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DNA-binding domain

Index DNA-binding domain

A DNA-binding domain (DBD) is an independently folded protein domain that contains at least one structural motif that recognizes double- or single-stranded DNA. [1]

69 relations: Alpha helix, Arabidopsis thaliana, B3 domain, Basic helix-loop-helix, Beta sheet, Biomolecular structure, BZIP domain, Caenorhabditis elegans, Calorimetry, Candida albicans, Chromatin, Cold shock response, Comparison of nucleic acid simulation software, CRISPR, Critical Reviews in Biochemistry and Molecular Biology, Cross-link, Deoxyribonuclease I, DNA, DNA footprinting, DNA methylation, DNA repair, DNA replication, DNA-binding protein, Drosophila melanogaster, Electron paramagnetic resonance, Enzyme, Gel electrophoresis, Genetic recombination, Helix-turn-helix, HMG-box, Homeobox, Hydrogen bond, Immunoglobulin domain, Leucine, Leucine zipper, Microscale thermophoresis, Molecular geometry, Molecular recognition, Mutation, Nuclear magnetic resonance, Nucleic acid sequence, Oligonucleotide, Oligosaccharide, PROSITE, Protein, Protein domain, Protein structure, R.EcoRII, Recognition sequence, Regulation of gene expression, ..., Restriction enzyme, Saccharomyces cerevisiae, Signal transduction, Single-stranded binding protein, Structural motif, Surface plasmon resonance, TAL effector, TALE-likes, Telomerase, Telomere, Transcription (biology), Transcription factor, Transcriptional regulation, Translation (biology), Ultracentrifuge, Vascular plant, Winged-helix transcription factors, X-ray crystallography, Zinc finger. Expand index (19 more) »

Alpha helix

The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a righthand-spiral conformation (i.e. helix) in which every backbone N−H group donates a hydrogen bond to the backbone C.

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Arabidopsis thaliana

Arabidopsis thaliana, the thale cress, mouse-ear cress or arabidopsis, is a small flowering plant native to Eurasia and Africa.

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B3 domain

The B3 DNA binding domain (DBD) is a highly conserved domain found exclusively in transcription factors, from higher plants (≥40 species) combined with other domains.

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Basic helix-loop-helix

A basic helix-loop-helix (bHLH) is a protein structural motif that characterizes one of the largest families of dimerizing transcription factors.

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Beta sheet

The β-sheet (also β-pleated sheet) is a common motif of regular secondary structure in proteins.

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Biomolecular structure

Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function.

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BZIP domain

The Basic Leucine Zipper Domain (bZIP domain) is found in many DNA binding eukaryotic proteins.

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Caenorhabditis elegans

Caenorhabditis elegans is a free-living (not parasitic), transparent nematode (roundworm), about 1 mm in length, that lives in temperate soil environments.

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Calorimetry is the science or act of measuring changes in state variables of a body for the purpose of deriving the heat transfer associated with changes of its state due, for example, to chemical reactions, physical changes, or phase transitions under specified constraints.

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Candida albicans

Candida albicans is an opportunistic pathogenic yeast that is a common member of the human gut flora.

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Chromatin is a complex of macromolecules found in cells, consisting of DNA, protein, and RNA.

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Cold shock response

Cold shock response is the physiological response of organisms to sudden cold, especially cold water.

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Comparison of nucleic acid simulation software

This is a list of computer programs that are used for nucleic acids simulations.

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CRISPR is a family of DNA sequences in bacteria and archaea.

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Critical Reviews in Biochemistry and Molecular Biology

Critical Reviews in Biochemistry and Molecular Biology is a bimonthly scientific journal that publishes comprehensive review articles in the areas of biochemistry and molecular biology.

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A cross-link is a bond that links one polymer chain to another.

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Deoxyribonuclease I

Deoxyribonuclease I (usually called DNase I), is an endonuclease coded by the human gene DNASE1.

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Deoxyribonucleic acid (DNA) is a thread-like chain of nucleotides carrying the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses.

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DNA footprinting

DNA footprinting is a method of investigating the sequence specificity of DNA-binding proteins in vitro.

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DNA methylation

DNA methylation is a process by which methyl groups are added to the DNA molecule.

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DNA repair

DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome.

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DNA replication

In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule.

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DNA-binding protein

DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or double-stranded DNA.

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Drosophila melanogaster

Drosophila melanogaster is a species of fly (the taxonomic order Diptera) in the family Drosophilidae.

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Electron paramagnetic resonance

Electron paramagnetic resonance (EPR) or electron spin resonance (ESR) spectroscopy is a method for studying materials with unpaired electrons.

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Enzymes are macromolecular biological catalysts.

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Gel electrophoresis

Gel electrophoresis is a method for separation and analysis of macromolecules (DNA, RNA and proteins) and their fragments, based on their size and charge.

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Genetic recombination

Genetic recombination (aka genetic reshuffling) is the production of offspring with combinations of traits that differ from those found in either parent.

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In proteins, the helix-turn-helix (HTH) is a major structural motif capable of binding DNA.

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In molecular biology, the HMG-box (high mobility group box) is a protein domain which is involved in DNA binding.

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A homeobox is a DNA sequence, around 180 base pairs long, found within genes that are involved in the regulation of patterns of anatomical development (morphogenesis) in animals, fungi and plants.

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Hydrogen bond

A hydrogen bond is a partially electrostatic attraction between a hydrogen (H) which is bound to a more electronegative atom such as nitrogen (N), oxygen (O), or fluorine (F), and another adjacent atom bearing a lone pair of electrons.

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Immunoglobulin domain

The immunoglobulin domain is a type of protein domain that consists of a 2-layer sandwich of 7-9 antiparallel β-strands arranged in two β-sheets with a Greek key topology, consisting of about 125 amino acids.

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Leucine (symbol Leu or L) is an essential amino acid that is used in the biosynthesis of proteins.

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Leucine zipper

A leucine zipper (or leucine scissors) is a common three-dimensional structural motif in proteins.

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Microscale thermophoresis

Microscale thermophoresis (MST) is a technology for the interaction analysis of biomolecules.

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Molecular geometry

Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule.

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Molecular recognition

The term molecular recognition refers to the specific interaction between two or more molecules through noncovalent bonding such as hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, π-π interactions, halogen bonding, electrostatic and/or electromagnetic effects.

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In biology, a mutation is the permanent alteration of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal DNA or other genetic elements.

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Nuclear magnetic resonance

Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a magnetic field absorb and re-emit electromagnetic radiation.

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Nucleic acid sequence

A nucleic acid sequence is a succession of letters that indicate the order of nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule.

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Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics.

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An oligosaccharide (from the Greek ὀλίγος olígos, "a few", and σάκχαρ sácchar, "sugar") is a saccharide polymer containing a small number (typically three to ten) of monosaccharides (simple sugars).

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PROSITE is a protein database.

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Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues.

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Protein domain

A protein domain is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain.

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Protein structure

Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule.

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Restriction endonuclease (REase) EcoRII (pronounced "eco R two") is an enzyme of restriction modification system (RM) naturally found in Escherichia coli, a Gram-negative bacteria.

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Recognition sequence

The recognition sequence, sometimes also referred to as recognition site, of any DNA-binding protein motif that exhibits binding specificity, refers to the DNA sequence (or subset thereof), to which the domain is specific.

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Regulation of gene expression

Regulation of gene expression includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA), and is informally termed gene regulation.

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Restriction enzyme

A restriction enzyme or restriction endonuclease is an enzyme that cleaves DNA into fragments at or near specific recognition sites within the molecule known as restriction sites.

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Saccharomyces cerevisiae

Saccharomyces cerevisiae is a species of yeast.

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Signal transduction

Signal transduction is the process by which a chemical or physical signal is transmitted through a cell as a series of molecular events, most commonly protein phosphorylation catalyzed by protein kinases, which ultimately results in a cellular response.

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Single-stranded binding protein

Single-stranded binding proteins (SSBs) are a class of proteins that have been identified in both viruses and organisms from bacteria to humans.

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Structural motif

In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a supersecondary structure, which also appears in a variety of other molecules.

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Surface plasmon resonance

Surface plasmon resonance (SPR) is the resonant oscillation of conduction electrons at the interface between negative and positive permittivity material stimulated by incident light.

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TAL effector

TAL (transcription activator-like) effectors (often referred to as TALEs, but not to be confused with the three amino acid loop extension homeobox class of proteins) are proteins secreted by Xanthomonas bacteria via their type III secretion system when they infect various plant species.

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Transcription Activator Like Effector Likes (TALE-likes) are a group of bacterial DNA binding proteins named for the first and still best studied group, the TALEs of Xanthomonas bacteria.

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Telomerase, also called terminal transferase, is a ribonucleoprotein that adds a species-dependent telomere repeat sequence to the 3' end of telomeres.

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A telomere is a region of repetitive nucleotide sequences at each end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes.

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Transcription (biology)

Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA (especially mRNA) by the enzyme RNA polymerase.

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Transcription factor

In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence.

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Transcriptional regulation

In molecular biology and genetics, transcriptional regulation is the means by which a cell regulates the conversion of DNA to RNA (transcription), thereby orchestrating gene activity.

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Translation (biology)

In molecular biology and genetics, translation is the process in which ribosomes in the cytoplasm or ER synthesize proteins after the process of transcription of DNA to RNA in the cell's nucleus.

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The ultracentrifuge is a centrifuge optimized for spinning a rotor at very high speeds, capable of generating acceleration as high as (approx.). There are two kinds of ultracentrifuges, the preparative and the analytical ultracentrifuge.

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Vascular plant

Vascular plants (from Latin vasculum: duct), also known as tracheophytes (from the equivalent Greek term trachea) and also higher plants, form a large group of plants (c. 308,312 accepted known species) that are defined as those land plants that have lignified tissues (the xylem) for conducting water and minerals throughout the plant.

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Winged-helix transcription factors

Consisting of about 110 amino acids, the domain in winged-helix transcription factors (see Regulation of gene expression) has four helices and a two-strand beta-sheet.

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X-ray crystallography

X-ray crystallography is a technique used for determining the atomic and molecular structure of a crystal, in which the crystalline atoms cause a beam of incident X-rays to diffract into many specific directions.

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Zinc finger

A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) in order to stabilize the fold.

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DNA binding domain, DNA-binding domains, Dna binding domain, Dna binding domains, Protein-DNA recognition, ProteinDNA recognition.


[1] https://en.wikipedia.org/wiki/DNA-binding_domain

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