Dna superhelical. Medical search. Web

Circular duplex DNA isolated from viruses, bacteria and mitochondria in supercoiled or supertwisted form. This superhelical DNA is endowed with free energy. During transcription, the magnitude of RNA initiation is proportional to the DNA superhelicity.

The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.

Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)

DNA TOPOISOMERASES that catalyze ATP-independent breakage of one of the two strands of DNA, passage of the unbroken strand through the break, and rejoining of the broken strand. DNA Topoisomerases, Type I enzymes reduce the topological stress in the DNA structure by relaxing the superhelical turns and knotted rings in the DNA helix.

A trypanocidal agent and possible antiviral agent that is widely used in experimental cell biology and biochemistry. Ethidium has several experimentally useful properties including binding to nucleic acids, noncompetitive inhibition of nicotinic acetylcholine receptors, and fluorescence among others. It is most commonly used as the bromide.

(T-4)-Osmium oxide (OsO4). A highly toxic and volatile oxide of osmium used in industry as an oxidizing agent. It is also used as a histological fixative and stain and as a synovectomy agent in arthritic joints. Its vapor can cause eye, skin, and lung damage.

Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.

Deoxyribonucleic acid that makes up the genetic material of viruses.

A species of POLYOMAVIRUS originally isolated from Rhesus monkey kidney tissue. It produces malignancy in human and newborn hamster kidney cell cultures.

Electrophoresis in which agar or agarose gel is used as the diffusion medium.

Enzymes that catalyze the hydrolysis of the internal bonds and thereby the formation of polynucleotides or oligonucleotides from ribo- or deoxyribonucleotide chains. EC 3.1.-.

Enzymes which catalyze the hydrolases of ester bonds within DNA. EC 3.1.-.

Viruses whose host is Escherichia coli.

A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.

Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.

A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).

Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.

Carbodiimides are chemical compounds containing two nitrogen atoms and one carbon atom, often used in biochemistry for the formation of amide bonds, particularly in peptide synthesis and cross-linking of proteins or other biomolecules.

Proteins conjugated with deoxyribonucleic acids (DNA) or specific DNA.

A group of 13 or more deoxyribonucleotides in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.

A brominating agent that replaces hydrogen atoms in benzylic or allylic positions. It is used in the oxidation of secondary alcohols to ketones and in controlled low-energy brominations. (From Miall's Dictionary of Chemistry, 5th ed; Hawley's Condensed Chemical Dictionary, 12th ed,).

Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.

The concentration of osmotically active particles in solution expressed in terms of osmoles of solute per liter of solution. Osmolality is expressed in terms of osmoles of solute per kilogram of solvent.

A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.

The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.

The repeating structural units of chromatin, each consisting of approximately 200 base pairs of DNA wound around a protein core. This core is composed of the histones H2A, H2B, H3, and H4.

Deoxyribonucleic acid that makes up the genetic material of bacteria.

A polypeptide antibiotic mixture obtained from Bacillus brevis. It consists of a mixture of three tyrocidines (60%) and several gramicidins (20%) and is very toxic to blood, liver, kidneys, meninges, and the olfactory apparatus. It is used topically.

Separation of particles according to density by employing a gradient of varying densities. At equilibrium each particle settles in the gradient at a point equal to its density. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

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)

Proteins conjugated with nucleic acids.

The rate dynamics in chemical or physical systems.

Replication-dependent marking of DNA by PCNA facilitates CAF-1-coupled inheritance of chromatin. (1/1746)

Chromatin assembly factor 1 (CAF-1) is required for inheritance of epigenetically determined chromosomal states in vivo and promotes assembly of chromatin during DNA replication in vitro. Herein, we demonstrate that after DNA replication, replicated, but not unreplicated, DNA is also competent for CAF-1-dependent chromatin assembly. The proliferating cell nuclear antigen (PCNA), a DNA polymerase clamp, is a component of the replication-dependent marking of DNA for chromatin assembly. The clamp loader, replication factor C (RFC), can reverse this mark by unloading PCNA from the replicated DNA. PCNA binds directly to p150, the largest subunit of CAF-1, and the two proteins colocalize at sites of DNA replication in cells. We suggest that PCNA and CAF-1 connect DNA replication to chromatin assembly and the inheritance of epigenetic chromosome states. (+info)

Mutants of Tn3 resolvase which do not require accessory binding sites for recombination activity. (2/1746)

Tn3 resolvase promotes site-specific recombination between two res sites, each of which has three resolvase dimer-binding sites. Catalysis of DNA-strand cleavage and rejoining occurs at binding site I, but binding sites II and III are required for recombination. We used an in vivo screen to detect resolvase mutants that were active on res sites with binding sites II and III deleted (that is, only site I remaining). Mutations of amino acids Asp102 (D102) or Met103 (M103) were sufficient to permit catalysis of recombination between site I and a full res, but not between two copies of site I. A double mutant resolvase, with a D102Y mutation and an additional activating mutation at Glu124 (E124Q), recombined substrates containing only two copies of site I, in vivo and in vitro. In these novel site Ixsite I reactions, product topology is no longer restricted to the normal simple catenane, indicating synapsis by random collision. Furthermore, the mutants have lost the normal specificity for directly repeated sites and supercoiled substrates; that is, they promote recombination between pairs of res sites in linear molecules, or in inverted repeat in a supercoiled molecule, or in separate molecules. (+info)

Inhibition of DNA supercoiling-dependent transcriptional activation by a distant B-DNA to Z-DNA transition. (3/1746)

Negative DNA superhelicity can destabilize the local B-form DNA structure and can drive transitions to other conformations at susceptible sites. In a molecule containing multiple susceptible sites, superhelicity can couple these alternatives together, causing them to compete. In principle, these superhelically driven local structural transitions can be either facilitated or inhibited by proteins that bind at or near potential transition sites. If a DNA region that is susceptible to forming a superhelically induced alternate structure is stabilized in the B-form by a DNA-binding protein, its propensity for transition will be transferred to other sites within the same domain. If one of these secondary sites is in a promoter region, this transfer could facilitate open complex formation and thereby activate gene expression. We previously proposed that a supercoiling-dependent, DNA structural transmission mechanism of this type is responsible for the integration host factor-mediated activation of transcription from the ilvPG promoter of Escherichia coli (Sheridan, S. D., Benham, C. J. & Hatfield, G. W. (1998) J. Biol. Chem. 273, 21298-21308). In this report we confirm the validity of this mechanism by demonstrating the ability of a distant Z-DNA-forming site to compete with the superhelical destabilization that is required for integration host factor-mediated transcriptional activation, and thereby delay its occurrence. (+info)

Specific binding of high-mobility-group I (HMGI) protein and histone H1 to the upstream AT-rich region of the murine beta interferon promoter: HMGI protein acts as a potential antirepressor of the promoter. (4/1746)

The high-mobility-group I (HMGI) protein is a nonhistone component of active chromatin. In this work, we demonstrate that HMGI protein specifically binds to the AT-rich region of the murine beta interferon (IFN-beta) promoter localized upstream of the murine virus-responsive element (VRE). Contrary to what has been described for the human promoter, HMGI protein did not specifically bind to the VRE of the murine IFN-beta promoter. Stably transfected promoters carrying mutations on this HMGI binding site displayed delayed virus-induced kinetics of transcription. When integrated into chromatin, the mutated promoter remained repressed and never reached normal transcriptional activity. Such a phenomenon was not observed with transiently transfected promoters upon which chromatin was only partially reconstituted. Using UV footprinting, we show that the upstream AT-rich sequences of the murine IFN-beta promoter constitute a preferential binding region for histone H1. Transfection with a plasmid carrying scaffold attachment regions as well as incubation with distamycin led to the derepression of the IFN-beta promoter stably integrated into chromatin. In vitro, HMGI protein was able to displace histone H1 from the upstream AT-rich region of the wild-type promoter but not from the promoter carrying mutations on the upstream high-affinity HMGI binding site. Our results suggest that the binding of histone H1 to the upstream AT-rich region of the promoter might be partly responsible for the constitutive repression of the promoter. The displacement by HMGI protein of histone H1 could help to convert the IFN-beta promoter from a repressed to an active state. (+info)

Analysis of DNA cleavage by reverse gyrase from Sulfolobus shibatae B12. (5/1746)

Reverse gyrase is a type I-5' topoisomerase, which catalyzes a positive DNA supercoiling reaction in vitro. To ascertain how this reaction takes places, we looked at the DNA sequences recognized by reverse gyrase. We used linear DNA fragments of its preferred substrate, the viral SSV1 DNA, which has been shown to be positively supercoiled in vivo. The Sulfolobus shibatae B12 strain, an SSV1 virus host, was chosen for production of reverse gyrase. This naturally occurring system (SSV1 DNA-S. shibatae reverse gyrase) allowed us to determine which SSV1 DNA sequences are bound and cleaved by the enzyme with particularly high selectivity. We show that the presence of ATP decreases the number of cleaved complexes obtained whereas the non-hydrolyzable ATP analog adenosine 5'-[beta, gamma-imido]triphosphate increases it without changing the sequence specificity. (+info)

Expression and characterization of a DNase I-Fc fusion enzyme. (6/1746)

Recombinant human deoxyribonuclease I (DNase I) is an important clinical agent that is inhaled into the airways where it degrades DNA to lower molecular weight fragments, thus reducing the viscoelasticity of sputum and improving the lung function of cystic fibrosis patients. To investigate DNases with potentially improved properties, we constructed a molecular fusion of human DNase I with the hinge and Fc region of human IgG1 heavy chain, creating a DNase I-Fc fusion protein. Infection of Sf9 insect cells with recombinant baculovirus resulted in the expression and secretion of the DNase I-Fc fusion protein. The fusion protein was purified from the culture medium using protein A affinity chromatography followed by desalting by gel filtration and was characterized by amino-terminal sequence, amino acid composition, and a variety of enzyme-linked immunosorbent assays (ELISA) and activity assays. The purified fusion contains DNase I, as determined by a DNase I ELISA and an actin-binding ELISA, and an intact antibody Fc region, which was quantified by an Fc ELISA, in a 2:1 stoichiometric ratio, respectively. The dimeric DNase I-Fc fusion was functionally active in enzymatic DNA digestion assays, albeit about 10-fold less than monomeric DNase I. Cleavage of the DNase I-Fc fusion by papain resulted in a specific activity comparable to the monomeric enzyme. Salt was inhibitory for wild type monomeric DNase I but actually enhanced the activity of the dimeric DNase I-Fc fusion. The DNase I-Fc fusion protein was also less Ca2+-dependent than DNase I itself. These results are consistent with a higher affinity of the dimeric fusion protein to DNA than monomeric DNase I. The engineered DNase I-Fc fusion protein described herein has properties that may have clinical benefits. (+info)

Pokeweed antiviral protein cleaves double-stranded supercoiled DNA using the same active site required to depurinate rRNA. (7/1746)

Ribosome-inactivating proteins (RIPs) are N-glycosylases that remove a specific adenine from the sarcin/ricin loop of the large rRNA in a manner analogous to N-glycosylases that are involved in DNA repair. Some RIPs have been reported to remove adenines from single-stranded DNA and cleave double-stranded supercoiled DNA. The molecular basis for the activity of RIPs on double-stranded DNA is not known. Pokeweed antiviral protein (PAP), a single-chain RIP from Phytolacca americana, cleaves supercoiled DNA into relaxed and linear forms. Double-stranded DNA treated with PAP contains apurinic/apyrimidinic (AP) sites due to the removal of adenine. Using an active-site mutant of PAP (PAPx) which does not depurinate rRNA, we present evidence that double-stranded DNA treated with PAPx does not contain AP sites and is not cleaved. These results demonstrate for the first time that PAP cleaves supercoiled double-stranded DNA using the same active site that is required for depurination of rRNA. (+info)

Extracellular signal-regulated kinase activates topoisomerase IIalpha through a mechanism independent of phosphorylation. (8/1746)

The mitogen-activated protein (MAP) kinases, extracellular signal-related kinase 1 (ERK1) and ERK2, regulate cellular responses by mediating extracellular growth signals toward cytoplasmic and nuclear targets. A potential target for ERK is topoisomerase IIalpha, which becomes highly phosphorylated during mitosis and is required for several aspects of nucleic acid metabolism, including chromosome condensation and daughter chromosome separation. In this study, we demonstrated interactions between ERK2 and topoisomerase IIalpha proteins by coimmunoprecipitation from mixtures of purified enzymes and from nuclear extracts. In vitro, diphosphorylated active ERK2 phosphorylated topoisomerase IIalpha and enhanced its specific activity by sevenfold, as measured by DNA relaxation assays, whereas unphosphorylated ERK2 had no effect. However, activation of topoisomerase II was also observed with diphosphorylated inactive mutant ERK2, suggesting a mechanism of activation that depends on the phosphorylation state of ERK2 but not on its kinase activity. Nevertheless, activation of ERK by transient transfection of constitutively active mutant MAP kinase kinase 1 (MKK1) enhanced endogenous topoisomerase II activity by fourfold. Our findings indicate that ERK regulates topoisomerase IIalpha in vitro and in vivo, suggesting a potential target for the MKK/ERK pathway in the modulation of chromatin reorganization events during mitosis and in other phases of the cell cycle. (+info)

Superhelical DNA refers to a type of DNA structure that is formed when the double helix is twisted around itself. This occurs due to the presence of negative supercoiling, which results in an overtwisted state that can be described as having a greater number of helical turns than a relaxed circular DNA molecule.

Superhelical DNA is often found in bacterial and viral genomes, where it plays important roles in compacting the genome into a smaller volume and facilitating processes such as replication and transcription. The degree of supercoiling can affect the structure and function of DNA, with varying levels of supercoiling influencing the accessibility of specific regions of the genome to proteins and other regulatory factors.

Superhelical DNA is typically maintained in a stable state by topoisomerase enzymes, which introduce or remove twists in the double helix to regulate its supercoiling level. Changes in supercoiling can have significant consequences for cellular processes, as they can impact the expression of genes and the regulation of chromosome structure and function.

Nucleic acid conformation refers to the three-dimensional structure that nucleic acids (DNA and RNA) adopt as a result of the bonding patterns between the atoms within the molecule. The primary structure of nucleic acids is determined by the sequence of nucleotides, while the conformation is influenced by factors such as the sugar-phosphate backbone, base stacking, and hydrogen bonding.

Two common conformations of DNA are the B-form and the A-form. The B-form is a right-handed helix with a diameter of about 20 Å and a pitch of 34 Å, while the A-form has a smaller diameter (about 18 Å) and a shorter pitch (about 25 Å). RNA typically adopts an A-form conformation.

The conformation of nucleic acids can have significant implications for their function, as it can affect their ability to interact with other molecules such as proteins or drugs. Understanding the conformational properties of nucleic acids is therefore an important area of research in molecular biology and medicine.

Circular DNA is a type of DNA molecule that forms a closed loop, rather than the linear double helix structure commonly associated with DNA. This type of DNA is found in some viruses, plasmids (small extrachromosomal DNA molecules found in bacteria), and mitochondria and chloroplasts (organelles found in plant and animal cells).

Circular DNA is characterized by the absence of telomeres, which are the protective caps found on linear chromosomes. Instead, circular DNA has a specific sequence where the two ends join together, known as the origin of replication and the replication terminus. This structure allows for the DNA to be replicated efficiently and compactly within the cell.

Because of its circular nature, circular DNA is more resistant to degradation by enzymes that cut linear DNA, making it more stable in certain environments. Additionally, the ability to easily manipulate and clone circular DNA has made it a valuable tool in molecular biology and genetic engineering.

DNA topoisomerases are enzymes that modify the topological structure of DNA by regulating the number of twists or supercoils in the double helix. There are two main types of DNA topoisomerases: type I and type II.

Type I DNA topoisomerases function by cutting one strand of the DNA duplex, allowing the uncut strand to rotate around the break, and then resealing the break. This process can relieve both positive and negative supercoiling in DNA, as well as introduce single-stranded breaks into the DNA molecule.

Type I topoisomerases are further divided into three subtypes: type IA, type IB, and type IC. These subtypes differ in their mechanism of action and the structure of the active site tyrosine residue that makes the transient break in the DNA strand.

Overall, DNA topoisomerases play a crucial role in many cellular processes involving DNA, including replication, transcription, recombination, and chromosome segregation. Dysregulation of these enzymes has been implicated in various human diseases, including cancer and genetic disorders.

Ethidium is a fluorescent, intercalating compound that is often used in molecular biology to stain DNA. When ethidium bromide, a common form of ethidium, binds to DNA, it causes the DNA to fluoresce brightly under ultraviolet light. This property makes it useful for visualizing DNA bands on gels, such as agarose or polyacrylamide gels, during techniques like gel electrophoresis.

It is important to note that ethidium bromide is a mutagen and should be handled with care. It can cause damage to DNA, which can lead to mutations, and it can also be harmful if inhaled or ingested. Therefore, appropriate safety precautions must be taken when working with this compound.

Osmium tetroxide is not a medical term per se, but it is a chemical compound with the formula OsO4. It is used in some medical and scientific applications due to its properties as a strong oxidizing agent and its ability to form complexes with organic compounds.

In histology, osmium tetroxide is sometimes used as a fixative for electron microscopy because it reacts with unsaturated lipids and proteins in biological tissue, creating an electron-dense deposit that can be visualized under the microscope. It is also used to stain fatty acids and other lipids in biological samples.

However, osmium tetroxide is highly toxic and volatile, and it can cause damage to the eyes, skin, and respiratory system if not handled with appropriate precautions. Therefore, its use in medical and scientific settings is typically limited to specialized applications where its unique properties are required.

A plasmid is a small, circular, double-stranded DNA molecule that is separate from the chromosomal DNA of a bacterium or other organism. Plasmids are typically not essential for the survival of the organism, but they can confer beneficial traits such as antibiotic resistance or the ability to degrade certain types of pollutants.

Plasmids are capable of replicating independently of the chromosomal DNA and can be transferred between bacteria through a process called conjugation. They often contain genes that provide resistance to antibiotics, heavy metals, and other environmental stressors. Plasmids have also been engineered for use in molecular biology as cloning vectors, allowing scientists to replicate and manipulate specific DNA sequences.

Plasmids are important tools in genetic engineering and biotechnology because they can be easily manipulated and transferred between organisms. They have been used to produce vaccines, diagnostic tests, and genetically modified organisms (GMOs) for various applications, including agriculture, medicine, and industry.

Viral DNA refers to the genetic material present in viruses that consist of DNA as their core component. Deoxyribonucleic acid (DNA) is one of the two types of nucleic acids that are responsible for storing and transmitting genetic information in living organisms. Viruses are infectious agents much smaller than bacteria that can only replicate inside the cells of other organisms, called hosts.

Viral DNA can be double-stranded (dsDNA) or single-stranded (ssDNA), depending on the type of virus. Double-stranded DNA viruses have a genome made up of two complementary strands of DNA, while single-stranded DNA viruses contain only one strand of DNA.

Examples of dsDNA viruses include Adenoviruses, Herpesviruses, and Poxviruses, while ssDNA viruses include Parvoviruses and Circoviruses. Viral DNA plays a crucial role in the replication cycle of the virus, encoding for various proteins necessary for its multiplication and survival within the host cell.

Simian Virus 40 (SV40) is a polyomavirus that is found in both monkeys and humans. It is a DNA virus that has been extensively studied in laboratory settings due to its ability to transform cells and cause tumors in animals. In fact, SV40 was discovered as a contaminant of poliovirus vaccines that were prepared using rhesus monkey kidney cells in the 1950s and 1960s.

SV40 is not typically associated with human disease, but there has been some concern that exposure to the virus through contaminated vaccines or other means could increase the risk of certain types of cancer, such as mesothelioma and brain tumors. However, most studies have failed to find a consistent link between SV40 infection and cancer in humans.

The medical community generally agrees that SV40 is not a significant public health threat, but researchers continue to study the virus to better understand its biology and potential impact on human health.

Electrophoresis, Agar Gel is a laboratory technique used to separate and analyze DNA, RNA, or proteins based on their size and electrical charge. In this method, the sample is mixed with agarose gel, a gelatinous substance derived from seaweed, and then solidified in a horizontal slab-like format. An electric field is applied to the gel, causing the negatively charged DNA or RNA molecules to migrate towards the positive electrode. The smaller molecules move faster through the gel than the larger ones, resulting in their separation based on size. This technique is widely used in molecular biology and genetics research, as well as in diagnostic testing for various genetic disorders.

Endonucleases are enzymes that cleave, or cut, phosphodiester bonds within a polynucleotide chain, specifically within the same molecule of DNA or RNA. They can be found in all living organisms and play crucial roles in various biological processes, such as DNA replication, repair, and recombination.

Endonucleases can recognize specific nucleotide sequences (sequence-specific endonucleases) or have no sequence preference (non-specific endonucleases). Some endonucleases generate sticky ends, overhangs of single-stranded DNA after cleavage, while others produce blunt ends without any overhang.

These enzymes are widely used in molecular biology techniques, such as restriction digestion, cloning, and genome editing (e.g., CRISPR-Cas9 system). Restriction endonucleases recognize specific DNA sequences called restriction sites and cleave the phosphodiester bonds at or near these sites, generating defined fragment sizes that can be separated by agarose gel electrophoresis. This property is essential for various applications in genetic engineering and biotechnology.

Deoxyribonucleases (DNases) are a group of enzymes that cleave, or cut, the phosphodiester bonds in the backbone of deoxyribonucleic acid (DNA) molecules. DNases are classified based on their mechanism of action into two main categories: double-stranded DNases and single-stranded DNases.

Double-stranded DNases cleave both strands of the DNA duplex, while single-stranded DNases cleave only one strand. These enzymes play important roles in various biological processes, such as DNA replication, repair, recombination, and degradation. They are also used in research and clinical settings for applications such as DNA fragmentation analysis, DNA sequencing, and treatment of cystic fibrosis.

It's worth noting that there are many different types of DNases with varying specificities and activities, and the medical definition may vary depending on the context.

Coliphages are viruses that infect and replicate within certain species of bacteria that belong to the coliform group, particularly Escherichia coli (E. coli). These viruses are commonly found in water and soil environments and are frequently used as indicators of fecal contamination in water quality testing. Coliphages are not harmful to humans or animals, but their presence in water can suggest the potential presence of pathogenic bacteria or other microorganisms that may pose a health risk. There are two main types of coliphages: F-specific RNA coliphages and somatic (or non-F specific) DNA coliphages.

'Escherichia coli' (E. coli) is a type of gram-negative, facultatively anaerobic, rod-shaped bacterium that commonly inhabits the intestinal tract of humans and warm-blooded animals. It is a member of the family Enterobacteriaceae and one of the most well-studied prokaryotic model organisms in molecular biology.

While most E. coli strains are harmless and even beneficial to their hosts, some serotypes can cause various forms of gastrointestinal and extraintestinal illnesses in humans and animals. These pathogenic strains possess virulence factors that enable them to colonize and damage host tissues, leading to diseases such as diarrhea, urinary tract infections, pneumonia, and sepsis.

E. coli is a versatile organism with remarkable genetic diversity, which allows it to adapt to various environmental niches. It can be found in water, soil, food, and various man-made environments, making it an essential indicator of fecal contamination and a common cause of foodborne illnesses. The study of E. coli has contributed significantly to our understanding of fundamental biological processes, including DNA replication, gene regulation, and protein synthesis.

Single-strand specific DNA and RNA endonucleases are enzymes that cleave or cut single-stranded DNA or RNA molecules at specific sites, leaving a free 3'-hydroxyl group and a 5'-phosphate group on the resulting fragments. These enzymes recognize and bind to particular nucleotide sequences or structural motifs in single-stranded nucleic acids, making them useful tools for various molecular biology techniques such as DNA and RNA mapping, sequencing, and manipulation.

Examples of single-strand specific endonucleases include S1 nuclease (specific to single-stranded DNA), mung bean nuclease (specific to single-stranded DNA with a preference for 3'-overhangs), and RNase A (specific to single-stranded RNA). These enzymes have distinct substrate specificities, cleavage patterns, and optimal reaction conditions, which should be carefully considered when selecting them for specific applications.

Deoxyribonucleic acid (DNA) is the genetic material present in the cells of organisms where it is responsible for the storage and transmission of hereditary information. DNA is a long molecule that consists of two strands coiled together to form a double helix. Each strand is made up of a series of four nucleotide bases - adenine (A), guanine (G), cytosine (C), and thymine (T) - that are linked together by phosphate and sugar groups. The sequence of these bases along the length of the molecule encodes genetic information, with A always pairing with T and C always pairing with G. This base-pairing allows for the replication and transcription of DNA, which are essential processes in the functioning and reproduction of all living organisms.

Nucleic acid denaturation is the process of separating the two strands of a double-stranded DNA molecule, or unwinding the helical structure of an RNA molecule, by disrupting the hydrogen bonds that hold the strands together. This process is typically caused by exposure to high temperatures, changes in pH, or the presence of chemicals called denaturants.

Denaturation can also cause changes in the shape and function of nucleic acids. For example, it can disrupt the secondary and tertiary structures of RNA molecules, which can affect their ability to bind to other molecules and carry out their functions within the cell.

In molecular biology, nucleic acid denaturation is often used as a tool for studying the structure and function of nucleic acids. For example, it can be used to separate the two strands of a DNA molecule for sequencing or amplification, or to study the interactions between nucleic acids and other molecules.

It's important to note that denaturation is a reversible process, and under the right conditions, the double-stranded structure of DNA can be restored through a process called renaturation or annealing.

Carbodiimides are a class of chemical compounds with the general formula R-N=C=N-R, where R can be an organic group. They are widely used in the synthesis of various chemical and biological products due to their ability to act as dehydrating agents, promoting the formation of amide bonds between carboxylic acids and amines.

In the context of medical research and biochemistry, carbodiimides are often used to modify proteins, peptides, and other biological molecules for various purposes, such as labeling, cross-linking, or functionalizing. For example, the carbodiimide cross-linker EDC (1-ethyl-3-(3-dimethylaminopropyl)carbodiimide) is commonly used to create stable amide bonds between proteins and other molecules in a process known as "EDC coupling."

It's important to note that carbodiimides can be potentially toxic and should be handled with care. They can cause irritation to the skin, eyes, and respiratory tract, and prolonged exposure can lead to more serious health effects. Therefore, appropriate safety precautions should be taken when working with these compounds in a laboratory setting.

Deoxyribonucleoproteins are complexes formed by the association of DNA (deoxyribonucleic acid) with proteins. These complexes play a crucial role in various cellular processes, including the packaging and protection of DNA within the cell, as well as the regulation of gene expression.

In particular, deoxyribonucleoproteins are important components of chromatin, which is the material that makes up chromosomes. Histone proteins are among the most abundant proteins found in chromatin, and they play a key role in compacting DNA into a more condensed form. Other non-histone proteins also associate with DNA to regulate various cellular processes, such as transcription, replication, and repair.

Deoxyribonucleoproteins can also be found in viruses, where they are often referred to as nucleocapsids. In these cases, the deoxyribonucleoprotein complex serves to protect the viral genome and facilitate its replication and transmission between host cells.

I'm sorry for any confusion, but "Polydeoxyribonucleotides" is not a widely recognized or established medical term. It seems to be a made-up or very obscure term that combines "poly," meaning many, "deoxy," referring to the lack of a hydroxyl group at the 2' carbon position in the ribose sugar, and "ribonucleotides," which are the building blocks of RNA.

If you meant "Polydeoxynucleotides" instead, it would refer to long, synthetic chains of deoxynucleotides, which are the building blocks of DNA. These chains can be used in various biochemical and biological research applications, such as studying enzyme mechanisms or constructing genetic circuits.

Bromosuccinimide is a chemical compound with the formula C4H2BrNO2S. It is a white crystalline solid that is used as a brominating agent in organic synthesis. Bromosuccinimide is an important reagent for introducing bromine into organic molecules, and it is particularly useful for carrying out selective brominations of unsaturated compounds.

Bromosuccinimide is typically used in solution, and it can be prepared by reacting succinimide with bromine in the presence of a base. It is a relatively stable compound, but it can decompose if heated or if it is exposed to strong oxidizing agents. Bromosuccinimide is not commonly used in medical applications, but it may be encountered in laboratory settings where organic synthesis is performed.

Histones are highly alkaline proteins found in the chromatin of eukaryotic cells. They are rich in basic amino acid residues, such as arginine and lysine, which give them their positive charge. Histones play a crucial role in packaging DNA into a more compact structure within the nucleus by forming a complex with it called a nucleosome. Each nucleosome contains about 146 base pairs of DNA wrapped around an octamer of eight histone proteins (two each of H2A, H2B, H3, and H4). The N-terminal tails of these histones are subject to various post-translational modifications, such as methylation, acetylation, and phosphorylation, which can influence chromatin structure and gene expression. Histone variants also exist, which can contribute to the regulation of specific genes and other nuclear processes.

Osmolar concentration is a measure of the total number of solute particles (such as ions or molecules) dissolved in a solution per liter of solvent (usually water), which affects the osmotic pressure. It is expressed in units of osmoles per liter (osmol/L). Osmolarity and osmolality are related concepts, with osmolarity referring to the number of osmoles per unit volume of solution, typically measured in liters, while osmolality refers to the number of osmoles per kilogram of solvent. In clinical contexts, osmolar concentration is often used to describe the solute concentration of bodily fluids such as blood or urine.

Single-stranded DNA (ssDNA) is a form of DNA that consists of a single polynucleotide chain. In contrast, double-stranded DNA (dsDNA) consists of two complementary polynucleotide chains that are held together by hydrogen bonds.

In the double-helix structure of dsDNA, each nucleotide base on one strand pairs with a specific base on the other strand through hydrogen bonding: adenine (A) with thymine (T), and guanine (G) with cytosine (C). This base pairing provides stability to the double-stranded structure.

Single-stranded DNA, on the other hand, lacks this complementary base pairing and is therefore less stable than dsDNA. However, ssDNA can still form secondary structures through intrastrand base pairing, such as hairpin loops or cruciform structures.

Single-stranded DNA is found in various biological contexts, including viral genomes, transcription bubbles during gene expression, and in certain types of genetic recombination. It also plays a critical role in some laboratory techniques, such as polymerase chain reaction (PCR) and DNA sequencing.

A base sequence in the context of molecular biology refers to the specific order of nucleotides in a DNA or RNA molecule. In DNA, these nucleotides are adenine (A), guanine (G), cytosine (C), and thymine (T). In RNA, uracil (U) takes the place of thymine. The base sequence contains genetic information that is transcribed into RNA and ultimately translated into proteins. It is the exact order of these bases that determines the genetic code and thus the function of the DNA or RNA molecule.

A nucleosome is a basic unit of DNA packaging in eukaryotic cells, consisting of a segment of DNA coiled around an octamer of histone proteins. This structure forms a repeating pattern along the length of the DNA molecule, with each nucleosome resembling a "bead on a string" when viewed under an electron microscope. The histone octamer is composed of two each of the histones H2A, H2B, H3, and H4, and the DNA wraps around it approximately 1.65 times. Nucleosomes play a crucial role in compacting the large DNA molecule within the nucleus and regulating access to the DNA for processes such as transcription, replication, and repair.

Bacterial DNA refers to the genetic material found in bacteria. It is composed of a double-stranded helix containing four nucleotide bases - adenine (A), thymine (T), guanine (G), and cytosine (C) - that are linked together by phosphodiester bonds. The sequence of these bases in the DNA molecule carries the genetic information necessary for the growth, development, and reproduction of bacteria.

Bacterial DNA is circular in most bacterial species, although some have linear chromosomes. In addition to the main chromosome, many bacteria also contain small circular pieces of DNA called plasmids that can carry additional genes and provide resistance to antibiotics or other environmental stressors.

Unlike eukaryotic cells, which have their DNA enclosed within a nucleus, bacterial DNA is present in the cytoplasm of the cell, where it is in direct contact with the cell's metabolic machinery. This allows for rapid gene expression and regulation in response to changing environmental conditions.

Tyrothricin is not typically considered a medical term, but it is a chemical compound with some medical applications. Medically, tyrothricin is often referred to as a polypeptide antibiotic, which is derived from the gram-positive bacteria Bacillus brevis. It is a complex mixture of several chemically related polypeptides, including tyrocidine and gramicidin. Tyrothricin has broad-spectrum antimicrobial activity against many gram-positive and gram-negative bacteria, as well as some fungi and viruses. However, its clinical use is limited due to its potential toxicity and the availability of safer and more effective antibiotics.

Centrifugation, Density Gradient is a medical laboratory technique used to separate and purify different components of a mixture based on their size, density, and shape. This method involves the use of a centrifuge and a density gradient medium, such as sucrose or cesium chloride, to create a stable density gradient within a column or tube.

The sample is carefully layered onto the top of the gradient and then subjected to high-speed centrifugation. During centrifugation, the particles in the sample move through the gradient based on their size, density, and shape, with heavier particles migrating faster and further than lighter ones. This results in the separation of different components of the mixture into distinct bands or zones within the gradient.

This technique is commonly used to purify and concentrate various types of biological materials, such as viruses, organelles, ribosomes, and subcellular fractions, from complex mixtures. It allows for the isolation of pure and intact particles, which can then be collected and analyzed for further study or use in downstream applications.

In summary, Centrifugation, Density Gradient is a medical laboratory technique used to separate and purify different components of a mixture based on their size, density, and shape using a centrifuge and a density gradient medium.

Novobiocin is an antibiotic derived from the actinomycete species Streptomyces niveus. It belongs to the class of drugs known as aminocoumarins, which function by inhibiting bacterial DNA gyrase, thereby preventing DNA replication and transcription. Novobiocin has activity against a narrow range of gram-positive bacteria, including some strains of Staphylococcus aureus (particularly those resistant to penicillin and methicillin), Streptococcus pneumoniae, and certain mycobacteria. It is used primarily in the treatment of serious staphylococcal infections and is administered orally or intravenously.

It's important to note that Novobiocin has been largely replaced by other antibiotics due to its narrow spectrum of activity, potential for drug interactions, and adverse effects. It is not widely used in clinical practice today.

Nucleoproteins are complexes formed by the association of proteins with nucleic acids (DNA or RNA). These complexes play crucial roles in various biological processes, such as packaging and protecting genetic material, regulating gene expression, and replication and repair of DNA. In these complexes, proteins interact with nucleic acids through electrostatic, hydrogen bonding, and other non-covalent interactions, leading to the formation of stable structures that help maintain the integrity and function of the genetic material. Some well-known examples of nucleoproteins include histones, which are involved in DNA packaging in eukaryotic cells, and reverse transcriptase, an enzyme found in retroviruses that transcribes RNA into DNA.

In the context of medicine and pharmacology, "kinetics" refers to the study of how a drug moves throughout the body, including its absorption, distribution, metabolism, and excretion (often abbreviated as ADME). This field is called "pharmacokinetics."

1. Absorption: This is the process of a drug moving from its site of administration into the bloodstream. Factors such as the route of administration (e.g., oral, intravenous, etc.), formulation, and individual physiological differences can affect absorption.

2. Distribution: Once a drug is in the bloodstream, it gets distributed throughout the body to various tissues and organs. This process is influenced by factors like blood flow, protein binding, and lipid solubility of the drug.

3. Metabolism: Drugs are often chemically modified in the body, typically in the liver, through processes known as metabolism. These changes can lead to the formation of active or inactive metabolites, which may then be further distributed, excreted, or undergo additional metabolic transformations.

4. Excretion: This is the process by which drugs and their metabolites are eliminated from the body, primarily through the kidneys (urine) and the liver (bile).

Understanding the kinetics of a drug is crucial for determining its optimal dosing regimen, potential interactions with other medications or foods, and any necessary adjustments for special populations like pediatric or geriatric patients, or those with impaired renal or hepatic function.

Å of DNA length. Wr, called "writhe," is the number of superhelical twists. Since biological circular DNA is usually underwound ... DNA supercoiling is important for DNA packaging within all cells. Because the length of DNA can be thousands of times that of a ... Negative supercoiling is also thought to favour the transition between B-DNA and Z-DNA, and moderate the interactions of DNA ... Supercoiling is also required for DNA/RNA synthesis. Because DNA must be unwound for DNA/RNA polymerase action, supercoils will ...

https://en.wikipedia.org/wiki/DNA_supercoil

"Preferential binding of IFI16 protein to cruciform structure and superhelical DNA". Biochemical and Biophysical Research ... Cruciform DNA is a form of non-B DNA, or an alternative DNA structure. The formation of cruciform DNA requires the presence of ... B-DNA can form transient structures of cruciform DNA that act as recognition signals near origins of replication in the DNA of ... Cruciform DNA is found in both prokaryotes and eukaryotes and has a role in DNA transcription and DNA replication, double ...

https://en.wikipedia.org/wiki/Cruciform_DNA

"Effect of the potential triplex DNA region on the in vitro expression of bacterial beta-lactamase gene in superhelical ... Triple-stranded DNA (also known as H-DNA or Triplex-DNA) is a DNA structure in which three oligonucleotides wind around each ... There are two different types of intramolecular triplex DNA: H-DNA and H*-DNA. Formation of H-DNA is stabilized under acidic ... Wang G, Vasquez KM (July 2014). "Impact of alternative DNA structures on DNA damage, DNA repair, and genetic instability". DNA ...

https://en.wikipedia.org/wiki/Triple-stranded_DNA

Woelfle MA, Xu Y, Qin X, Johnson CH (November 2007). "Circadian rhythms of superhelical status of DNA in cyanobacteria". ... in which the circadian clock orchestrates dramatic circadian changes in DNA topology, which causes a change in the ...

https://en.wikipedia.org/wiki/Bacterial_circadian_rhythm

DNA supercoil (superhelical DNA) Knot theory Fuller, F. Brock (1971). "The writhing number of a space curve" (PDF). Proceedings ... In DNA this property does not change and can only be modified by specialized enzymes called topoisomerases. ... DNA Structure and Topology at Molecular Biochemistry II: The Bello Lectures. (Helices, Molecular biology, Molecular topology). ... This study originated in response to questions that arise in the study of supercoiled double-stranded DNA rings. About the ...

https://en.wikipedia.org/wiki/Superhelix

Chu, Y; Hsu, M T (1992). "Ellipticine increases the superhelical density of intracellular SV40 DNA by intercalation". Nucleic ... Further DNA damage results from the formation of covalent DNA adducts following enzymatic activation of ellipticine by with ... increasing the superhelical density of the DNA. Intercalated ellipticine binds directly to topoisomerase II, an enzyme involved ... DNA replication inhibitors, Prodrugs, Topoisomerase inhibitors, DNA intercalaters, Plant toxins). ...

https://en.wikipedia.org/wiki/Ellipticine

It is the melting of the DNA which is not induced by a promoter, but purely by the superhelical (also called topological) ... sites in superhelical DNA". Bioinformatics. 20 (9): 1477-1479. doi:10.1093/bioinformatics/bth304. PMID 15130924. [1] v t e (All ... nature of the DNA. It is based on a statistical mechanics treatment of DNA made by Craig J. Benham and Richard M. Fye. This ... "Activation of Gene Expression by a Novel DNA Structural Transmission Mechanism That Requires Supercoiling-induced DNA Duplex ...

https://en.wikipedia.org/wiki/SIDD

Negative superhelical tension causes approximately one turn of DNA to unwind and form the transcription bubble. The template ... Subunits within TFIIH that have ATPase and helicase activity create negative superhelical tension in the DNA. ... and DNA helicase activity (unwinds DNA at promoter). It also recruits nucleotide-excision repair proteins. ... Kim TK, Lagrange T, Wang YH, Griffith JD, Reinberg D, Ebright RH (November 1997). "Trajectory of DNA in the RNA polymerase II ...

https://en.wikipedia.org/wiki/Transcription_preinitiation_complex

This negative superhelical tension causes approximately one turn of DNA to unwind and form the transcription bubble. The ... Subunits within TFIIH that have ATPase and helicase activity create negative superhelical tension in the DNA. ... on DNA to activate transcription of genetic information from DNA to messenger RNA. GTFs, RNA polymerase, and the mediator (a ... It attaches to the promoter of the DNA (e.i., TATA box) and helps position the RNA polymerase II to the gene transcription ...

https://en.wikipedia.org/wiki/General_transcription_factor

... superhelical DNA packaged in capsid proteins. They are around 2.0-31kb in length. Viral replication is nuclear. DNA-templated ... Fleming, J.-A. G. W. & Summers, M. D. (1991). "Polydnavirus DNA is integrated in the DNA of its parasitoid wasp host". ... DNA, as contrasted with positive- or negative-sense single-strand DNA or RNA, as found in some other viruses) with each segment ... "The Domestication of a Large DNA Virus by the Wasp Venturia canescens Involves Targeted Genome Reduction through ...

https://en.wikipedia.org/wiki/Polydnavirus

These circular sequences can withstand superhelical stresses, resulting in the formation of DNA supercoils. Whilst such ... To this end, minicircles of DNA (closed double-stranded DNA sequences) have been proposed as model systems. Harris developed ... Her publications include: Parmbsc1: a refined force field for DNA simulations Cooperativity in drug-DNA recognition: a ... Circular DNA sequences are present in bacterial, mitochondrial and cancer genomes, and offer promise for the design of gene ...

https://en.wikipedia.org/wiki/Sarah_Harris_(scientist)

Kikuchi A, Asai K (21 June 1984). "Reverse gyrase--a topoisomerase which introduces positive superhelical turns into DNA". ... Where DNA gyrase forms a tetramer and is capable of cleaving a double-stranded region of DNA, reverse gyrase can only cleave ... how many times a strand of DNA is wrapped around the other strand) of the DNA strand as they are renatured. Following ATP ... initiates an unwinding of approximately 20 base pairs upon binding to a DNA structure. Upon initial binding to the DNA, the ...

https://en.wikipedia.org/wiki/Reverse_gyrase

Z-DNA is a relatively rare left-handed double-helix. Given the proper sequence and superhelical tension, it can be formed in ... B-DNA is the most common form of DNA in vivo and is a more narrow, elongated helix than A-DNA. Its wide major groove makes it ... A-DNA, is a form of the DNA duplex observed under dehydrating conditions. It is shorter and wider than B-DNA. RNA adopts this ... Biology portal Biomolecular structure Crosslinking of DNA DNA nanotechnology DNA supercoil Gene structure Non-helical models of ...

https://en.wikipedia.org/wiki/Nucleic_acid_structure

DNA polymerase III is then able to start DNA replication. DnaA is made up of four domains: the first is the N-terminal that ... When bound to ATP, but not to ADP, DnaA forms a super-helical structure with four monomers per turn. The structure of sphere I ... When DNA replication is about to commence, DnaA occupies all of the high and low affinity binding sites. The denatured AT-rich ... In contrary to dnaA mutants, the PC2 strain has a mutation in the dnaC gene, which codes for the loading factor for the DNA ...

https://en.wikipedia.org/wiki/DnaA

Any mutational event that disrupts the superhelical structure of DNA carries with it the potential to compromise the genetic ... It nicks unmethylated DNA and the unmethylated strand of hemimethylated DNA but does not nick fully methylated DNA. Experiments ... DNA methylase then rapidly methylates the daughter strand. When bound, the MutS2 dimer bends the DNA helix and shields ... Sporadic cancers with a DNA repair deficiency only rarely have a mutation in a DNA repair gene, but they instead tend to have ...

https://en.wikipedia.org/wiki/DNA_mismatch_repair

H-NS has a specific topology that allows it to condense bacterial DNA into a superhelical structure based on evidence from X- ... H-NS is responsible for formation of nucleofilaments along the DNA and DNA-DNA bridges. H-NS is known as a passive DNA bridger ... The C-Terminal domain, also known as the DNA Binding Domain (DBD), shows high affinity for regions in DNA that are rich in ... Alpha helices 3 and 4 are then responsible for creating the superhelical structure of H-NS-DNA interactions by head to head ...

https://en.wikipedia.org/wiki/Histone-like_nucleoid-structuring_protein

... large hydrophobic interface that allows for subunit rotation which may be driven by superhelical torsion within the protein-DNA ... of DNA invertases in which it relies on the active site serine to initiate DNA cleavage and recombination. The related protein ... including structures bound to DNA and reaction intermediates. Hin functions to invert a 900 base pair (bp) DNA segment within ... The DNA cleavage event also requires the divalent metal cation magnesium. A large conformational change reveals a ...

https://en.wikipedia.org/wiki/Hin_recombinase

The number of superhelical turns introduced into an initially relaxed circular DNA has been calculated to be approximately ... Upon binding to DNA (the "Gyrase-DNA" state), there is a competition between DNA wrapping and dissociation, where increasing ... DNA cleavage and reunion is performed by a catalytic center located in DNA-gates build by all gyrase subunits. C-gates are ... This process occurs in bacteria, whose single circular DNA is cut by DNA gyrase and the two ends are then twisted around each ...

https://en.wikipedia.org/wiki/DNA_gyrase

DNA)-like particle). Around 146 base pairs (bp) of DNA wrap around this core particle 1.65 times in a left-handed super-helical ... Without histones, unwound DNA in chromosomes would be very long. For example, each human cell has about 1.8 meters of DNA if ... Histones prevent DNA from becoming tangled and protect it from DNA damage. In addition, histones play important roles in gene ... Marking sites of DNA damage is an important function for histone modifications. Without a repair marker, DNA would get ...

https://en.wikipedia.org/wiki/Histone

I purified from Xenopus egg extracts is a DNA-stimulated ATPase and displays the ability to introduce positive superhelical ... Early single-DNA-molecule experiments also demonstrated in real time that condensin I is able to compact DNA in an ATP- ... It has been proposed that condensin I anchors DNA between Ycg1-Brn1 subunits and pulls DNA asymmetrically to form large loops. ... For eukaryotic complexes, it has been reported that HEAT repeat subunits contribute to part of DNA binding and to the assembly ...

https://en.wikipedia.org/wiki/Condensin

... thereby generating superhelical torsion that facilitates melting of the adjacent AT-rich DUE. DNA strand separation is ... bends DNA and negative supercoiling has been reported to enhance DNA binding of this complex, suggesting that DNA shape and ... This can either involve the replication of DNA in living organisms such as prokaryotes and eukaryotes, or that of DNA or RNA in ... However, Orc1/Cdc6 severely underwinds and bends DNA, suggesting that it relies on a mix of both DNA sequence and context- ...

https://en.wikipedia.org/wiki/Origin_of_replication

The nucleosome core particle consists of approximately 146 base pairs (bp) of DNA wrapped in 1.67 left-handed superhelical ... The DNA is non-uniformly bent and also contains twist defects. The twist of free B-form DNA in solution is 10.5 bp per turn. ... DNA twist defects are when the addition of one or a few base pairs from one DNA segment are transferred to the next segment ... Because DNA portions of nucleosome core particles are less accessible for DNAse than linking sections, DNA gets digested into ...

https://en.wikipedia.org/wiki/Nucleosome

... negative super coiling during DNA replication Cell death can occur through the inability of bacteria to maintain the DNA super helical ... It exerts its antibacterial effect by interfering with the bacterial enzyme DNA gyrase, which is needed for the maintenance and ... Difloxacin inhibits DNA gyrase (also known as Topoisomerase II), an enzyme required for ... The primary mode of action of fluoroquinolones involves interaction with enzymes essential for major DNA functions such as ...

https://en.wikipedia.org/wiki/Difloxacin

DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical ... separating the DNA of daughter chromosomes after DNA replication, and relax DNA. These enzymes have several functions: to ... DNA topoisomerases are divided into two classes: type I enzymes (EC; topoisomerases I, III and V) break single-strand DNA, and ... The topoisomerase also does not use ATP during uncoiling of the DNA; rather, the torque present in the DNA drives the uncoiling ...

https://en.wikipedia.org/wiki/Type_I_topoisomerase

Z-DNA, stem-loop, and other conformations under superhelical stress. Between the strand-biased microsatellite repeats and C:G ... Satellite DNA consists of very large arrays of tandemly repeating, non-coding DNA. Satellite DNA is the main component of ... Satellite DNA, together with minisatellite and microsatellite DNA, constitute the tandem repeats. The size of satellite DNA ... The name "satellite DNA" refers to the phenomenon that repetitions of a short DNA sequence tend to produce a different ...

https://en.wikipedia.org/wiki/Satellite_DNA

It catalyses the relaxation of negatively or positively superhelical DNA and is employed in phage DNA replication during ... A strand of DNA, called the gate, or G-segment, is bound by a central DNA-binding gate (DNA-gate). A second strand of DNA, ... Roca J, Wang JC (May 1994). "DNA transport by a type II DNA topoisomerase: evidence in favor of a two-gate mechanism". Cell. 77 ... The structures formed a novel beta barrel, which bends DNA by wrapping the nucleic acid around itself. The bending of DNA by ...

https://en.wikipedia.org/wiki/Type_II_topoisomerase

... in the form of coiled ring structures that appear to correspond to multiply looped DNA configurations in which superhelical ... T7 DNA polymerase, assisted by E. coli thioredoxin, performs both leading and lagging-strand DNA synthesis. In phage T7, DNA ... PMID 10792729 Yu M, Masker W. T7 single strand DNA binding protein but not T7 helicase is required for DNA double strand break ... T7 polymerase uses E. coli's endogenous thioredoxin, a REDOX protein, as a sliding DNA clamp during phage DNA replication ( ...

https://en.wikipedia.org/wiki/T7_phage

DNA, superhelical MeSH D13.444.308.291 - DNA, concatenated MeSH D13.444.308.295 - DNA, cruciform MeSH D13.444.308.300 - DNA, ... DNA adducts MeSH D13.444.308.142 - DNA, a-form MeSH D13.444.308.148 - DNA, algal MeSH D13.444.308.150 - DNA, antisense MeSH ... DNA, bacterial MeSH D13.444.308.227 - DNA, c-form MeSH D13.444.308.243 - DNA, catalytic MeSH D13.444.308.283 - DNA, circular ... DNA, ribosomal spacer MeSH D13.444.308.425 - DNA, neoplasm MeSH D13.444.308.435 - DNA, plant MeSH D13.444.308.435.275 - DNA, ...

https://en.wikipedia.org/wiki/List_of_MeSH_codes_(D13)

"Chemists slide a splitting catalyst over DNA for the first time". ""Alle data van de wereld op een draadje plastic", Trouw, ... Some of these formed super helical structures by a process in which information is transferred stepwise from the building ... More recently, he developed a synthetic catalyst that can move along a DNA chain and cleave it. He furthermore designed ... "A clamp-like biohybrid catalyst for DNA oxidation". Nature Chemistry. 5 (11): 945-51. Bibcode:2013NatCh...5..945V. doi:10.1038/ ...

https://en.wikipedia.org/wiki/Roeland_Nolte

DNA-dependent protein kinase) Fanconi anemia responsible protein FANCF (FANCF) Damaged DNA-binding protein AlkD (Alkylpurin DNA ... HEAT repeats form extended superhelical structures which are often involved in intracellular transport; they are structurally ... regulation Elongation factor eEF3 Initiation factor eIF4G Aminoacyl tRNA synthetase transfer protein Cex1p DNA repair DNA-PK ( ... "Crystal structure of DNA-PKcs reveals a large open-ring cradle comprised of HEAT repeats". Nature. 463 (7277): 118-121. doi: ...

https://en.wikipedia.org/wiki/HEAT_repeat

A number of different assay methods have been used to study repair of strand breaks in DNA after exposure of cells to ionizing ... Repair of strand breaks in superhelical dna of ataxia telangiectasia lymphoblastoid cells. J Cell Sci (1981) 48 (1): 383-391. ... Inhibition of DNA synthesis and alteration to DNA structure by the phenacetin analog p-aminophenol ... Differences in the DNA Supercoiling Response of Irradiated Cell Lines from Ataxia-telangiectasia Versus Unaffected Individuals ...

https://journals.biologists.com/jcs/crossref-citedby/59080

The superhelical status of the DNA in the reconstructed complexes is indistinguishable from that found in control nucleoids ... These nucleoids contain all the nuclear RNA and DNA but few of the proteins characteristic of chromatin. Their DNA is ... Experiments with micrococcal nuclease confirm that the DNA in the reconstructed complexes is organized into nucleosome-like ... histones without breaking the DNA. We have probed the integrity and structure of the reconstructed complexes using a non- ...

https://www.neuroscience.ox.ac.uk/publications/4665

Coliphages, DNA, Bacterial, DNA, Recombinant, DNA, Single-Stranded, DNA, Viral, Escherichia coli, Genes, Nucleic Acid ... When a mixture of superhelical DNA (RFI) of phage phiX174 am3 and fragments of single-stranded DNA from wild-type phiX174 was ... Recombination promoted by superhelical DNA and the recA gene of Escherichia coli.. ... Recombination promoted by superhelical DNA and the recA gene of Escherichia coli.. ...

https://microbiology.weill.cornell.edu/recombination-promoted-superhelical-dna-and-reca-gene-escherichia-coli

https://en.wikipedia.org/wiki/DNA_supercoil

DNA Repair / genetics* * DNA, Superhelical / genetics * Gene Targeting / methods* * Genetic Therapy / methods ... showed a similar gene correction frequency to chimeric RNA-DNA oligonucleotide, measured using the same system. The in vitro ... at a similar frequency as the chimeric RNA-DNA oligonucleotide. ...

https://pubmed.ncbi.nlm.nih.gov/11313816/

... nucleosomes function as the most basic unit of chromosome organization directly binding and assembling on DNA to modulate DNA ... Likewise, superhelical tension forms on the daughter strands as a consequence of polymerase synthesis. Polymerases must travel ... They consist of a dimer of dimers with two copies each of the histones H3, H4, H2A and H2B, that tightly bind and wrap DNA, ... Resolution of superhelical tension is critical to ensure replication fork progression and avoid chromosome damage. To date, ...

https://www.biochem.mpg.de/duderstadt/research

30 DNA-PKcs in DNA-PK holoenzyme (PDB ID: 5Y3R),32 and ATR in ATR-ATRIP complex (PDB ID: 5YZ0).31 The structures are shown in ... 2). (1) In other PIKK family members, the N-HEAT domains more or less adopt a twisted super-helical conformation. In contrast, ... b-e The structures of SMG1 (b), mTOR (c), ATR (d) and DNA-PKcs (e) are shown as in a. f Close-up view of the superimposed KDs ... g-j Close-up views of the four-way junction of SMG1 (g), and equivalent regions in mTOR (h), ATR (i) and DNA-PKcs (j). SMG1 and ...

https://www.nature.com/articles/s41422-019-0255-3?error=cookies_not_supported&code=6f330600-c08a-4d4d-9e27-11dff43ab4b5

Human mitochondrial mTERF wraps around DNA through a left-handed superhelical tandem repeat ... Structure and inhibition of herpesvirus DNA packaging terminase nuclease domain. Nadal M, Mas PJ, Blanco AG, Arnan C, Solà M, ...

https://www.irbbarcelona.org/en/research/research-publications?page=9

ATP-dependent breakage, passage and rejoining of double-stranded DNA.. -!- The enzyme can introduce negative superhelical turns ... into double- stranded circular DNA. -!- One unit has nicking-closing activity, and another catalyzes super- twisting and ...

http://cathdb.info/version/latest/domain/1bgwA05

... the N-terminal domain of human DNA polymerase epsilon subunit B revealed a domain that consists of a left-handed superhelical ... DNA polymerase epsilon subunit 2. Names. DNA polymerase II subunit 2. DNA polymerase epsilon subunit B. polymerase (DNA ... DNA_pol_E_B; DNA polymerase alpha/epsilon subunit B. pfam12213. Location:4 → 73. Dpoe2NT; DNA polymerases epsilon N terminal. ... DNA_pol_E_B; DNA polymerase alpha/epsilon subunit B. pfam12213. Location:4 → 73. Dpoe2NT; DNA polymerases epsilon N terminal. ...

https://www.ncbi.nlm.nih.gov/gene/5427

We will discuss the mechanism of DNA supercoiling and the role of superhelical stress in DNA structure and function. Mechanism ... Introduction DNA supercoiling is the twisting or coiling of the double helix structure of DNA, resulting in a strain on the ... Principle of DNA MicroarrayThe principle of DNA microarray technology is based on the hybridization of complementary sequences ... Introduction DNA microarrays are powerful tools for analysing gene expression patterns, detecting DNA mutations, and ...

https://www.tutorialspoint.com/articles/category/genetics

... are DNA elements that serve to compartmentalize the chromatin into structural and functional domains.... , Find, read and cite ... protein-DNA complexes. We find that although protein binding may bend the DNA, bending alone is not sufficient to kink the DNA ... also susceptible to superhelical stress-induced duplex desta-. bilization (56). OriC is one such element that contains AT ... and has been used as a method of choice for studying DNA conformation, secondary DNA structure transition and DNA damage. In ...

https://www.researchgate.net/publication/334204983_Mapping_of_scaffoldmatrix_attachment_regions_in_human_genome_a_data_mining_exercise

The results reveal that SV 40 DNA I contains about -13 superhelical turns in concentrated salt solutions. ... The number of superhelical turns, τ, present in I is calculated at each dye concentration using Fuller and Warings (1964) ... The theory is applied to the specific cases of the binding of ethidium bromide to SV 40 DNA and of the binding of mercury and ... of τ from a consideration of the effect of the superhelical turns upon the binding isotherm of ethidium bromide to SV 40 DNA I ...

https://thesis.library.caltech.edu/9624/

Thus FACT has been a sensor and mediator of a novel type of cell stress-DNA superhelical or torsional stress, which is the ... We also believe that FACT may be involved in the protection of our genome from DNA damage through the control of DNA topology. ... Our current focus area is chromatin remodeling factors, their role in normal development and disease, DNA damage detection and ... Specifically, she identified a new class of prospective anticancer agents named curaxins which interfere with DNA binding to ...

https://www.roswellpark.org/katerina-gurova

Transcription Elongation Provides Superhelical Tension for the DNA. Immediately following it offers initiated transcription, ... not, because the chatted about into the Chapter cuatro, DNA when you look at the eucaryotic tissue was packaged to the ... Indeed, these additional necessary protein assemblies get get in touch with one another away from the DNA and start to become ... Just like the demonstrated into the Chapter 7, these necessary protein join to certain brief sequences into the DNA. In the ...

http://elsafwany.com/polymerase-ii-and-additionally-need-activator/

DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical ... Topoisomerases I promote the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex ... CRYSTAL STRUCTURE OF HUMAN TOPOISOMERASE I DNA COMPLEX. 1k4s. HUMAN DNA TOPOISOMERASE I IN COVALENT COMPLEX WITH A 22 BASE PAIR ... HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE POISON TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX. ...

https://smart.embl.de/smart/do_annotation.pl?DOMAIN=Blast:TOPEUc&START=245&END=321&E_VALUE=9e-19&TYPE=BLAST&BLAST=DGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNDEKNTITNLSKCDFTQMSQYFKAQSEARKQM

... into a lefthanded superhelical path that mimics the DNA conformation in the nucleosome crystal structure [4]. (B) Fraction of ... So your DNA could stretch to the sun and back 61 times. That is one persons DNA." For all FEELguide stories related to DNA be ... SEE ALSO: Digital DNA: A Mindblowing Conversation About The Future Of Synthetic DNA In The Digital Age. SEE ALSO: Researchers ... SEE ALSO: Scientists Stunned By Meditations Ability To Regrow DNAs Age-Defying Telomeres In Cancer Patients. SEE ALSO: DNA ...

https://www.feelguide.com/2021/03/16/the-wow-files-scientists-confirm-a-second-layer-of-information-has-been-found-hiding-inside-dna/

Intramolecular DNA triplexes, bent DNA and DNA unwinding elements in the initiation region of an amplified dihydrofolate ... Formation of DNA triplexes accounts for arrests of DNA synthesis at d(TC)n and d(GA)n tracts. scientific article published on ... Formation of DNA triplexes accounts for arrests of DNA synthesis at d(TC)n and d(GA)n tracts (English) ... The DNA sequence of sea urchin (S. purpuratus) H2A, H2B and H3 histone coding and spacer regions ...

https://m.wikidata.org/wiki/Q37373852

DNA, Superhelical (MeSH) * Electrophoresis, Agar Gel (MeSH) * Models, Theoretical (MeSH) * Nucleic Acid Conformation (MeSH) ... The partition coefficient also increased with increasing ionic strength due to the compaction of the DNA associated with the ...

https://experts.mcmaster.ca/display/publication1338244

DNA, Superhelical. Circular duplex DNA isolated from viruses, bacteria and mitochondria in supercoiled or supertwisted form. ... It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into ... Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a ... GeneticDNA, SuperhelicalMicrococcal NucleaseRibosome Subunits, Large, EukaryoticDNACentromereTranscription FactorsProtein ...

https://lookformedical.com/en/search/chromatin-assembly-factor-1

The procaryotic transposon Tn5 inserts into many different sites within a single gene, but some sites (hotspots) are targeted repeatedly. Hotspots are not closely related in sequence, but most have G/C pairs at the ends of the nine base pairs duplicated by Tn5 insertion. In pBR322, the major hotspot coincides with the -10 region of the tet promoter. We mutated the G/C pairs at this hotspot and assayed for insertion into hotspot I, resistance to tetracycline, and plasmid supercoiling. We found that changing the G/C pairs to A/T pairs reduced the frequency of insertion into the hotspot by at least fivefold. The reduction in hotspot use caused by these G/C to A/T changes was not attributable to changes in plasmid supercoiling or tet promoter strength.. ...

https://scholars.duke.edu/publication/1508782

Dive into the research topics of The C-terminal domain of DNA gyrase A adopts a DNA-bending β-pinwheel fold. Together they ... The C-terminal domain of DNA gyrase A adopts a DNA-bending β-pinwheel fold. ... DNA Gyrase 100% * DNA Topoisomerase IV 54% * DNA 38% * Superhelical DNA 25% ...

https://pure.johnshopkins.edu/en/publications/the-c-terminal-domain-of-dna-gyrase-a-adopts-a-dna-bending-%CE%B2-pinw-4/fingerprints/

keywords = "Catalysis, DNA Gyrase/chemistry, DNA, Superhelical/chemistry, DNA-Binding Proteins/chemistry, Escherichia coli/ ... N2 - Bacterial DNA gyrase introduces negative supercoils into chromosomal DNA and relaxes positive supercoils introduced by ... AB - Bacterial DNA gyrase introduces negative supercoils into chromosomal DNA and relaxes positive supercoils introduced by ... Bacterial DNA gyrase introduces negative supercoils into chromosomal DNA and relaxes positive supercoils introduced by ...

https://pure.york.ac.uk/portal/en/publications/single-molecule-imaging-of-dna-gyrase-activity-in-living-escheric

Superhelical DNA Medicine & Life Sciences 15% * Dynamic Light Scattering Medicine & Life Sciences 13% ... For digestion by S1 nuclease, which selectively cleaves single strand DNA, the pressurized plasmid DNA was easily degraded ... For digestion by S1 nuclease, which selectively cleaves single strand DNA, the pressurized plasmid DNA was easily degraded ... For digestion by S1 nuclease, which selectively cleaves single strand DNA, the pressurized plasmid DNA was easily degraded ...

https://okayama.elsevierpure.com/en/publications/characteristics-of-compacted-plasmid-dna-by-high-pressurization

Why are there different topological forms of DNA? The answer is related to superhelical voltage and sequence distortion. ... DNA in bacteria. In bacteria, there is no nucleus for DNA. Instead, DNA is contained in a structure called a nucleoid (Figure ... Structure of DNA strands. Each DNA strand is assembled from dNTPs by the formation of a phosphodiester bond, catalyzed by DNA ... First, voltage can provide energy to "reverse" the structure of DNA. Z-DNA may emerge as a means of relaxation. Second, DNA can ...

https://rainis.pics/article/2-6-structure-and-function-nucleic-acids

The nucleosome core particle (shown in the figure) consists of about 146[5] bp of DNA wrapped in 1.67 left-handed superhelical ... The nucleosome core particle consists of approximately 147[5] base pairs of DNA wrapped in 1.67 left-handed superhelical turns ... The DNA is non-uniformly bent and also contains twist defects. The twist of free B-form DNA in solution is 10.5 bp per turn, ... DNA site exposure. Work from the Widom laboratory has shown that nucleosomal DNA is in equilibrium between a wrapped and ...

https://fr.wikidoc.org/index.php/Nucleosome

Signature of positive selection in mitochondrial DNA in Cetartiodactyla. Genes Genet Syst. 2018 Sep 15; 93(2):65-73. ...

https://connects.catalyst.harvard.edu/Profiles/display/Concept/Artiodactyla

Recent studies have shown that DNA structural properties, such as curvature, stacking energy, and stress-induced duplex ... Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress. ... DNA structural features are increasingly being recognized as an important tool for detecting promoters. Promoter prediction ... Wang H, Noordewier M, Benham CJ: Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely ...

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-S6-S17

Human mitochondrial mTERF wraps around DNA through a left-handed superhelical tandem repeat. Nature Structural and Molecular ... DNA Site-X and Site-Y, similar to and downstream from LSP, unexpectedly show distinct DNA-structure features and TFAM binds to ... Human mitochondrial mTERF wraps around DNA through a left-handed superhelical tandem repeat. Nature Structural and Molecular ... DNA specificities modulate the binding of human transcription factor A to mitochondrial DNA control region. Nucleic Acids ...

https://www.ibmb.csic.es/en/department-of-structural-and-molecular-biology/mitochondrial-macromolecules/

A pH-dependent structural transition in the homopurine-homopyrimidine tract in superhelical DNA ... Stimulation of DNA synthesis in hepatocytes by serum fractions of hepatectomized rats ...

http://biopolymers.org.ua/content/2/3/

BACs are circular DNA molecules that are derived from the F-factor plasmid found in the bacterium E. coli. (tutorialspoint.com)
Magnesium ion-dependent triple-helix structure formed by homopurine-homopyrimidine sequences in supercoiled plasmid DNA. (wikidata.org)
Characteristics of compacted plasmid DNA by high pressurization. (elsevierpure.com)
In order to investigate the effect of pressure on the tertiary structure of plasmid DNA having the supercoiled and relaxed forms, the solution of plasmid DNA was hydrostatically pressurized at different atmosphere and 40 degrees C for various times. (elsevierpure.com)
For dynamic light scattering (DLS) measurement of the pressurized plasmid DNA, the hydrodynamic diameters of the super-coiled and relaxed plasmid DNA were decreased with increasing pressure. (elsevierpure.com)
Also, at constant pressure, a long period of pressure treatment effectively induced the decrease in plasmid DNA. (elsevierpure.com)
These results suggest that the plasmid DNA was condensed by high hydrostatic pressurization. (elsevierpure.com)
The circular dichroism (CD) spectrum of the pressurized plasmid DNA was slightly changed. (elsevierpure.com)
For digestion by S1 nuclease, which selectively cleaves single strand DNA, the pressurized plasmid DNA was easily degraded compared to the non-pressurized plasmid DNA, suggesting that the double helix of plasmid DNA was partly dissociated to single strand by the pressure-induced compaction of plasmid DNA. (elsevierpure.com)
These results indicate that high hydrostatic pressurization is one of powerful tools for preparing the compacted plasmid DNA. (elsevierpure.com)
Dive into the research topics of 'Characteristics of compacted plasmid DNA by high pressurization. (elsevierpure.com)
The effect of radiations on supercoiled plasmid DNA has been investigated by using atomic force microscopy (AFM). (ox.ac.uk)
The miniF plasmid C protein: sequence, purification and DNA binding. (shengsci.com)
The C protein has been purified from cells carrying the Ptrp-C plasmid, and a preliminary study of C protein-DNA binding properties has been carried out. (shengsci.com)
We describe an improved model of DNA replication in Xenopus egg extracts, in which a circular plasmid immobilized on paramagnetic beads is used as a template. (shengsci.com)
DNA synthesis occurred on either circular or linear plasmids coupled to the beads, but only DNA synthesis on the circular plasmid was inhibited by geminin and a. (shengsci.com)

Experiments with micrococcal nuclease confirm that the DNA in the reconstructed complexes is organized into nucleosome-like structures. (ox.ac.uk)
Specifically, she identified a new class of prospective anticancer agents named curaxins which interfere with DNA binding to histones and cause nucleosome disassembly and chromatin decondensation, phenomenon which they named "chromatin damage. (roswellpark.org)
A) The rigid base-pair model is forced, using 28 constraints (indicated by red spheres), into a lefthanded superhelical path that mimics the DNA conformation in the nucleosome crystal structure [4]. (feelguide.com)
A histone chaperone that facilitates nucleosome assembly by mediating the formation of the histone octamer and its transfer to DNA. (lookformedical.com)
The nucleosome core particle consists of approximately 147 [5] base pairs of DNA wrapped in 1.67 left-handed superhelical turns around a histone octamer consisting of 2 copies each of the core histones H2A , H2B , H3 , and H4 . (wikidoc.org)
[6] Linker histones such as H1 and its isoforms are involved in chromatin compaction and sit at the base of the nucleosome near the DNA entry and exit binding to the linker region of the DNA. (wikidoc.org)
The crystal structure of the nucleosome core particle consisting of H2A , H2B , H3 and H4 and DNA. (wikidoc.org)
The nucleosome contains over 120 direct protein-DNA interactions and several hundred water mediated ones [13] . (wikidoc.org)
The translocase motor of the ATPase module engages with the edge of the nucleosome at superhelical location +2. (mbexc.de)
The human nucleosome core contains about seven turns of DNA for every full "superhelical" turn, rather than three as shown at Crooked Soley. (aloriaweaver.com)
Eukaryotic histones are basic and water-soluble nuclear proteins that form hetero-octameric nucleosome particles by wrapping 146 base pairs of DNA in a left-handed super-helical turn sequentially to form chromosomal fiber. (neobiotechnologies.com)

eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. (embl.de)
Bacterial DNA gyrase introduces negative supercoils into chromosomal DNA and relaxes positive supercoils introduced by replication and transiently by transcription. (york.ac.uk)
DNA gyrase is a class of Type II Topoisomerases that plays an important role in bacterial viability. (biomedicineonline.org)
The study focuses on DNA gyrase as a target and shows insights into future drug development. (biomedicineonline.org)
The research focuses on the discovery of novel plant-based therapeutic compounds to target DNA gyrase B activity. (biomedicineonline.org)
The study employs DNA gyrase as its target and provides information on potential therapeutic targets. (biomedicineonline.org)
The goal of the study is to identify innovative plant-based medicinal molecules that specifically target DNA gyrase B activity. (biomedicineonline.org)
Cozzarelli, N.R. DNA gyrase and the supercoiling of DNA. (biomedicineonline.org)

In a "relaxed" double-helical segment of B-DNA, the two strands twist around the helical axis once every 10.4-10.5 base pairs of sequence. (wikipedia.org)
Chromosome replication is performed by a large multisubunit assembly, known as the replisome, which couples the unpackaging of parental DNA with the synthesis of new daughter strands. (mpg.de)
Separation of the two single strands leads to the build-up of superhelical tension, which, if left unresolved, exerts extreme forces in the form of torque that disrupts critical enzymatic events on chromosomes. (mpg.de)
Likewise, superhelical tension forms on the daughter strands as a consequence of polymerase synthesis. (mpg.de)
PCNA is required for the coordinated synthesis of both leading and lagging strands at the replication fork during DNA replication. (lookformedical.com)
Removal of these positive supercoils is essential for replication fork progression and for the overall unlinking of the two duplex DNA strands, as well as for ongoing transcription. (york.ac.uk)
The double helix, made up of a pair of DNA strands, has bases in its core that are joined by hydrogen bonds to form base pairs: adenine always paired with thymine and guanine always paired with cytosine. (rainis.pics)
Two of these paired strands make up the DNA molecule, which then twists into a helix. (rainis.pics)
After irradiation, fragments (open circular and linearised strands) were observed corresponding to single strand breaks and double strand breaks in DNA. (ox.ac.uk)

These nucleoids contain all the nuclear RNA and DNA but few of the proteins characteristic of chromatin. (ox.ac.uk)
Based on the properties of intercalating molecules, i.e. fluorescing upon binding to DNA and unwinding of DNA base-pairs, in 2016, a single-molecule technique has been introduced to directly visualize individual plectonemes along supercoiled DNA which would further allow to study the interactions of DNA processing proteins with supercoiled DNA. (wikipedia.org)
The solution structure of the amino-terminal domain of human DNA polymerase epsilon subunit B is homologous to C-domains of AAA+ proteins. (nih.gov)
The way in which DNA is folded determines how the letters are read out, and therefore which proteins are actually made. (feelguide.com)
Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. (lookformedical.com)
Proteins which bind to DNA. (lookformedical.com)
The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases. (lookformedical.com)
Crucially, the sequence of bases in DNA contains the information for making proteins. (rainis.pics)
Early structural studies provided evidence that an octamer of histone proteins wraps DNA around itself in about two turns of a left-handed superhelix. (wikidoc.org)
Single-molecule kinetics reveal microscopic mechanism by which High-Mobility Group B proteins alter DNA flexibility. (shengsci.com)
Eukaryotic High-Mobility Group B (HMGB) proteins alter DNA elasticity while facilitating transcription, replication and DNA repair. (shengsci.com)

e.g. they bind selectively to DNA, stimulate transcription resulting in tissue-specific RNA synthesis and undergo specific changes in response to various hormones or phytomitogens. (lookformedical.com)
Nuclear antigen with a role in DNA synthesis, DNA repair, and cell cycle progression. (lookformedical.com)
The complementary structure immediately suggested to Watson and Crick how DNA could (and does) replicate, and further explains how information from DNA is transferred to RNA for protein synthesis. (rainis.pics)
A unique feature of mitochondria is that they possess their own genome, the mitochondrial DNA (mtDNA), which codes for subunits of the electron transport chain that eventually leads to the synthesis of the ATP molecule. (csic.es)
Trading places: how do DNA polymerases switch during translesion DNA synthesis? (academicinfluence.com)

A negatively supercoiled DNA molecule will produce either a one-start left-handed helix, the toroid, or a two-start right-handed helix with terminal loops, the plectoneme. (wikipedia.org)
Introduction DNA supercoiling is the twisting or coiling of the double helix structure of DNA, resulting in a strain on the molecule. (tutorialspoint.com)
The free energy of superhelix formation is calculated as a function of τ from a consideration of the effect of the superhelical turns upon the binding isotherm of ethidium bromide to SV 40 DNA I. The value of the free energy is about 100 kcal/mole DNA in the native molecule. (caltech.edu)
But today's announcement confirms what scientists have suspected since the 1980s - there is a secret "hidden" code found inside the specific way each DNA molecule is wrapped up and folded. (feelguide.com)
The process by which a DNA molecule is duplicated. (lookformedical.com)
In the more common B form, the DNA helix has a repeat of 10.5 base pairs per turn, with the sugar and phosphate forming the covalent phosphodiester "backbone" of the molecule, and the bases adenine, guanine, cytosine and thymine line up in the middle, where the base pairs we know today are, which look like the rungs of a ladder. (rainis.pics)
We developed a new single-molecule method to probe non-specific DNA interactions for two HMGB homologs: the human HMGB2 box A domain and yeast Nhp6Ap, along with chimeric mutants replacin. (shengsci.com)
The kind of IB molecule via variola malware (vTopo) has proven to be attractive dealing with mechanistic queries about topoisomerase operate since it varieties the relatively easy to fix 3′-phosphotyrosyl adduct using the DNA central source with a distinct goal sequence (5′-CCCTT-3′) from which Genetic re-energizing could proceed. (wee1-receptor.com)

In that study, Sytox Orange (an intercalating dye) was used to induce supercoiling on surface tethered DNA molecules. (wikipedia.org)
The microarray technology is based on the hybridization of labelled DNA or RNA molecules to complementary sequences that are immobilized on a solid substrate. (tutorialspoint.com)
Principle of DNA MicroarrayThe principle of DNA microarray technology is based on the hybridization of complementary sequences of nucleic acid molecules. (tutorialspoint.com)
In an application of this method it is found that HeLa cells contain in addition to closed circular mitochondrial DNA of mean length 4.81 microns, a heterogeneous group of smaller DNA molecules which vary in size from 0.2 to 3.5 microns and a paucidisperse group of multiples of the mitochondrial length. (caltech.edu)
Ever since Watson and Crick identified the structure of DNA molecules in 1953, scientists have assumed that the only information contained within each strand is the various combos of G, A, T and C inside the iconic double helix structure. (feelguide.com)
Nucleic acids, DNA and RNA, can be considered as the information molecules of the cell. (rainis.pics)
In this section, we examine the structures of DNA and RNA and how these structures relate to the functions of these molecules. (rainis.pics)
The DNA molecules were deposited on a substrate and observed by AFM. (ox.ac.uk)
H. influenzae , like many other pathogens, is naturally competent, able to actively transport environmental DNA through its cell membranes and incorporate homologous molecules into its chromosomes. (drexel.edu)

The mechanisms effecting establishment, maintenance, and modification of that specific physical conformation of CHROMATIN determining the transcriptional accessibility or inaccessibility of the DNA. (lookformedical.com)
We examined this issue in transient and stable assay systems using a 180-bp synthetic curved DNA with a left-handed superhelical conformation. (soken.ac.jp)
Curved DNA structures with a left-handed superhelical conformation can activate eukaryotic transcription. (soken.ac.jp)

Scaffold/matrix attachment regions (S/MARs) are DNA elements that serve to compartmentalize the chromatin into structural and functional domains. (researchgate.net)
Our current focus area is chromatin remodeling factors, their role in normal development and disease, DNA damage detection and prevention. (roswellpark.org)
not, because the chatted about into the Chapter cuatro, DNA when you look at the eucaryotic tissue was packaged to the nucleosomes, being further set up in highest-order chromatin structures. (elsafwany.com)
Which interest is required to help the RNA polymerase additionally the general transcription situations inside conquering the situation away from joining to help you DNA that is packed within the chromatin. (elsafwany.com)
Because the discussed for the Part cuatro, both type of minerals makes it possible for higher accessibility to the fresh new DNA present in chromatin, and by doing this, it helps the latest system of your own transcription initiation gadgets onto DNA. (elsafwany.com)
Eucaryotic RNA polymerases must contend with chromatin design while they circulate together a great DNA layout. (elsafwany.com)
The repeating structural units of chromatin, each consisting of approximately 200 base pairs of DNA wound around a protein core. (lookformedical.com)
Nucleosomes form the fundamental repeating units of eukaryotic chromatin [1] , which is used to pack the large eukaryotic genomes into the nucleus while still ensuring appropriate access to it (in mammalian cells approximately 2 m of linear DNA have to be packed into a nucleus of roughly 10 µm diameter). (wikidoc.org)
Epigenetics of a tandem DNA repeat: chromatin DNaseI sensitivity and opposite methylation changes in cancers. (shengsci.com)
DNA methylation and chromatin DNaseI sensitivity were analyzed in and adjacent to D4Z4 repeat arrays, which consist of 1 to approximately 100 tandem 3.3-kb units at subtelomeric 4q and 10q. (shengsci.com)
Over 80% of nucleosomes contain the linker Histone H1, derived from an intronless gene that interacts with linker DNA between nucleosomes and mediates compaction into higher order chromatin. (neobiotechnologies.com)

Transfection by fragments and superhelical DNA produced 20 to 100 times more recombinants than transfection by fragments and either nicked circular DNA or relaxed closed circular DNA. (cornell.edu)
a circular DNA strand assumes this shape to accommodate more or few helical twists. (wikipedia.org)
Lobal contortions of a circular DNA, such as the rotation of the figure-eight lobes above, are referred to as writhe. (wikipedia.org)
The enzyme can introduce negative superhelical turns into double- stranded circular DNA. (cathdb.info)
I. The structure and properties of closed circular duplex DNA. (caltech.edu)
I. The binding of the intercalating dye ethidium bromide to closed circular SV 40 DNA causes an unwinding of the duplex structure and a simultaneous and quantitatively equivalent unwinding of the superhelices. (caltech.edu)
A buoyant density method for the isolation and detection of closed circular DNA is described. (caltech.edu)
The method is based upon the reduced binding of the intercalating dye, ethidium bromide, by closed circular DNA. (caltech.edu)
Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA. (shengsci.com)
Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. (shengsci.com)
In 504 of those squares, the crop was left standing, so as to depict a closed-circular, double-helical DNA of three turns. (aloriaweaver.com)

In eukaryotic organisms, nucleosomes function as the most basic unit of chromosome organization directly binding and assembling on DNA to modulate DNA topology, drive compaction, and regulate transcription. (mpg.de)
The partition coefficient also increased with increasing ionic strength due to the compaction of the DNA associated with the shielding of the intramolecular electrostatic interactions. (mcmaster.ca)
Structural basis of mitochondrial DNA transcription and compaction. (csic.es)

The crystal structures of human topoisomerase I comprising the core and carboxyl-terminal domains in covalent and noncovalent complexes with 22-base pair DNA duplexes reveal an enzyme that 'clamps' around essentially B-form DNA. (embl.de)
The core domain and the first eight residues of the carboxyl-terminal domain of the enzyme, including the active-site nucleophile tyrosine-723, share significant structural similarity with the bacteriophage family of DNA integrases. (embl.de)
The antitumor drug camptothecin (CPT) and its analogs inhibit the rejoining step of the breakage/rejoining reaction, which traps the enzyme in covalent linkage with DNA (the cleavable complex). (tmu.edu.tw)

Signature of positive selection in mitochondrial DNA in Cetartiodactyla. (harvard.edu)

We seek to define the operating principles that guide replisome function and understand how replisomes recognize and process obstacles encountered on parental chromosomes such as DNA lesions, unfavorable topological structures, and architectural factors. (mpg.de)
FACT can detect abnormal or alternative DNA structures and convey signal to p53 activation. (roswellpark.org)
The theory suggests that mechanical cues within the DNA structures determine how preferentially DNA folds. (feelguide.com)
Structures of homopurine-homopyrimidine tract in superhelical DNA. (wikidata.org)
Our biochemical analyses showed that TFAM binds to DNA structures, such as G-quadruplexes (Lyonnais et al. (csic.es)

Recombination promoted by superhelical DNA and the recA gene of Escherichia coli. (cornell.edu)

The twist is the number of helical turns in the DNA and the writhe is the number of times the double helix crosses over on itself (these are the supercoils). (wikipedia.org)
Using this assay, it was found that the DNA sequence encodes for the position of plectonemic supercoils. (wikipedia.org)
Furthermore, DNA supercoils were found to be enriched at the transcription start sites in prokaryotes. (wikipedia.org)
In eukaryotes, DNA supercoiling exists on many levels of both plectonemic and solenoidal supercoils, with the solenoidal supercoiling proving most effective in compacting the DNA. (wikipedia.org)

It is found in all bacteria and is involved in replication, repair, recombination, and DNA transcription. (biomedicineonline.org)

Many topoisomerase enzymes sense supercoiling and either generate or dissipate it as they change DNA topology. (wikipedia.org)
DNA topoisomerase (ATP-hydrolyzing). (cathdb.info)
Structure and mechanism of DNA topoisomerase II. (cathdb.info)
This entry represents the C-terminal region of DNA topoisomerase I enzymes from eukaryotes (type IB enzymes). (embl.de)
Tse, Y.C., Wang, J.C. E. coli and M. luteus DNA topoisomerase I can catalyze catenation or decatenation of double-stranded DNA rings. (biomedicineonline.org)
A unique real regardless of whether topoisomerase action will be managed with the topological condition of the particular DNA, therefore offering the selleckchem system pertaining to ideal chemical in order to very supercoiled Genetic domain names within genomes. (wee1-receptor.com)
Topoisomerase I (TOP1) relaxes superhelical DNA through a breakage/rejoining reaction in which the active site tyrosine links covalently to a 3' phosphate at the break site as a transient intermediate. (tmu.edu.tw)

Many of us infer in which the two superhelical density and transient associates involving vTopo and also the rotating DNA decide the efficiency regarding supercoil rejuvinating. (wee1-receptor.com)

The amount of a strand's supercoiling affects a number of biological processes, such as compacting DNA and regulating access to the genetic code (which strongly affects DNA metabolism and possibly gene expression). (wikipedia.org)
Because the length of DNA can be thousands of times that of a cell, packaging this genetic material into the cell or nucleus (in eukaryotes) is a difficult feat. Supercoiling of DNA reduces the space and allows for DNA to be packaged. (wikipedia.org)
While the double-helical structure of duplex DNA is advantageous for the storage and maintenance of genetic information, it poses major challenges during essential cellular processes, such as transcription and replication, when the information-rich DNA bases must be accessed. (mpg.de)
Introduction DNA microarrays are powerful tools for analysing gene expression patterns, detecting DNA mutations, and identifying genetic variations. (tutorialspoint.com)
Introduction Bacterial Artificial Chromosome (BAC) is a powerful tool in Genetic Research Bacterial Artificial Chromosome (BAC) is a widely used tool in genetic research for the manipulation and study of DNA. (tutorialspoint.com)
We start with DNA, the genetic information in every cell that is copied and passed from generation to generation. (rainis.pics)
DNA was discovered by Friedrich Miescher in 1869 and identified as genetic material in experiments conducted by Oswald Avery, Colin MacLeod, and Maclyn McCarty in the 1940s. (rainis.pics)
This sort of factors could be crucial in governing the steady-state superhelical occurrence involving Genetic domain names within the cell.Trial and error findings of the angular distribution regarding tiny droplets during lazer ablation along with deposition regarding 's skinny movies tend to be introduced along with discussed. (wee1-receptor.com)

When a mixture of superhelical DNA (RFI) of phage phiX174 am3 and fragments of single-stranded DNA from wild-type phiX174 was added to spheroplasts of E. coli carrying an amber suppressor, several percent of the progeny phage were recombinant. (cornell.edu)
Surprisingly, these short single-stranded oligonucleotides (ODN) showed a similar gene correction frequency to chimeric RNA-DNA oligonucleotide, measured using the same system. (nih.gov)
Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. (embl.de)

Using a simple and rapid procedure we have reconstructed nucleohistone complexes from nucleoids and the 'core' histones without breaking the DNA. (ox.ac.uk)
The superhelical status of the DNA in the reconstructed complexes is indistinguishable from that found in control nucleoids containing core histones. (ox.ac.uk)
They consist of a dimer of dimers with two copies each of the histones H3, H4, H2A and H2B, that tightly bind and wrap DNA, while leaving long exposed tails available for post-translational modification that can carry epigenetic information. (mpg.de)
Due to the highly basic charge of all four core histones, the histone octamer is only stable in the presence of DNA or very high salt concentrations. (wikidoc.org)

Reconstruction of complexes of histone and superhelical nuclear DNA. (ox.ac.uk)
We have probed the integrity and structure of the reconstructed complexes using a non-destructive fluorometric approach, which provides a general method for detecting agents that bind to DNA and alter its supercoiling. (ox.ac.uk)
This partial requirement for recA was bypassed by transfection with complexes of RFI AM3 DNA and am+ fragments made in vitro. (cornell.edu)
2019). In these studies we showed that TFAM/DNA complexes multimerize at higher concentrations. (csic.es)

The noun form "supercoil" is often used when describing DNA topology. (wikipedia.org)
We also believe that FACT may be involved in the protection of our genome from DNA damage through the control of DNA topology. (roswellpark.org)
Topology and formation of triple-stranded H-DNA. (wikidata.org)
The amount of each class of topology enables a quantitative response to be determined for both types of radiation (alpha, X). A value of the radiosensitivity of DNA was obtained as a function of the scavenger concentration. (ox.ac.uk)

We will discuss the mechanism of DNA supercoiling and the role of superhelical stress in DNA structure and function. (tutorialspoint.com)
2017). This protein also bears two HMG-boxes but the mechanism of binding is from one side of the DNA, as a staple. (csic.es)
Localization of a gene in the nucleus often plays an important role in its expression and this phenomenon may also have a curved DNA-dependent mechanism. (soken.ac.jp)
Brown, P.O., Cozzarelli, N.R. A sign inversion mechanism for enzymatic supercoiling of DNA. (biomedicineonline.org)
Molecular modeling and computational analyses suggests that the Sinorhizobium meliloti periplasmic regulator protein ExoR adopts a superhelical fold and is controlled by a unique mechanism of proteolysis. (cuny.edu)

ATP-dependent breakage, passage and rejoining of double-stranded DNA. (cathdb.info)

DNA supercoiling is important for DNA packaging within all cells, and seems to also play a role in gene expression. (wikipedia.org)
Purification, cDNA cloning, and gene mapping of the small subunit of human DNA polymerase epsilon. (nih.gov)
Gene duplication occurs through several mechanisms, including chromosomal duplication, retro transposition, and DNA replication errors. (tutorialspoint.com)
Earliest, gene regulatory healthy protein known as transcriptional activators join to particular sequences inside DNA which help to attract RNA polymerase II for the start point away from transcription (Contour six-19). (elsafwany.com)
this both compacts DNA and creates an added layer of regulatory control which ensures correct gene expression. (wikidoc.org)
However, whether the curved DNA segment can affect localization of a reporter gene is an open question. (soken.ac.jp)

A histone chaperone protein that plays a role in the deposition of NUCLEOSOMES on newly synthesized DNA. (lookformedical.com)
[7] Non-condensed nucleosomes without the linker histone resemble "beads on a string of DNA" under an electron microscope . (wikidoc.org)
Adjacent nucleosomes are joined by a stretch of free DNA termed "linker DNA" which varies from 10 - 80 bp in length depending on species and tissue type [10] ). (wikidoc.org)

In contrast to most eukaryotic cells mature sperm cells largely use protamines to package their genomic DNA, most likely to achieve an even higher packaging ratio. (wikidoc.org)

The new design to own transcription initiation just discussed was depending by the discovering the experience regarding RNA polymerase II and its own standard transcription situations to the refined DNA themes for the vitro. (elsafwany.com)
Because of this, transcription initiation within the an effective eucaryotic telephone is far more complex and needs a whole lot more healthy protein than it does towards the filtered DNA. (elsafwany.com)
Here we simply remember that the visibility into DNA becomes necessary for transcription initiation into the an effective eucaryotic phone. (elsafwany.com)
Thus, promoters with this kind of curved DNA can adopt a more open structure, facilitating transcription initiation. (soken.ac.jp)

To ensure genome integrity, this sophisticated molecular machine must coordinate events over a broad range of time and length scales, from the breaking and reformation of chemical bonds within DNA polymerases to the large-scale structural rearrangements of chromosomes. (mpg.de)
Structural polymorphism of homopurine--homopyrimidine sequences: the secondary DNA structure adopted by a d(GA.CT)22 sequence in the presence of zinc ions. (wikidata.org)
Recent studies have shown that DNA structural properties, such as curvature, stacking energy, and stress-induced duplex destabilization (SIDD) are useful in promoter prediction, as well. (biomedcentral.com)

DNA supercoiling refers to the amount of twist in a particular DNA strand, which determines the amount of strain on it. (wikipedia.org)
Certain enzymes, such as topoisomerases, change the amount of DNA supercoiling to facilitate functions such as DNA replication and transcription. (wikipedia.org)
The amount of supercoiling in a given strand is described by a mathematical formula that compares it to a reference state known as "relaxed B-form" DNA. (wikipedia.org)
DNA supercoiling is important for DNA packaging within all cells. (wikipedia.org)
Supercoiling is an essential process that occurs in all living organisms and is critical for a variety of cellular processes, including DNA replication, transcription, and repair. (tutorialspoint.com)
Negative supercoiling of bacterial DNA by DNA gyr B is essential in replication which further influences all the metabolic activities. (biomedicineonline.org)

Just like the demonstrated into the Chapter 7, these necessary protein join to certain brief sequences into the DNA. (elsafwany.com)
Indeed, these additional necessary protein assemblies get get in touch with one another away from the DNA and start to become brought to DNA as preformed subcomplexes. (elsafwany.com)
The replication terminator protein of E. coli is a DNA sequence-specific contra-helicase. (wikidata.org)
Direct protein - DNA interactions are not spread evenly about the octamer surface but rather located at discrete sites. (wikidoc.org)
The body module serves as a scaffold for the four flexible modules that we call DNA-interacting, ATPase, arm and actin-related protein (ARP) modules. (mbexc.de)
The SAD1/RAD53 protein kinase controls multiple checkpoints and DNA damage-induced transcription in yeast. (academicinfluence.com)

Resolution of superhelical tension is critical to ensure replication fork progression and avoid chromosome damage. (mpg.de)
To date, studies of this important problem have been focused on topoisomerases, which are a specialized class of enzymes that can resolve superhelical tension. (mpg.de)

The DNA of most organisms is usually negatively supercoiled. (wikipedia.org)

These types of circumstances typically connect with RNA polymerase just after initiation possess happened that assist polymerases to move from wide selection of other DNA sequences which can be included in genetics. (elsafwany.com)

Investigation of radiation damage in DNA by using atomic force microscopy. (ox.ac.uk)

Nuclease treatment of the cell lysate to remove the covalently linked DNA from TOP1 revealed a distinct ladder of higher molecular weight bands having properties indicative of multi-ubiquitin (Ub) conjugates of TOP1. (tmu.edu.tw)

Wang, J.C. Cellular roles of DNA topoisomerases: a molecular perspective. (biomedicineonline.org)

The number of superhelical turns, τ, present in I is calculated at each dye concentration using Fuller and Waring's (1964) estimate of the angle of duplex unwinding per intercalation. (caltech.edu)

Polymerases must travel on a helical path during successive rounds of nucleotide incorporation to generate a helical, double-stranded DNA product. (mpg.de)
The Y-family of DNA polymerases. (academicinfluence.com)

Two apparently homologous TFAM binding sites, DNA Site-X and Site-Y, similar to and downstream from LSP, unexpectedly show distinct DNA-structure features and TFAM binds to them in opposite directions, imposing again a U-turn (Cuppari el al. (csic.es)
The DNA-interacting module binds extra-nucleosomal DNA and is involved in the recognition of promoter DNA elements that influence RSC functionality. (mbexc.de)

The race to unravel the structure of DNA was one of the greatest scientific stories of the 20th century. (rainis.pics)
Today, every biology student knows about the double helix structure of DNA and how G pairs with C and A pairs with T. (rainis.pics)

Transfection of a recA- strain by RFI DNA and fragments yielded 5-10% as many recombinants as transfection of a rec+ strain. (cornell.edu)

In the yeast Saccharomyces cerevisiae, the essential SWI/SNF complex RSC contains 16 subunits, including the ATP-dependent DNA translocase Sth1. (mbexc.de)

Mutations/polymorphisms in the 55 kDa subunit of DNA polymerase epsilon in human colorectal cancer. (nih.gov)

If a DNA segment under twist strain is closed into a circle by joining its two ends, and then allowed to move freely, it takes on different shape, such as a figure-eight. (wikipedia.org)
This strain is known as superhelical stress. (tutorialspoint.com)

These results show that a relatively short ODN can make a sequence-specific change in the target sequence in mammalian cells, at a similar frequency as the chimeric RNA-DNA oligonucleotide. (nih.gov)
When CPT-treated cells were lysed with either SDS or alkali and analyzed by Western blotting, greater than 90% of the TOP1 was linked to DNA. (tmu.edu.tw)
These results demonstrate that independent of DNA replication, the TOP1 clearable complex is ubiquitinated and destroyed in cells treated with antitumor drugs that block the religation step of the TOP1 reaction. (tmu.edu.tw)

Alternatively, DNA at different scavenger concentrations was initially exposed to different types of radiations (alpha and X rays) at various doses. (ox.ac.uk)

The view is from the top through the superhelical axis. (wikidoc.org)

Anatomy1

Organisms3

Chemicals and Drugs21

Analytical, Diagnostic and Therapeutic Techniques and Equipment3

Phenomena and Processes10

Information Science1

Replication-dependent marking of DNA by PCNA facilitates CAF-1-coupled inheritance of chromatin. (1/1746)

Mutants of Tn3 resolvase which do not require accessory binding sites for recombination activity. (2/1746)

Inhibition of DNA supercoiling-dependent transcriptional activation by a distant B-DNA to Z-DNA transition. (3/1746)

Specific binding of high-mobility-group I (HMGI) protein and histone H1 to the upstream AT-rich region of the murine beta interferon promoter: HMGI protein acts as a potential antirepressor of the promoter. (4/1746)

Analysis of DNA cleavage by reverse gyrase from Sulfolobus shibatae B12. (5/1746)

Expression and characterization of a DNase I-Fc fusion enzyme. (6/1746)

Pokeweed antiviral protein cleaves double-stranded supercoiled DNA using the same active site required to depurinate rRNA. (7/1746)

Extracellular signal-regulated kinase activates topoisomerase IIalpha through a mechanism independent of phosphorylation. (8/1746)

DNA, Superhelical

Nucleic Acid Conformation

DNA, Circular

DNA Topoisomerases, Type I

Ethidium

Osmium Tetroxide

Plasmids

DNA, Viral

Simian virus 40

Electrophoresis, Agar Gel

Endonucleases

Deoxyribonucleases

Coliphages

Escherichia coli

Single-Strand Specific DNA and RNA Endonucleases

DNA

Nucleic Acid Denaturation

Carbodiimides

Deoxyribonucleoproteins

Polydeoxyribonucleotides

Bromosuccinimide

Histones

Osmolar Concentration

DNA, Single-Stranded

Base Sequence

Nucleosomes

DNA, Bacterial

Tyrothricin

Centrifugation, Density Gradient

Novobiocin

Nucleoproteins

Kinetics

Replication-dependent marking of DNA by PCNA facilitates CAF-1-coupled inheritance of chromatin. (1/1746)

Mutants of Tn3 resolvase which do not require accessory binding sites for recombination activity. (2/1746)

Inhibition of DNA supercoiling-dependent transcriptional activation by a distant B-DNA to Z-DNA transition. (3/1746)

Specific binding of high-mobility-group I (HMGI) protein and histone H1 to the upstream AT-rich region of the murine beta interferon promoter: HMGI protein acts as a potential antirepressor of the promoter. (4/1746)

Analysis of DNA cleavage by reverse gyrase from Sulfolobus shibatae B12. (5/1746)

Expression and characterization of a DNase I-Fc fusion enzyme. (6/1746)

Pokeweed antiviral protein cleaves double-stranded supercoiled DNA using the same active site required to depurinate rRNA. (7/1746)

Extracellular signal-regulated kinase activates topoisomerase IIalpha through a mechanism independent of phosphorylation. (8/1746)

DNA supercoil

Cruciform DNA

Triple-stranded DNA

Bacterial circadian rhythm

Superhelix

Ellipticine

SIDD

Transcription preinitiation complex

General transcription factor

Polydnavirus

Sarah Harris (scientist)

Reverse gyrase

Nucleic acid structure

DnaA

DNA mismatch repair

Histone-like nucleoid-structuring protein

Hin recombinase

DNA gyrase

Histone

Condensin

Origin of replication

Nucleosome

Difloxacin

Type I topoisomerase

Satellite DNA

Type II topoisomerase

T7 phage

List of MeSH codes (D13)

Roeland Nolte

HEAT repeat

Repair of strand breaks in superhelical dna of ataxia telangiectasia lymphoblastoid cells | Citedby Results | Journal of Cell...

Reconstruction of complexes of histone and superhelical nuclear DNA. - Oxford Neuroscience

Recombination promoted by superhelical DNA and the recA gene of Escherichia coli. | Microbiology and Immunology

DNA supercoil - Wikipedia

Targeted gene correction by small single-stranded oligonucleotides in mammalian cells

Research | Max Planck Institute of Biochemistry

Cryo-EM structure of SMG1-SMG8-SMG9 complex | Cell Research

Research publications | IRB Barcelona

CATH Domain 1bgwA05

POLE2 DNA polymerase epsilon 2, accessory subunit [Homo sapiens (human)] - Gene - NCBI