Target type: biologicalprocess
A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands. [GOC:mah, ISBN:0198506732]
DNA replication is a fundamental process in all living organisms, where a double-stranded DNA molecule is copied to produce two identical DNA molecules. This process is essential for cell division and heredity. Here's a detailed description of the process:
**1. Initiation:**
- The process begins at specific sites on the DNA called origins of replication.
- The DNA molecule unwinds at the origin, forming a replication bubble.
- Two replication forks are formed at each end of the bubble, where replication proceeds bidirectionally.
- Specific proteins, including initiator proteins and helicase, unwind the DNA double helix.
- Single-stranded binding proteins (SSBs) stabilize the unwound strands, preventing them from re-annealing.
**2. Elongation:**
- DNA polymerase, the primary enzyme in DNA replication, synthesizes new DNA strands using the original strands as templates.
- DNA polymerase can only add nucleotides to the 3'-hydroxyl end of a pre-existing DNA strand.
- This leads to the synthesis of one continuous leading strand and one discontinuous lagging strand.
- The leading strand is synthesized continuously in the 5' to 3' direction.
- The lagging strand is synthesized in short fragments called Okazaki fragments, which are later joined together by DNA ligase.
- Primase, an RNA polymerase, synthesizes short RNA primers that provide a starting point for DNA polymerase.
- DNA polymerase removes the RNA primers and replaces them with DNA nucleotides.
**3. Termination:**
- As the replication forks progress, they eventually meet and terminate replication.
- The newly synthesized DNA molecules are separated, resulting in two identical DNA molecules.
- These molecules are then packaged into chromosomes and distributed to daughter cells during cell division.
**Key Enzymes and Proteins:**
- DNA polymerase: Synthesizes new DNA strands.
- Helicase: Unwinds the DNA double helix.
- Single-stranded binding proteins (SSBs): Stabilize the unwound strands.
- Primase: Synthesizes RNA primers.
- DNA ligase: Joins Okazaki fragments together.
- Topoisomerases: Relieve torsional stress in the DNA molecule.
**Accuracy and Fidelity:**
- DNA replication is remarkably accurate, with a very low error rate.
- This accuracy is ensured by several mechanisms, including:
- Proofreading activity of DNA polymerase.
- Mismatch repair systems that correct errors missed by DNA polymerase.
**Regulation:**
- DNA replication is tightly regulated to ensure that the genome is replicated only once per cell cycle.
- This regulation involves a complex network of proteins and signaling pathways.
**Importance of DNA Replication:**
- Essential for cell division and growth.
- Allows for the transmission of genetic information from one generation to the next.
- Provides the basis for genetic variation through mutations.
- Plays a role in various cellular processes, including repair and recombination.'
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Protein | Definition | Taxonomy |
---|---|---|
DNA gyrase subunit B | A DNA gyrase subunit B that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0AES6] | Escherichia coli K-12 |
DNA gyrase subunit A | A DNA gyrase subunit A that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0AES4] | Escherichia coli K-12 |
DNA polymerase nu | A DNA polymerase nu that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q7Z5Q5] | Homo sapiens (human) |
DNA polymerase subunit gamma-1 | A DNA polymerase subunit gamma-1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P54098] | Homo sapiens (human) |
DNA polymerase delta catalytic subunit | A DNA polymerase delta catalytic subunit that is encoded in the genome of human. [PRO:DNx, UniProtKB:P28340] | Homo sapiens (human) |
DNA polymerase beta | A DNA polymerase beta that is encoded in the genome of human. [PRO:CNA] | Homo sapiens (human) |
Compound | Definition | Classes | Roles |
---|---|---|---|
digallic acid | digallic acid: structure given in first source | benzoate ester; gallate ester | |
ciprofloxacin | ciprofloxacin : A quinolone that is quinolin-4(1H)-one bearing cyclopropyl, carboxylic acid, fluoro and piperazin-1-yl substituents at positions 1, 3, 6 and 7, respectively. Ciprofloxacin: A broad-spectrum antimicrobial carboxyfluoroquinoline. | aminoquinoline; cyclopropanes; fluoroquinolone antibiotic; N-arylpiperazine; quinolinemonocarboxylic acid; quinolone; quinolone antibiotic; zwitterion | antibacterial drug; antiinfective agent; antimicrobial agent; DNA synthesis inhibitor; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor; environmental contaminant; topoisomerase IV inhibitor; xenobiotic |
enoxacin | enoxacin : A 1,8-naphthyridine derivative that is 1,4-dihydro-1,8-naphthyridine with an ethyl group at the 1 position, a carboxy group at the 3-position, an oxo sustituent at the 4-position, a fluoro substituent at the 5-position and a piperazin-1-yl group at the 7 position. An antibacterial, it is used in the treatment of urinary-tract infections and gonorrhoea. Enoxacin: A broad-spectrum 6-fluoronaphthyridinone antibacterial agent that is structurally related to NALIDIXIC ACID. | 1,8-naphthyridine derivative; amino acid; fluoroquinolone antibiotic; monocarboxylic acid; N-arylpiperazine; quinolone antibiotic | antibacterial drug; DNA synthesis inhibitor |
foscarnet | Foscarnet: An antiviral agent used in the treatment of cytomegalovirus retinitis. Foscarnet also shows activity against human herpesviruses and HIV. phosphonoformic acid : Phosphoric acid in which one of the hydroxy groups is replaced by a carboxylic acid group. It is used as the trisodium salt as an antiviral agent in the treatment of cytomegalovirus retinitis (CMV retinitis, an inflamation of the retina that can lead to blindness) and as an alternative to ganciclovir for AIDS patients who require concurrent antiretroviral therapy but are unable to tolerate ganciclovir due to haematological toxicity. | carboxylic acid; one-carbon compound; phosphonic acids | antiviral drug; geroprotector; HIV-1 reverse transcriptase inhibitor; sodium-dependent Pi-transporter inhibitor |
isoniazid | Hydra: A genus of freshwater polyps in the family Hydridae, order Hydroida, class HYDROZOA. They are of special interest because of their complex organization and because their adult organization corresponds roughly to the gastrula of higher animals. hydrazide : Compounds derived from oxoacids RkE(=O)l(OH)m (l =/= 0) by replacing -OH by -NRNR2 (R groups are commonly H). (IUPAC). | carbohydrazide | antitubercular agent; drug allergen |
nalidixic acid | 1,8-naphthyridine derivative; monocarboxylic acid; quinolone antibiotic | antibacterial drug; antimicrobial agent; DNA synthesis inhibitor | |
norfloxacin | norfloxacin : A quinolinemonocarboxylic acid with broad-spectrum antibacterial activity against most gram-negative and gram-positive bacteria. Norfloxacin is bactericidal and its mode of action depends on blocking of bacterial DNA replication by binding itself to an enzyme called DNA gyrase. Norfloxacin: A synthetic fluoroquinolone (FLUOROQUINOLONES) with broad-spectrum antibacterial activity against most gram-negative and gram-positive bacteria. Norfloxacin inhibits bacterial DNA GYRASE. | fluoroquinolone antibiotic; N-arylpiperazine; quinolinemonocarboxylic acid; quinolone; quinolone antibiotic | antibacterial drug; DNA synthesis inhibitor; environmental contaminant; xenobiotic |
ofloxacin | 9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid : An oxazinoquinoline that is 2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinolin-7-one substituted by methyl, carboxy, fluoro, and 4-methylpiperazin-1-yl groups at positions 3, 6, 9, and 10, respectively. ofloxacin : A racemate comprising equimolar amounts of levofloxacin and dextrofloxacin. It is a synthetic fluoroquinolone antibacterial agent which inhibits the supercoiling activity of bacterial DNA gyrase, halting DNA replication. Ofloxacin: A synthetic fluoroquinolone antibacterial agent that inhibits the supercoiling activity of bacterial DNA GYRASE, halting DNA REPLICATION. | 3-oxo monocarboxylic acid; N-arylpiperazine; N-methylpiperazine; organofluorine compound; oxazinoquinoline | |
gatifloxacin | gatifloxacin : A monocarboxylic acid that is 4-oxo-1,4-dihydroquinoline-3-carboxylic acid which is substituted on the nitrogen by a cyclopropyl group and at positions 6, 7, and 8 by fluoro, 3-methylpiperazin-1-yl, and methoxy groups, respectively. Gatifloxacin is an antibiotic of the fourth-generation fluoroquinolone family, that like other members of that family, inhibits the bacterial topoisomerase type-II enzymes. Gatifloxacin: A fluoroquinolone antibacterial agent and DNA TOPOISOMERASE II inhibitor that is used as an ophthalmic solution for the treatment of BACTERIAL CONJUNCTIVITIS. | N-arylpiperazine; organofluorine compound; quinolinemonocarboxylic acid; quinolone; quinolone antibiotic | antiinfective agent; antimicrobial agent; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor |
triclosan | aromatic ether; dichlorobenzene; monochlorobenzenes; phenols | antibacterial agent; antimalarial; drug allergen; EC 1.3.1.9 [enoyl-[acyl-carrier-protein] reductase (NADH)] inhibitor; EC 1.5.1.3 (dihydrofolate reductase) inhibitor; fungicide; persistent organic pollutant; xenobiotic | |
pamoic acid | pamoic acid: RN given refers to parent cpd; structure | dicarboxylic acid | |
Dillapiole | 5-allyl 6,7-dimethoxy 1,3-benzodioxole: a plant based insecticide; structure in first source | benzodioxoles | metabolite |
oleanolic acid | hydroxy monocarboxylic acid; pentacyclic triterpenoid | plant metabolite | |
4-cumylphenol | diarylmethane | ||
4-phenoxyphenol | phenoxyphenol | ||
bis(4-oxyphenyl)sulfide | 4,4'-thiodiphenol: structure in first source | phenols | |
ochracin | ochracin: produced by Aspergillus alutaceus; structure in first source | isochromanes | |
zidovudine | zidovudine : A pyrimidine 2',3'-dideoxyribonucleoside compound having a 3'-azido substituent and thymine as the nucleobase. Zidovudine: A dideoxynucleoside compound in which the 3'-hydroxy group on the sugar moiety has been replaced by an azido group. This modification prevents the formation of phosphodiester linkages which are needed for the completion of nucleic acid chains. The compound is a potent inhibitor of HIV replication, acting as a chain-terminator of viral DNA during reverse transcription. It improves immunologic function, partially reverses the HIV-induced neurological dysfunction, and improves certain other clinical abnormalities associated with AIDS. Its principal toxic effect is dose-dependent suppression of bone marrow, resulting in anemia and leukopenia. | azide; pyrimidine 2',3'-dideoxyribonucleoside | antimetabolite; antiviral drug; HIV-1 reverse transcriptase inhibitor |
ursolic acid | hydroxy monocarboxylic acid; pentacyclic triterpenoid | geroprotector; plant metabolite | |
thymidine 5'-triphosphate | dTTP : A thymidine phosphate having a triphosphate group at the 5'-position. thymidine 5'-triphosphate: RN given refers to parent cpd | pyrimidine 2'-deoxyribonucleoside 5'-triphosphate; thymidine phosphate | Escherichia coli metabolite; mouse metabolite |
betulinic acid | hydroxy monocarboxylic acid; pentacyclic triterpenoid | anti-HIV agent; anti-inflammatory agent; antimalarial; antineoplastic agent; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor; plant metabolite | |
calanolide a | (+)-calanolide A : An organic heterotetracyclic compound that is 11,12-dihydro-2H,6H,10H-dipyrano[2,3-f:2',3'-h]chromen-2-one substituted by a hydroxy group at position 12, methyl groups at positions 6, 6, 10 and 11 and a propyl group at position 4 (the 10R,11S,12S stereoisomer). Isolated from Calophyllum lanigerum var austrocoriaceum and Calophyllum brasiliense, it exhibits potent activity against HIV-1 reverse transcriptase. calanolide A: NSC 661122 and costatolide are isomers; a novel HIV-inhibitory class of coumarin derivatives from the tropical rainforest tree, Calophyllum lanigerum (Clusiaceae); structure in first source | cyclic ether; delta-lactone; organic heterotetracyclic compound; secondary alcohol | HIV-1 reverse transcriptase inhibitor; plant metabolite |
2',3'-dideoxythymidine triphosphate | ddTTP : A pyrimidine 2',3'-dideoxyribonucleoside 5'-triphosphate having thymine as the nucleobase. | pyrimidine 2',3'-dideoxyribonucleoside 5'-triphosphate; thymidine phosphate | |
2',3'-dideoxyadenosine triphosphate | purine deoxyribonucleoside triphosphate | ||
zidovudine triphosphate | |||
illimaquinone | illimaquinone: structure given in first source; isolated from the Red Sea sponge Smenospongia; inhibits the RNase H. activity of HIV-1 reverse transcriptase | monohydroxy-1,4-benzoquinones; prenylquinone | metabolite |
moxifloxacin | moxifloxacin : A quinolone that consists of 4-oxo-1,4-dihydroquinoline-3-carboxylic acid bearing a cyclopropyl substituent at position 1, a fluoro substitiuent at position 6, a (4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl group at position 7 and a methoxy substituent at position 8. A member of the fluoroquinolone class of antibacterial agents. Moxifloxacin: A fluoroquinolone that acts as an inhibitor of DNA TOPOISOMERASE II and is used as a broad-spectrum antibacterial agent. | aromatic ether; cyclopropanes; fluoroquinolone antibiotic; pyrrolidinopiperidine; quinolinemonocarboxylic acid; quinolone; quinolone antibiotic | antibacterial drug |
sitosterol, (3beta)-isomer | sitosterol : A member of the class of phytosterols that is stigmast-5-ene substituted by a beta-hydroxy group at position 3. Sobatum: tradename; active fraction of Solanum trilobatum; reduces side-effects of radiation-induced toxicity | 3beta-hydroxy-Delta(5)-steroid; 3beta-sterol; C29-steroid; phytosterols; stigmastane sterol | anticholesteremic drug; antioxidant; mouse metabolite; plant metabolite; sterol methyltransferase inhibitor |
linezolid | acetamides; morpholines; organofluorine compound; oxazolidinone | antibacterial drug; protein synthesis inhibitor | |
TTP | pyrimidine ribonucleoside 5'-triphosphate | ||
aphidicolin | aphidicolin : A tetracyclic diterpenoid that has an tetradecahydro-8,11a-methanocyclohepta[a]naphthalene skeleton with two hydroxymethyl substituents at positions 4 and 9, two methyl substituents at positions 4 and 11b and two hydroxy substituents at positions 3 and 9. An antibiotic with antiviral and antimitotical properties. Aphidicolin is a reversible inhibitor of eukaryotic nuclear DNA replication. Aphidicolin: An antiviral antibiotic produced by Cephalosporium aphidicola and other fungi. It inhibits the growth of eukaryotic cells and certain animal viruses by selectively inhibiting the cellular replication of DNA polymerase II or the viral-induced DNA polymerases. The drug may be useful for controlling excessive cell proliferation in patients with cancer, psoriasis or other dermatitis with little or no adverse effect upon non-multiplying cells. | tetracyclic diterpenoid | antimicrobial agent; antimitotic; antineoplastic agent; antiviral drug; apoptosis inducer; Aspergillus metabolite; DNA synthesis inhibitor; EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitor; fungal metabolite |
pnu183792 | PNU183792: structure in first source | ||
stigmasterol | stigmasta-5,22-dien-3-ol: isolated from freeze-dried powder of Blackberries (Rubus ursinus L.) which showed an activity on inhibition of chemocarcinogen stigmasterol : A 3beta-sterol that consists of 3beta-hydroxystigmastane having double bonds at the 5,6- and 22,23-positions. | 3beta-hydroxy-Delta(5)-steroid; 3beta-sterol; phytosterols; stigmastane sterol | plant metabolite |
pecilocin | pecilocin: fungicidal antibiotic produced by Paecilomyces varioti Bainier var. antibioticus; structure | N-acylpyrrolidine | |
lyoniside | daucosterol : A steroid saponin that is sitosterol attached to a beta-D-glucopyranosyl residue at position 3 via a glycosidic linkage. It has bee isolated from Panax japonicus var. major and Breynia fruticosa. | beta-D-glucoside; monosaccharide derivative; steroid saponin | plant metabolite |
corosolic acid | triterpenoid | metabolite | |
gemifloxacin | gemifloxacin : A 1,4-dihydro-1,8-naphthyridine with a carboxy group at the 3-position, an oxo sustituent at the 4-position, a fluoro substituent at the 5-position and a substituted pyrrolin-1-yl group at the 7-position. Gemifloxacin: A naphthyridine and fluoroquinolone derivative antibacterial agent and DNA TOPOISOMERASE II inhibitor that is used for the treatment of community-acquired pneumonia and acute bacterial infections associated with chronic bronchitis. | 1,8-naphthyridine derivative; fluoroquinolone antibiotic; monocarboxylic acid; quinolone antibiotic | antibacterial drug; antimicrobial agent; topoisomerase IV inhibitor |
edgeworin | edgeworin: from Dirca occidentalis Gray; structure given in first source | ||
pd 0305970 | |||
sch 725680 | Sch 725680: an aazaphilone from Aspergillus sp.; structure in first source | ||
gsk299423 | GSK299423: structure in first source | ||
raltegravir | 1,2,4-oxadiazole; dicarboxylic acid amide; hydroxypyrimidine; monofluorobenzenes; pyrimidone; secondary carboxamide | antiviral drug; HIV-1 integrase inhibitor | |
novobiocin | novobiocin : A coumarin-derived antibiotic obtained from Streptomyces niveus. Novobiocin: An antibiotic compound derived from Streptomyces niveus. It has a chemical structure similar to coumarin. Novobiocin binds to DNA gyrase, and blocks adenosine triphosphatase (ATPase) activity. (From Reynolds, Martindale The Extra Pharmacopoeia, 30th ed, p189) | carbamate ester; ether; hexoside; hydroxycoumarin; monocarboxylic acid amide; monosaccharide derivative; phenols | antibacterial agent; antimicrobial agent; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor; Escherichia coli metabolite; hepatoprotective agent |
clorobiocin | clorobiocin: chlorine-containing antibiotic related to novobiocin | ||
GS-443902 | GS-441524 triphosphate: intracellular active metabolite of remdesivir GS-443902 : An organic triphosphate that is GS-441524 in which the 5'-hydroxy group has been replaced by a triphosphate group. It is the active metabolite of remdesivir. | aromatic amine; C-nucleoside; nitrile; organic triphosphate; pyrrolotriazine | anticoronaviral agent; antiviral drug; drug metabolite |
pinophilin b | pinophilin B: from cultures of a fungus (Penicillium pinophilum Hedgcok) derived from a seaweed; structure in first source | ||
deoxyguanosine triphosphate | deoxyguanosine phosphate; guanyl deoxyribonucleotide; purine 2'-deoxyribonucleoside 5'-triphosphate | Arabidopsis thaliana metabolite; Escherichia coli metabolite; human metabolite; mouse metabolite; plant metabolite; Saccharomyces cerevisiae metabolite | |
acyclovir triphosphate |