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Regions of DNA capable of binding to biomolecules
DNA binding sites are a type of binding site found in DNA where other molecules may bind. DNA binding sites are distinct from other binding sites in that
DNA_binding_site
Proteins that bind with DNA
DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or double-stranded DNA. Sequence-specific
DNA-binding_protein
Protein that regulates the rate of DNA transcription
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 DNA sequences
Transcription_factor
Protein found in humans
Transactive response DNA binding protein 43 kDa (TAR DNA-binding protein 43 or TDP-43) is a protein that in humans is encoded by the TARDBP gene. TDP-43
TAR_DNA-binding_protein_43
Class of enzymes that divide DNA
is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzymes are
Restriction_enzyme
Class of proteins
two-subunit DNA polymerase, a helicase–primase complex and a single-stranded DNA-binding protein. The human herpesvirus 1 (HHV-1) single-strand DNA-binding protein
Single-stranded binding protein
Single-stranded_binding_protein
Process of copying a segment of DNA into RNA
about half of EGR1 binding sites are located in promoters and half in enhancers. The binding of EGR1 to its target DNA binding site is insensitive to cytosine
Transcription_(biology)
Molecule that carries genetic information
articles) DNA binding site prediction on protein DNA the Double Helix Game From the official Nobel Prize web site DNA under electron microscope Dolan DNA Learning
DNA
Sequence of nucleotides
A ribosome binding site, or ribosomal binding site (RBS), is a sequence of nucleotides upstream of the start codon of an mRNA transcript that is responsible
Ribosome-binding_site
Small structural protein motif found mostly in transcriptional proteins
to the CpG site. It is used in mammals for antiviral defense. Various protein engineering techniques can be used to alter the DNA-binding specificity
Zinc_finger
Enzyme that synthesizes RNA from DNA during Transcription
mediator complex must be attached to a DNA binding site called a promoter region before RNAP can initiate the DNA unwinding at that position. RNAP not only
RNA_polymerase
Self-stabilizing region of a protein that binds to specific DNA sequences
single-stranded DNA. A DBD can recognize a specific DNA sequence (a recognition sequence) or have a general affinity to DNA. Some DNA-binding domains may
DNA-binding_domain
Method used to analyze protein interactions with DNA
interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated
ChIP_sequencing
Method used to analyze protein interactions with DNA
DNA sequencing to identify the binding sites of DNA-associated proteins. It can be used to map global DNA binding sites precisely for any protein of interest
CUT&RUN_sequencing
Basic structural unit of DNA packaging in eukaryotes
two types of DNA binding sites within the octamer; the α1α1 site, which uses the α1 helix from two adjacent histones, and the L1L2 site formed by the
Nucleosome
Region of DNA encouraging transcription
gene. Promoters contain specific DNA sequences such as response elements that provide a secure initial binding site for RNA polymerase and for proteins
Promoter_(genetics)
properties of DNA provide important constraints on the binding sites formed on surfaces of DNA-binding proteins. Characteristics of such binding sites may be
Protein–DNA interaction site predictor
Protein–DNA_interaction_site_predictor
Bioinformatic graphic
create sequence logos, related DNA, RNA or protein sequences, or DNA sequences that have common conserved binding sites, are aligned so that the most conserved
Sequence_logo
Set genes encoding proteins and enzymes for lactose metabolism
genes starts with the binding of the enzyme RNA polymerase (RNAP), a DNA-binding protein, which binds to a specific DNA binding site, the promoter, immediately
Lac_operon
Protein
DnaA binding to 9-mer (9-bp) repeats upstream of oriC. Binding of DnaA leads to strand separation at the 13-mer repeats. This binding causes the DNA to
DnaA
Bacterial DNA primase
noncovalent binding of DnaG to the DnaB helicase protein. The zinc-binding domain, the domain responsible for recognizing sequence specific DNA binding sites, is
DnaG
primer binding site is a region of a nucleotide sequence where an RNA or DNA single-stranded primer binds to start replication. The primer binding site is
Primer_binding_site
Lab technique
DNA adenine methyltransferase identification, often abbreviated DamID, is a molecular biology protocol used to map the binding sites of DNA- and chromatin-binding
DNA adenine methyltransferase identification
DNA_adenine_methyltransferase_identification
Protein that increases transcription of a gene or set of genes
to occur. Most activators are DNA-binding proteins that bind to enhancers or promoter-proximal elements. The DNA site bound by the activator is referred
Activator_(genetics)
Protein-coding gene in the species Homo sapiens
The TATA-binding protein (TBP) is a general transcription factor that binds to a DNA sequence called the TATA box. This DNA sequence is found about 30
TATA-binding_protein
Method used to analyze protein interactions with DNA
DNA sequencing to identify the binding sites of DNA-associated proteins. It can be used to map global DNA binding sites precisely for any protein of interest
CUT&Tag_sequencing
Region within a prokaryotic cell containing genetic material
than the number of specific binding sites in the genome. Therefore, it is reasoned that NAPs bind to the chromosomal DNA mostly in the non-sequence specific
Nucleoid
AP-1 binding site, also known as the AP-1 promoter site, is a DNA sequence to which AP-1 transcription factors are able to bind. The AP-1 binding site, in
AP-1_binding_site
Region of non-coding DNA that regulates the transcription of neighboring genes
target site that contain transcription factor binding sites. The original definition presented cis-regulatory modules as enhancers of cis-acting DNA, which
Cis-regulatory_element
Sequence in a genome
conserved DNA repeats that are specifically recognized by DnaA (called DnaA-boxes), an AT-rich DNA unwinding element (DUE), and binding sites for proteins
Origin_of_replication
Drugs acting on the estrogen receptor
some cofactors bind to ER through the terminals, the DNA-binding site or other binding sites. Thus, one compound can be an ER agonist in a tissue rich
Selective estrogen receptor modulator
Selective_estrogen_receptor_modulator
Bacteria use a variety of DNA-binding proteins, generally basic in pH. Since bacterial binding proteins have a diversity of functions, it has been difficult
Bacterial_DNA_binding_protein
Database of human and mouse transcription factor binding sites
transcription factors, their DNA binding site motifs, and motif subtypes. Transcription factors (TFs) are proteins that bind DNA and thus regulate the transcription
HOCOMOCO
Change in proteins expressed by bacteria
DNA-binding proteins and the presence or absence of DNA binding sites) and a site-specific recombinase. There is a change in orientation of the DNA that
Phase_variation
Restriction enzyme
N-terminal DNA-binding domain and a non sequence-specific DNA cleavage domain at the C-terminal. Once the protein is bound to duplex DNA via its DNA-binding domain
FokI
Initiation site for the opening of the DNA double helix
Eddy. The DNA unwinding allows for access of replication machinery to the newly single strands. In eukaryotes, DUEs are the binding site for DNA-unwinding
DNA_unwinding_element
Biological process
certain number of DnaA proteins are also required for DNA replication — each time the origin is copied, the number of binding sites for DnaA doubles, requiring
DNA_replication
Molecular biology technique
Selection and amplification binding assay (SAAB) is a molecular biology technique typically used to find the DNA binding site for proteins. It was developed
Selection and amplification binding assay
Selection_and_amplification_binding_assay
Class of enzymes
identify protein binding sites. When DNA polymerase makes an error resulting in a mismatched base-pair or a small insertion or deletion during DNA synthesis
DNA_adenine_methylase
Enzyme that repairs DNA damage
the other. Half of all progeny DNA derived from the mutated template inherit a shift from GC to AU at the mutation site. UDG excises uracil in both AU
Uracil-DNA_glycosylase
DNA structure
Triple-stranded DNA (also known as H-DNA or Triplex-DNA) is a DNA structure in which three oligonucleotides wind around each other and form a triple helix
Triple-stranded_DNA
DNA sequence
the TATA box in TATA-containing genes. The TATA box is the binding site of the TATA-binding protein (TBP) and other transcription factors in some eukaryotic
TATA_box
Male fertility gene in Drosophila
from Caf40, a DNA-binding protein. It differs by 107 amino acid substitutions. It retains approximately 30% of Caf40's DNA-binding sites but over the past
Zeus_(gene)
Protein family
molecular biology, origin recognition complex (ORC) is a multi-subunit DNA binding complex (6 subunits) that binds in all eukaryotes and archaea in an ATP-dependent
Origin_recognition_complex
Protein-coding gene in the species Homo sapiens
PMID 2028256. S2CID 38000717. Christy B, Nathans D (November 1989). "DNA binding site of the growth factor-inducible protein Zif268". Proceedings of the
EGR1
Chromodomain helicase DNA-binding (CHD) proteins is a subfamily of ATP-dependent chromatin remodeling complexes (remodelers). All remodelers fall under
Chromodomain helicase DNA-binding (CHD) subfamily
Chromodomain_helicase_DNA-binding_(CHD)_subfamily
DNA-binding protein
The lac repressor (LacI) is a DNA-binding protein that inhibits the expression of genes coding for proteins involved in the metabolism of lactose in bacteria
Lac_repressor
Regulatory protein in bacteria
a conformational change that allows CRP to bind tightly to a specific DNA site in the promoters of the genes it controls. CRP then activates transcription
CAMP_receptor_protein
Bacteriophage that infects Escherichia coli
ori site, and P protein binds the DnaB subunit of the host replication machinery as well as binding O. This effectively commandeers the host DNA polymerase
Lambda_phage
Protein domain
is found in many DNA binding eukaryotic proteins. One part of the domain contains a region that mediates sequence specific DNA binding properties and the
BZIP_domain
Substance that forms a complex with a biomolecule
protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein. The binding typically results
Ligand_(biochemistry)
Fluorescent dye used to stain DNA
Hoechst dyes cannot reach their optimal binding site. Binding of Hoechst dyes is even stronger to BrdU-substituted DNA; however, no fluorescence ensues. Hoechst
Hoechst_stain
protein bound to DNA often protects it from enzymatic cleavage. This makes it possible to locate a protein binding site on a particular DNA molecule. The
DNase_footprinting_assay
Segment of nucleic acid that affects the expression of associated genes
about half of EGR1 binding sites are located in promoters and half in enhancers. The binding of EGR1 to its target DNA binding site is insensitive to cytosine
Regulatory_sequence
Family of transcription factors
and synthesis of DNA in mammalian cells. E2Fs as TFs bind to the TTTCCCGC (or slight variations of this sequence) consensus binding site in the target promoter
E2F
Enzyme
by competitive inhibition of energy transduction of DNA gyrase by binding to the ATPase active site on the GyrB subunit. The quinolones (including nalidixic
DNA_gyrase
Molecular biology technique
DNA footprinting is a method of in vitro DNA analysis that assists researchers in determining transcription factor (TF) associated binding proteins. This
DNA_footprinting
One of many possible double helical structures of DNA
in the DNA. A Z-DNA high affinity binding protein, hZαADAR1, was used at varying concentrations to induce the transformation from B-DNA to Z-DNA. The smFRET
Z-DNA
Sort of RNA-binding protein in molecular genetics
a DNA- or RNA-binding protein that inhibits the expression of one or more genes by binding to the operator or associated silencers. A DNA-binding repressor
Repressor
Protein that initiates male sex determination in therian mammals
Sex-determining region Y protein (SRY), or testis-determining factor (TDF), is a DNA-binding protein (also known as gene-regulatory protein/transcription factor)
Sex-determining region Y protein
Sex-determining_region_Y_protein
Molecule-specific coordinate bonding area in biological systems
molecular biology, a binding site is a region on a macromolecule such as a protein that binds to another molecule with specificity. The binding partner of the
Binding_site
Group of bacterial ferritin proteins that protect DNA against oxidative damage
DNA-binding proteins from starved cells (Dps) are bacterial proteins that belong to the ferritin superfamily and are characterized by strong similarities
DNA-binding protein from starved cells
DNA-binding_protein_from_starved_cells
DNA-binding protein involved in methylation
base pair 152,878,611. MECP2 is an important reader of DNA methylation. Its methyl-CpG-binding (MBD) domain recognizes and binds 5-mC regions. MECP2 is
MECP2
Bocaparvoviruses known to infect humans
motifs form the nucleoside triphosphate binding pocket, the metal ion coordination site, the DNA-binding site and the sensory element. These motifs are
Human_bocavirus
Method for identifying the sequence-specific target site of a DNA-binding domain
system is a method for identifying the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed
Bacterial_one-hybrid_system
DNA replication in eukaryotic organisms
many eukaryotic genomes with the difference being their diverged DNA binding sites. The most widely studied origin recognition complex is that of Saccharomyces
Eukaryotic_DNA_replication
Process in molecular biology
acceptor site affect splice site selection. Also, point mutations in the underlying DNA or errors during transcription can activate a cryptic splice site in
RNA_splicing
Class of enzymes
domain containing catalytic and cofactor binding sites, and a smaller DNA recognition domain. Highly conserved DNA methyltransferases of the m4C, m5C, and
DNA_methyltransferase
Oncogenic protein
euchromatin at EWS/FLI1 DNA-binding sites effectively generating de novo enhancers. The C-terminus of EWS/FLI1 retains the DNA-binding domain of FLI1. While
EWS/FLI
Protein-coding gene in the species Homo sapiens
mice. They bind the DNA via their winged-helix-turn-helix DNA binding motif known as the Ets domain that specifically recognizes DNA sequences that contain
ETS1
Restriction enzyme
changes upon DNA recognition. This allows the DNA to maintain its normal B-DNA conformation without distorting to facilitate enzyme binding. BamHI is a
BamHI
Molecular complex
(primase or DNA polymerase alpha) Ensuring processivity (clamp loading factors, ring-shaped clamp proteins, strand binding proteins) High-fidelity DNA replication
Replisome
Technology for screening small molecule compounds
the linkage of a small molecule to an identifier DNA code allows the facile identification of binding molecules. DELs are subjected to affinity selection
DNA-encoded_chemical_library
Nucleotide or amino-acid sequence pattern
sometimes the case. For example, many DNA binding proteins that have affinity for specific DNA binding sites bind DNA in only its double-helical form. They
Sequence_motif
Commonly used representation of patterns in biological sequences
MC (2009). "A reexamination of information theory-based methods for DNA-binding site identification". BMC Bioinformatics. 10: 57. doi:10.1186/1471-2105-10-57
Position_weight_matrix
The Ribose repressor (RbsR) is a bacterial DNA-binding transcription repressor protein and a member of the LacI/GalR protein family. This group of proteins
Ribose_repressor
Database of eukaryotic transcription factors
genomic binding sites and DNA binding profiles. The contents of the database can be used to predict potential transcription factor binding sites. The origin
TRANSFAC
DNA-binding structural motif
bZIP domain is 60 to 80 amino acids in length with a highly conserved DNA binding basic region and a more diversified leucine zipper dimerization region
Leucine_zipper
Most common variant of a genetic sequence across samples
sequence is a model for a putative DNA binding site: it is obtained by aligning all known examples of a certain recognition site and defined as the idealized
Consensus_sequence
To identify peptides binding a target
linked to an mRNA:cDNA which encodes it. The immobilized target is mixed with the library in a binding step, then those peptide-mRNA:cDNA fusions which do
MRNA_display
epigenetic modification at the site in question. The engineered proteins used for epigenome editing are composed of a DNA binding domain that targets specific
Epigenome_editing
Protein-coding gene in the species Homo sapiens
of a strand break. The BRCT domain is a phosphopeptide binding domain that is common among DNA repair proteins and is likely involved in coordinating
DNA_polymerase_lambda
Protein family
of two dimerization sites, a linker region that is unstructured and a C-terminal domain (CTD) that is responsible for DNA-binding. Though it is a small
Histone-like nucleoid-structuring protein
Histone-like_nucleoid-structuring_protein
Method of DNA sequencing
method led to the Methylation Interference Assay, used to map DNA-binding sites for DNA-binding proteins. An automated Maxam–Gilbert sequencing protocol was
Maxam–Gilbert_sequencing
Biomolecules capable of binding to DNA by unwinding the Double Helix
DNA-binding metallo-intercalators are positively charged, planar, polycyclic, aromatic compounds that unwind the DNA double helix and insert themselves
DNA-binding metallo-intercalators
DNA-binding_metallo-intercalators
Mechanism in molecular recognition
the binding site. The mechanism of conformational proofreading is utilized in the system of homologous recombination to discern between similar DNA sequences
Conformational_proofreading
Description of the structure and function of a genome
regions in DNA, which was achieved thanks to the appearance of methods to analyze transcription factor binding sites, DNA methylation sites, chromatin
DNA_annotation
Enzymes that catalyze DNA formation
the purine towards the minor groove. Relative to the shape of DNA polymerase's binding pocket, steric clashes occur between the purine and residues in
DNA_polymerase
End-to-end chemical orientation of a single strand of nucleic acid
along strands of nucleic acid, including genes and various protein binding sites, are usually noted as being either upstream (towards the 5′-end) or
Directionality (molecular biology)
Directionality_(molecular_biology)
Mammalian protein found in humans
factor by binding DNA as a tetramer, a structure that is essential for its stability and effective DNA binding activity. Once bound to DNA, p53 induces
P53
The DNA binding site, which contains the catalytic domain, is composed of two parts on either side of the cutting point. The half-binding sites can be
Meganuclease
Protein-coding gene in the species Homo sapiens
Methyl-CpG-binding domain protein 2 is a protein that in humans is encoded by the MBD2 gene. DNA methylation is the major modification of eukaryotic genomes
Methyl-CpG-binding domain protein 2
Methyl-CpG-binding_domain_protein_2
Transcription factor
average of about 55,000 DNA sites in 19 diverse cell types (12 normal and 7 immortal) and in total 77,811 distinct binding sites across all 19 cell types
CTCF
Type of genetic engineering
recombinase is an enzyme that removes DNA by homologous recombination between binding sequences known as Lox-P sites. The Flip-FRT system operates in a similar
Genome_editing
Control of DNA to RNA conversion in cells
about half of EGR1 binding sites are located in promoters and half in enhancers. The binding of EGR1 to its target DNA binding site is insensitive to cytosine
Transcriptional_regulation
Conversion of a gene's sequence into a mature gene product or products
binding sites around the coding region with the specific function of regulating transcription. There are many classes of regulatory DNA binding sites
Gene_expression
of three parts that flank the DNA sequence of interest. There is the flow cell binding sequence, the primer binding site, and also tagged barcoded regions
Adapter_(genetics)
Protein-coding gene in the species Drosophila melanogaster
of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site". Journal of Molecular Biology. 356 (5): 1137–1151. doi:10.1016/j.jmb
Homeotic_protein_bicoid
glucose concentrations. Upon arabinose binding to AraC, the N-terminal arm of AraC is released from its DNA binding domain via a “light switch” mechanism
PBAD_promoter
a bacterial DNA binding protein complex that facilitates genetic recombination, replication, and transcription by binding to specific DNA sequences and
Integration_host_factor
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