of short DNA segments called Okazaki fragments . Each Okazaki fragment requires a separate RNA primer. As the Okazaki fragments are synthesized, the RNA primers are replaced with DNA nucleotides and the fragments are bonded together in a continuous complementary strand. Damage of nuclear DNA is a persistent problem arising from a variety of disruptive endogenous and exogenous sources. Eukaryotes have evolved

1600-473: A short sequence of RNA nucleotides, complementary to a small, initial section of the DNA strand being prepared for replication. DNA polymerase is then able to add DNA nucleotides to the RNA primer and thus begin the process of constructing a new complementary strand of DNA. Later the RNA primer is enzymatically removed and replaced with the appropriate sequence of DNA nucleotides. Because the two complementary strands of

1700-423: A similar manner, Cdc7 is also required through S phase to activate replication origins. Cdc7 is not active throughout the cell cycle, and its activation is strictly timed to avoid premature initiation of DNA replication. In late G1, Cdc7 activity rises abruptly as a result of association with the regulatory subunit DBF4 , which binds Cdc7 directly and promotes its protein kinase activity. Cdc7 has been found to be

1800-422: A template DNA molecule. Polymerase chain reaction (PCR), ligase chain reaction (LCR), and transcription-mediated amplification (TMA) are examples. In March 2021, researchers reported evidence suggesting that a preliminary form of transfer RNA , a necessary component of translation , the biological synthesis of new proteins in accordance with the genetic code , could have been a replicator molecule itself in

1900-420: A template to guide the synthesis of the new complementary polynucleotide of DNA. The DNA single-strand template serves to guide the synthesis of a complementary strand of DNA. DNA replication begins at a specific site in the DNA molecule called the origin of replication . The enzyme helicase unwinds and separates a portion of the DNA molecule after which single-strand binding proteins react with and stabilize

2000-528: Is a single molecule that contains 247 million base pairs ). In most cases, naturally occurring DNA molecules are double-stranded and RNA molecules are single-stranded. There are numerous exceptions, however—some viruses have genomes made of double-stranded RNA and other viruses have single-stranded DNA genomes, and, in some circumstances, nucleic acid structures with three or four strands can form. Nucleic acids are linear polymers (chains) of nucleotides. Each nucleotide consists of three components:

2100-447: Is a structure that forms within the long helical DNA during DNA replication. It is produced by enzymes called helicases that break the hydrogen bonds that hold the DNA strands together in a helix. The resulting structure has two branching "prongs", each one made up of a single strand of DNA. These two strands serve as the template for the leading and lagging strands, which will be created as DNA polymerase matches complementary nucleotides to

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2200-524: Is complete, ensuring that assembly cannot occur again until all Cdk activity is reduced in late mitosis. In budding yeast, inhibition of assembly is caused by Cdk-dependent phosphorylation of pre-replication complex components. At the onset of S phase, phosphorylation of Cdc6 by Cdk1 causes the binding of Cdc6 to the SCF ubiquitin protein ligase , which causes proteolytic destruction of Cdc6. Cdk-dependent phosphorylation of Mcm proteins promotes their export out of

2300-401: Is complete, it does not occur again in the same cell cycle. This is made possible by the division of initiation of the pre-replication complex . In late mitosis and early G1 phase , a large complex of initiator proteins assembles into the pre-replication complex at particular points in the DNA, known as " origins ". In E. coli the primary initiator protein is Dna A ; in yeast , this

2400-524: Is completed by Pol ε. As DNA synthesis continues, the original DNA strands continue to unwind on each side of the bubble, forming a replication fork with two prongs. In bacteria, which have a single origin of replication on their circular chromosome, this process creates a " theta structure " (resembling the Greek letter theta: θ). In contrast, eukaryotes have longer linear chromosomes and initiate replication at multiple origins within these. The replication fork

2500-421: Is composed of a five-carbon sugar, a phosphate group, and an organic base. Nucleotides are distinguished by their bases: purines , large bases that include adenine and guanine ; and pyrimidines , small bases that include thymine and cytosine . Chargaff's rules state that adenine always pairs with thymine, and guanine always with cytosine. The phosphate groups are held together by a phosphodiester bond and

2600-411: Is continuously extended from the primer by a DNA polymerase with high processivity , while the lagging strand is extended discontinuously from each primer forming Okazaki fragments . RNase removes the primer RNA fragments, and a low processivity DNA polymerase distinct from the replicative polymerase enters to fill the gaps. When this is complete, a single nick on the leading strand and several nicks on

2700-495: Is controlled within the context of the cell cycle . As the cell grows and divides, it progresses through stages in the cell cycle; DNA replication takes place during the S phase (synthesis phase). The progress of the eukaryotic cell through the cycle is controlled by cell cycle checkpoints . Progression through checkpoints is controlled through complex interactions between various proteins, including cyclins and cyclin-dependent kinases . Unlike bacteria, eukaryotic DNA replicates in

2800-523: Is critical — without it, the union of two gametes during fertilization would result in offspring with twice the normal number of chromosomes. Meiosis creates new combinations of genetic material in each of the four daughter cells. These new combinations result from the exchange of DNA between paired chromosomes. Such an exchange means that the gametes produced through meiosis often exhibit considerable genetic variation. Meiosis involves two rounds of nuclear division, not just one. Prior to undergoing meiosis,

2900-504: Is distinguished from naturally occurring DNA or RNA by changes to the backbone of the molecules. DNA replication 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

3000-510: Is known as the molecule of life and contains the genetic instructions for the development of all eukaryotic organisms. It is found in almost every cell in the human body, with exceptions such as red blood cells . Everyone has a unique genetic blueprint, even identical twins. Forensic departments such as the Bureau of Criminal Apprehension (BCA) and Federal Bureau of Investigation (FBI) are able to use techniques involving nuclear DNA to compare samples in

3100-411: Is one of four types of molecules called nucleobases (informally, bases). It is the sequence of these four nucleobases along the backbone that encodes genetic information. This information specifies the sequence of the amino acids within proteins according to the genetic code . The code is read by copying stretches of DNA into the related nucleic acid RNA in a process called transcription. Within cells, DNA

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3200-553: Is one of the hallmarks of cancer. Termination requires that the progress of the DNA replication fork must stop or be blocked. Termination at a specific locus, when it occurs, involves the interaction between two components: (1) a termination site sequence in the DNA, and (2) a protein which binds to this sequence to physically stop DNA replication. In various bacterial species, this is named the DNA replication terminus site-binding protein, or Ter protein . Because bacteria have circular chromosomes, termination of replication occurs when

3300-409: Is opposite to the direction of the growing replication fork. The leading strand is the strand of new DNA which is synthesized in the same direction as the growing replication fork. This sort of DNA replication is continuous. The lagging strand is the strand of new DNA whose direction of synthesis is opposite to the direction of the growing replication fork. Because of its orientation, replication of

3400-453: Is organized into long sequences called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, providing each cell its own complete set of chromosomes. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast, prokaryotes (bacteria and archaea) store their DNA only in

3500-473: Is particularly prone to mutation. Mutations arising in the nuclear DNA of the germline are most often neutral or adaptively disadvantageous. However, the small proportion of mutations that prove to be advantageous provide the genetic variation upon which natural selection operates to generate new adaptations. Nucleic acid Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides , which are

3600-561: Is the nucleotide , each of which contains a pentose sugar ( ribose or deoxyribose ), a phosphate group, and a nucleobase . Nucleic acids are also generated within the laboratory, through the use of enzymes (DNA and RNA polymerases) and by solid-phase chemical synthesis . Nucleic acids are generally very large molecules. Indeed, DNA molecules are probably the largest individual molecules known. Well-studied biological nucleic acid molecules range in size from 21 nucleotides ( small interfering RNA ) to large chromosomes ( human chromosome 1

3700-405: Is the origin recognition complex . Sequences used by initiator proteins tend to be "AT-rich" (rich in adenine and thymine bases), because A-T base pairs have two hydrogen bonds (rather than the three formed in a C-G pair) and thus are easier to strand-separate. In eukaryotes, the origin recognition complex catalyzes the assembly of initiator proteins into the pre-replication complex. In addition,

3800-431: Is the presence of a hydroxyl group ). Also, the nucleobases found in the two nucleic acid types are different: adenine , cytosine , and guanine are found in both RNA and DNA, while thymine occurs in DNA and uracil occurs in RNA. The sugars and phosphates in nucleic acids are connected to each other in an alternating chain (sugar-phosphate backbone) through phosphodiester linkages. In conventional nomenclature ,

3900-433: Is to create many short DNA regions rather than a few very long regions. In eukaryotes , the low-processivity enzyme, Pol α, helps to initiate replication because it forms a complex with primase. In eukaryotes, leading strand synthesis is thought to be conducted by Pol ε; however, this view has recently been challenged, suggesting a role for Pol δ. Primer removal is completed Pol δ while repair of DNA during replication

4000-478: The University of Tübingen , Germany. He discovered a new substance, which he called nuclein and which - depending on how his results are interpreted in detail - can be seen in modern terms either as a nucleid acid- histone complex or as the actual nucleid acid. Phoeber Aaron Theodor Levene, an American biochemist determined the basic structure of nucleic acids. In the early 1880s, Albrecht Kossel further purified

4100-660: The monomer components: a 5-carbon sugar , a phosphate group and a nitrogenous base . The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). If the sugar is ribose , the polymer is RNA; if the sugar is deoxyribose , a variant of ribose, the polymer is DNA. Nucleic acids are chemical compounds that are found in nature. They carry information in cells and make up genetic material. These acids are very common in all living things, where they create, encode, and store information in every living cell of every life-form on Earth. In turn, they send and express that information inside and outside

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4200-570: The mutations and epigenetic alterations that such damages cause, are considered to be a major cause of cancer . Nuclear DNA damages are also implicated in aging and neurodegenerative diseases . Nuclear DNA is subject to mutation . A major cause of mutation is inaccurate DNA replication , often by specialized DNA polymerases that synthesize past DNA damages in the template strand (error-prone trans-lesion synthesis ). Mutations also arise by inaccurate DNA repair. The microhomology-mediated end joining pathway for repair of double-strand breaks

4300-574: The nucleus , and for the presence of phosphate groups (related to phosphoric acid). Although first discovered within the nucleus of eukaryotic cells, nucleic acids are now known to be found in all life forms including within bacteria , archaea , mitochondria , chloroplasts , and viruses (There is debate as to whether viruses are living or non-living ). All living cells contain both DNA and RNA (except some cells such as mature red blood cells), while viruses contain either DNA or RNA, but usually not both. The basic component of biological nucleic acids

4400-599: The sequence of nucleotides . Nucleotide sequences are of great importance in biology since they carry the ultimate instructions that encode all biological molecules, molecular assemblies, subcellular and cellular structures, organs, and organisms, and directly enable cognition, memory, and behavior. Enormous efforts have gone into the development of experimental methods to determine the nucleotide sequence of biological DNA and RNA molecules, and today hundreds of millions of nucleotides are sequenced daily at genome centers and smaller laboratories worldwide. In addition to maintaining

4500-417: The "3′ (three-prime) end" and the "5′ (five-prime) end". By convention, if the base sequence of a single strand of DNA is given, the left end of the sequence is the 5′ end, while the right end of the sequence is the 3′ end. The strands of the double helix are anti-parallel, with one being 5′ to 3′, and the opposite strand 3′ to 5′. These terms refer to the carbon atom in deoxyribose to which the next phosphate in

4600-405: The 5′ to 3′ direction—this is often confused). Four distinct mechanisms for DNA synthesis are recognized: Cellular organisms use the first of these pathways since it is the most well-known. In this mechanism, once the two strands are separated, primase adds RNA primers to the template strands. The leading strand receives one RNA primer while the lagging strand receives several. The leading strand

4700-493: The A/B/Y families that are involved in DNA replication and repair. In eukaryotic replication, the primase forms a complex with Pol α. Multiple DNA polymerases take on different roles in the DNA replication process. In E. coli , DNA Pol III is the polymerase enzyme primarily responsible for DNA replication. It assembles into a replication complex at the replication fork that exhibits extremely high processivity, remaining intact for

4800-430: The DNA helix. Bare single-stranded DNA tends to fold back on itself forming secondary structures ; these structures can interfere with the movement of DNA polymerase. To prevent this, single-strand binding proteins bind to the DNA until a second strand is synthesized, preventing secondary structure formation. Double-stranded DNA is coiled around histones that play an important role in regulating gene expression so

4900-490: The DNA into a complex molecular machine called the replisome . The following is a list of major DNA replication enzymes that participate in the replisome: In vitro single-molecule experiments (using optical tweezers and magnetic tweezers ) have found synergetic interactions between the replisome enzymes ( helicase , polymerase , and Single-strand DNA-binding protein ) and with the DNA replication fork enhancing DNA-unwinding and DNA-replication. These results lead to

5000-407: The DNA molecule are oriented in opposite directions and the DNA polymerase can only accommodate replication in one direction, two different mechanisms for copying the strands of DNA are employed. One strand is replicated continuously towards unwinding, separating the portion of the original DNA molecule; while the other strand is replicated discontinuously in the opposite direction with the formation of

5100-551: The DNA via ATP-dependent protein remodeling. The loading of the Mcm complex onto the origin DNA marks the completion of pre-replication complex formation. If environmental conditions are right in late G1 phase, the G1 and G1/S cyclin - Cdk complexes are activated, which stimulate expression of genes that encode components of the DNA synthetic machinery. G1/S-Cdk activation also promotes the expression and activation of S-Cdk complexes, which may play

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5200-563: The GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. Deoxyribonucleic acid (DNA) is a nucleic acid containing the genetic instructions used in the development and functioning of all known living organisms. The chemical DNA

5300-502: The bases are held together by hydrogen bonds . Nuclear DNA and mitochondrial DNA differ in many ways, starting with location and structure. Nuclear DNA is located within the nucleus of eukaryote cells and usually has two copies per cell while mitochondrial DNA is located in the mitochondria and contains 100–1,000 copies per cell. The structure of nuclear DNA chromosomes is linear with open ends and includes 46 chromosomes and contains for example 3 billion nucleotides in humans while

5400-520: The carbons to which the phosphate groups attach are the 3'-end and the 5'-end carbons of the sugar. This gives nucleic acids directionality , and the ends of nucleic acid molecules are referred to as 5'-end and 3'-end. The nucleobases are joined to the sugars via an N -glycosidic linkage involving a nucleobase ring nitrogen ( N -1 for pyrimidines and N -9 for purines) and the 1' carbon of the pentose sugar ring. Non-standard nucleosides are also found in both RNA and DNA and usually arise from modification of

5500-446: The cell nucleus. From the inner workings of the cell to the young of a living thing, they contain and provide information via the nucleic acid sequence . This gives the RNA and DNA their unmistakable 'ladder-step' order of nucleotides within their molecules. Both play a crucial role in directing protein synthesis . Strings of nucleotides are bonded to form spiraling backbones and assembled into chains of bases or base-pairs selected from

5600-434: The chain attaches. Directionality has consequences in DNA synthesis, because DNA polymerase can synthesize DNA in only one direction by adding nucleotides to the 3′ end of a DNA strand. The pairing of complementary bases in DNA (through hydrogen bonding ) means that the information contained within each strand is redundant. Phosphodiester (intra-strand) bonds are stronger than hydrogen (inter-strand) bonds. The actual job of

5700-498: The chromatids into daughter cells after DNA replication. Because sister chromatids after DNA replication hold each other by Cohesin rings, there is the only chance for the disentanglement in DNA replication. Fixing of replication machineries as replication factories can improve the success rate of DNA replication. If replication forks move freely in chromosomes, catenation of nuclei is aggravated and impedes mitotic segregation. Eukaryotes initiate DNA replication at multiple points in

5800-522: The chromatin throughout the cell cycle. Cdc6 and Cdt1 then associate with the bound origin recognition complex at the origin in order to form a larger complex necessary to load the Mcm complex onto the DNA. In eukaryotes, the Mcm complex is the helicase that will split the DNA helix at the replication forks and origins. The Mcm complex is recruited at late G1 phase and loaded by the ORC-Cdc6-Cdt1 complex onto

5900-424: The chromosome, so replication forks meet and terminate at many points in the chromosome. Because eukaryotes have linear chromosomes, DNA replication is unable to reach the very end of the chromosomes. Due to this problem, DNA is lost in each replication cycle from the end of the chromosome. Telomeres are regions of repetitive DNA close to the ends and help prevent loss of genes due to this shortening. Shortening of

6000-404: The clamp enables DNA to be threaded through it. Once the polymerase reaches the end of the template or detects double-stranded DNA, the sliding clamp undergoes a conformational change that releases the DNA polymerase. Clamp-loading proteins are used to initially load the clamp, recognizing the junction between template and RNA primers. At the replication fork, many replication enzymes assemble on

6100-458: The confines of the nucleus. The G1/S checkpoint (restriction checkpoint) regulates whether eukaryotic cells enter the process of DNA replication and subsequent division. Cells that do not proceed through this checkpoint remain in the G0 stage and do not replicate their DNA. Once the DNA has gone through the "G1/S" test, it can only be copied once in every cell cycle. When the Mcm complex moves away from

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6200-621: The cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed. Ribonucleic acid (RNA) functions in converting genetic information from genes into the amino acid sequences of proteins. The three universal types of RNA include transfer RNA (tRNA), messenger RNA (mRNA), and ribosomal RNA (rRNA). Messenger RNA acts to carry genetic sequence information between DNA and ribosomes, directing protein synthesis and carries instructions from DNA in

6300-420: The development of kinetic models accounting for the synergetic interactions and their stability. Replication machineries consist of factors involved in DNA replication and appearing on template ssDNAs. Replication machineries include primosotors are replication enzymes; DNA polymerase, DNA helicases, DNA clamps and DNA topoisomerases, and replication proteins; e.g. single-stranded DNA binding proteins (SSB). In

6400-465: The double-helix structure of DNA . Experimental studies of nucleic acids constitute a major part of modern biological and medical research , and form a foundation for genome and forensic science , and the biotechnology and pharmaceutical industries . The term nucleic acid is the overall name for DNA and RNA, members of a family of biopolymers , and is a type of polynucleotide . Nucleic acids were named for their initial discovery within

6500-448: The entire replication cycle. In contrast, DNA Pol I is the enzyme responsible for replacing RNA primers with DNA. DNA Pol I has a 5′ to 3′ exonuclease activity in addition to its polymerase activity, and uses its exonuclease activity to degrade the RNA primers ahead of it as it extends the DNA strand behind it, in a process called nick translation . Pol I is much less processive than Pol III because its primary function in DNA replication

6600-425: The eukaryotic nucleus are usually linear double-stranded DNA molecules. Most RNA molecules are linear, single-stranded molecules, but both circular and branched molecules can result from RNA splicing reactions. The total amount of pyrimidines in a double-stranded DNA molecule is equal to the total amount of purines. The diameter of the helix is about 20 Å . One DNA or RNA molecule differs from another primarily in

6700-632: The five primary, or canonical, nucleobases . RNA usually forms a chain of single bases, whereas DNA forms a chain of base pairs. The bases found in RNA and DNA are: adenine , cytosine , guanine , thymine , and uracil . Thymine occurs only in DNA and uracil only in RNA. Using amino acids and protein synthesis , the specific sequence in DNA of these nucleobase-pairs helps to keep and send coded instructions as genes . In RNA, base-pair sequencing helps to make new proteins that determine most chemical processes of all life forms. Nucleic acid was, partially, first discovered by Friedrich Miescher in 1869 at

6800-515: The initiation and continuation of DNA synthesis . Most prominently, DNA polymerase synthesizes the new strands by adding nucleotides that complement each (template) strand. DNA replication occurs during the S-stage of interphase . DNA replication (DNA amplification) can also be performed in vitro (artificially, outside a cell). DNA polymerases isolated from cells and artificial DNA primers can be used to start DNA synthesis at known sequences in

6900-517: The lagging strand can be found. Ligase works to fill these nicks in, thus completing the newly replicated DNA molecule. The primase used in this process differs significantly between bacteria and archaea / eukaryotes . Bacteria use a primase belonging to the DnaG protein superfamily which contains a catalytic domain of the TOPRIM fold type. The TOPRIM fold contains an α/β core with four conserved strands in

7000-403: The lagging strand is more complicated as compared to that of the leading strand. As a consequence, the DNA polymerase on this strand is seen to "lag behind" the other strand. The lagging strand is synthesized in short, separated segments. On the lagging strand template , a primase "reads" the template DNA and initiates synthesis of a short complementary RNA primer. A DNA polymerase extends

7100-492: The lagging strand. As helicase unwinds DNA at the replication fork, the DNA ahead is forced to rotate. This process results in a build-up of twists in the DNA ahead. This build-up creates a torsional load that would eventually stop the replication fork. Topoisomerases are enzymes that temporarily break the strands of DNA, relieving the tension caused by unwinding the two strands of the DNA helix; topoisomerases (including DNA gyrase ) achieve this by adding negative supercoils to

7200-455: The new cells receives its own copy of the DNA. The cell possesses the distinctive property of division, which makes replication of DNA essential. DNA is made up of a double helix of two complementary strands . The double helix describes the appearance of a double-stranded DNA which is thus composed of two linear strands that run opposite to each other and twist together to form. During replication, these strands are separated. Each strand of

7300-402: The newly synthesized DNA Strand from the original strand sequence. Together, these three discrimination steps enable replication fidelity of less than one mistake for every 10 nucleotides added. The rate of DNA replication in a living cell was first measured as the rate of phage T4 DNA elongation in phage-infected E. coli . During the period of exponential DNA increase at 37 °C, the rate

7400-515: The nucleid acid substance and discovered its highly acidic properties. He later also identified the nucleobases . In 1889 Richard Altmann created the term nucleic acid – at that time DNA and RNA were not differentiated. In 1938 Astbury and Bell published the first X-ray diffraction pattern of DNA. In 1944 the Avery–MacLeod–McCarty experiment showed that DNA is the carrier of genetic information and in 1953 Watson and Crick proposed

7500-503: The nucleus along with Cdt1 during S phase, preventing the loading of new Mcm complexes at origins during a single cell cycle. Cdk phosphorylation of the origin replication complex also inhibits pre-replication complex assembly. The individual presence of any of these three mechanisms is sufficient to inhibit pre-replication complex assembly. However, mutations of all three proteins in the same cell does trigger reinitiation at many origins of replication within one cell cycle. In animal cells,

7600-515: The nucleus to ribosome . Ribosomal RNA reads the DNA sequence, and catalyzes peptide bond formation. Transfer RNA serves as the carrier molecule for amino acids to be used in protein synthesis, and is responsible for decoding the mRNA. In addition, many other classes of RNA are now known. Artificial nucleic acid analogues have been designed and synthesized. They include peptide nucleic acid , morpholino - and locked nucleic acid , glycol nucleic acid , and threose nucleic acid . Each of these

7700-418: The origin replication complex, inactivating and disassembling the pre-replication complex. Loading the preinitiation complex onto the origin activates the Mcm helicase, causing unwinding of the DNA helix. The preinitiation complex also loads α-primase and other DNA polymerases onto the DNA. After α-primase synthesizes the first primers, the primer-template junctions interact with the clamp loader, which loads

7800-480: The origin, the pre-replication complex is dismantled. Because a new Mcm complex cannot be loaded at an origin until the pre-replication subunits are reactivated, one origin of replication can not be used twice in the same cell cycle. Activation of S-Cdks in early S phase promotes the destruction or inhibition of individual pre-replication complex components, preventing immediate reassembly. S and M-Cdks continue to block pre-replication complex assembly even after S phase

7900-403: The original DNA molecule then serves as a template for the production of its counterpart, a process referred to as semiconservative replication . As a result of semi-conservative replication, the new helix will be composed of an original DNA strand as well as a newly synthesized strand. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication. In

8000-418: The phosphate-deoxyribose backbone of the DNA double helix with the nucleobases pointing inward (i.e., toward the opposing strand). Nucleobases are matched between strands through hydrogen bonds to form base pairs . Adenine pairs with thymine (two hydrogen bonds), and guanine pairs with cytosine (three hydrogen bonds ). DNA strands have a directionality , and the different ends of a single strand are called

8100-407: The phosphodiester bonds is where in DNA polymers connect the 5' carbon atom of one nucleotide to the 3' carbon atom of another nucleotide, while the hydrogen bonds stabilize DNA double helices across the helix axis but not in the direction of the axis. This makes it possible to separate the strands from one another. The nucleotides on a single strand can therefore be used to reconstruct nucleotides on

8200-431: The primed segments, forming Okazaki fragments . The RNA primers are then removed and replaced with DNA, and the fragments of DNA are joined by DNA ligase . In all cases the helicase is composed of six polypeptides that wrap around only one strand of the DNA being replicated. The two polymerases are bound to the helicase hexamer. In eukaryotes the helicase wraps around the leading strand, and in prokaryotes it wraps around

8300-583: The protein geminin is a key inhibitor of pre-replication complex assembly. Geminin binds Cdt1, preventing its binding to the origin recognition complex. In G1, levels of geminin are kept low by the APC, which ubiquitinates geminin to target it for degradation. When geminin is destroyed, Cdt1 is released, allowing it to function in pre-replication complex assembly. At the end of G1, the APC is inactivated, allowing geminin to accumulate and bind Cdt1. Replication of chloroplast and mitochondrial genomes occurs independently of

8400-455: The reaction effectively irreversible. In general, DNA polymerases are highly accurate, with an intrinsic error rate of less than one mistake for every 10 nucleotides added. Some DNA polymerases can also delete nucleotides from the end of a developing strand in order to fix mismatched bases. This is known as proofreading. Finally, post-replication mismatch repair mechanisms monitor the DNA for errors, being capable of distinguishing mismatches in

8500-426: The replicated DNA must be coiled around histones at the same places as the original DNA. To ensure this, histone chaperones disassemble the chromatin before it is replicated and replace the histones in the correct place. Some steps in this reassembly are somewhat speculative. Clamp proteins act as a sliding clamp on DNA, allowing the DNA polymerase to bind to its template and aid in processivity. The inner face of

8600-421: The replication machineries these components coordinate. In most of the bacteria, all of the factors involved in DNA replication are located on replication forks and the complexes stay on the forks during DNA replication. Replication machineries are also referred to as replisomes, or DNA replication systems. These terms are generic terms for proteins located on replication forks. In eukaryotic and some bacterial cells

8700-671: The replisomes are not formed. In an alternative figure, DNA factories are similar to projectors and DNAs are like as cinematic films passing constantly into the projectors. In the replication factory model, after both DNA helicases for leading strands and lagging strands are loaded on the template DNAs, the helicases run along the DNAs into each other. The helicases remain associated for the remainder of replication process. Peter Meister et al. observed directly replication sites in budding yeast by monitoring green fluorescent protein (GFP)-tagged DNA polymerases α. They detected DNA replication of pairs of

8800-476: The second round of division, called meiosis II. Prior to cell division, the DNA material in the original cell must be duplicated so that after cell division, each new cell contains the full amount of DNA material. The process of DNA duplication is usually called replication . The replication is termed semiconservative since each new cell contains one strand of original DNA and one newly synthesized strand of DNA. The original polynucleotide strand of DNA serves as

8900-419: The separated, single-stranded sections of the DNA molecule. The enzyme complex DNA polymerase engages the separated portion of the molecule and initiates the process of replication. DNA polymerase can only connect new DNA nucleotides to a pre-existing chain of nucleotides. Therefore, replication begins as an enzyme called primase assembles an RNA primer at the origin of replication. The RNA primer consists of

9000-407: The sliding clamp onto the DNA to begin DNA synthesis. The components of the preinitiation complex remain associated with replication forks as they move out from the origin. DNA polymerase has 5′–3′ activity. All known DNA replication systems require a free 3′ hydroxyl group before synthesis can be initiated (note: the DNA template is read in 3′ to 5′ direction whereas a new strand is synthesized in

9100-483: The standard nucleosides within the DNA molecule or the primary (initial) RNA transcript. Transfer RNA (tRNA) molecules contain a particularly large number of modified nucleosides. Double-stranded nucleic acids are made up of complementary sequences, in which extensive Watson-Crick base pairing results in a highly repeated and quite uniform nucleic acid double-helical three-dimensional structure. In contrast, single-stranded RNA and DNA molecules are not constrained to

9200-400: The structure of Mitochondrial DNA chromosome is usually closed, circular, and contains for example 16,569 nucleotides in humans. Nuclear DNA in animals is diploid , ordinarily inheriting the DNA from two parents, while mitochondrial DNA is haploid , coming only from the mother. The mutation rate for nuclear DNA is less than 0.3% while that of mitochondrial DNA is generally higher. Nuclear DNA

9300-420: The tagged loci spaced apart symmetrically from a replication origin and found that the distance between the pairs decreased markedly by time. This finding suggests that the mechanism of DNA replication goes with DNA factories. That is, couples of replication factories are loaded on replication origins and the factories associated with each other. Also, template DNAs move into the factories, which bring extrusion of

9400-607: The telomeres is a normal process in somatic cells . This shortens the telomeres of the daughter DNA chromosome. As a result, cells can only divide a certain number of times before the DNA loss prevents further division. (This is known as the Hayflick limit .) Within the germ cell line, which passes DNA to the next generation, telomerase extends the repetitive sequences of the telomere region to prevent degradation. Telomerase can become mistakenly active in somatic cells, sometimes leading to cancer formation. Increased telomerase activity

9500-399: The template ssDNAs and new DNAs. Meister's finding is the first direct evidence of replication factory model. Subsequent research has shown that DNA helicases form dimers in many eukaryotic cells and bacterial replication machineries stay in single intranuclear location during DNA synthesis. Replication Factories Disentangle Sister Chromatids. The disentanglement is essential for distributing

9600-453: The templates; the templates may be properly referred to as the leading strand template and the lagging strand template. DNA is read by DNA polymerase in the 3′ to 5′ direction, meaning the new strand is synthesized in the 5' to 3' direction. Since the leading and lagging strand templates are oriented in opposite directions at the replication fork, a major issue is how to achieve synthesis of new lagging strand DNA, whose direction of synthesis

9700-463: The two replication forks meet each other on the opposite end of the parental chromosome. E. coli regulates this process through the use of termination sequences that, when bound by the Tus protein , enable only one direction of replication fork to pass through. As a result, the replication forks are constrained to always meet within the termination region of the chromosome. Within eukaryotes, DNA replication

9800-631: The very early development of life, or abiogenesis . DNA exists as a double-stranded structure, with both strands coiled together to form the characteristic double helix . Each single strand of DNA is a chain of four types of nucleotides . Nucleotides in DNA contain a deoxyribose sugar, a phosphate , and a nucleobase . The four types of nucleotide correspond to the four nucleobases adenine , cytosine , guanine , and thymine , commonly abbreviated as A, C, G, and T. Adenine and guanine are purine bases, while cytosine and thymine are pyrimidines . These nucleotides form phosphodiester bonds , creating

9900-469: Was 749 nucleotides per second. The mutation rate per base pair per replication during phage T4 DNA synthesis is 1.7 per 10 . DNA replication, like all biological polymerization processes, proceeds in three enzymatically catalyzed and coordinated steps: initiation, elongation and termination. For a cell to divide , it must first replicate its DNA. DNA replication is an all-or-none process; once replication begins, it proceeds to completion. Once replication

10000-672: Was discovered in 1869, but its role in genetic inheritance was not demonstrated until 1943. The DNA segments that carry this genetic information are called genes. Other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Along with RNA and proteins, DNA is one of the three major macromolecules that are essential for all known forms of life. DNA consists of two long polymers of monomer units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands are oriented in opposite directions to each other and are, therefore, antiparallel . Attached to each sugar

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