| GOID Link to GO |
Functional Category | Description | Protein Count link to protein list |
|---|---|---|---|
| GO:0043565 | sequence-specific DNA binding | Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. | 490 |
| GO:0003697 | single-stranded DNA binding | Interacting selectively and non-covalently with single-stranded DNA. | 272 |
| GO:0003690 | double-stranded DNA binding | Interacting selectively and non-covalently with double-stranded DNA. | 181 |
| GO:0044212 | transcription regulatory region DNA binding | Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. | 143 |
| GO:0003684 | damaged DNA binding | Interacting selectively and non-covalently with damaged DNA. | 112 |
| GO:0003688 | DNA replication origin binding | Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally. | 83 |
| GO:0001046 | core promoter sequence-specific DNA binding | Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region composed of the transcription start site and binding sites for the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon. | 53 |
| GO:0008301 | DNA binding, bending | The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence. | 49 |
| GO:0000977 | RNA polymerase II regulatory region sequence-specific DNA binding | Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II. | 49 |
| GO:0000978 | RNA polymerase II core promoter proximal region sequence-specific DNA binding | Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II. | 38 |
| GO:0001047 | core promoter binding | Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. | 33 |
| GO:0031490 | chromatin DNA binding | Interacting selectively and non-covalently with DNA that is assembled into chromatin. | 29 |
| GO:0000182 | rDNA binding | Interacting selectively and non-covalently with DNA sequences encoding ribosomal RNA. | 22 |
| GO:0003680 | AT DNA binding | Interacting selectively and non-covalently with oligo(A) and oligo(T) tracts of DNA (AT DNA). | 21 |
| GO:0043566 | structure-specific DNA binding | Interacting selectively and non-covalently with DNA of a specific structure or configuration e.g. triplex DNA binding or bent DNA binding. | 21 |
| GO:0043047 | single-stranded telomeric DNA binding | Interacting selectively and non-covalently with single-stranded telomere-associated DNA. | 19 |
| GO:0031492 | nucleosomal DNA binding | Interacting selectively and non-covalently with the DNA portion of a nucleosome. | 18 |
| GO:0019237 | centromeric DNA binding | Interacting selectively and non-covalently with a centromere, a region of chromosome where the spindle fibers attach during mitosis and meiosis. | 17 |
| GO:0000405 | bubble DNA binding | Interacting selectively and non-covalently with DNA that contains a bubble. A bubble occurs when DNA contains a region of unpaired, single-stranded DNA flanked on both sides by regions of paired, double-stranded DNA. | 16 |
| GO:0001163 | RNA polymerase I regulatory region sequence-specific DNA binding | Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase I. | 16 |
| GO:0008327 | methyl-CpG binding | Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide. | 15 |
| GO:0003689 | DNA clamp loader activity | Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the opening of the ring structure of the PCNA complex, or any of the related sliding clamp complexes, and their closing around the DNA duplex. | 15 |
| GO:0001158 | enhancer sequence-specific DNA binding | Interacting selectively and non-covalently with a specific sequence of DNA that is part of an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter. | 13 |
| GO:0032137 | guanine/thymine mispair binding | Interacting selectively and non-covalently with double-stranded DNA containing a G/T mispair. | 10 |
| GO:0003691 | double-stranded telomeric DNA binding | Interacting selectively and non-covalently with double-stranded telomere-associated DNA. | 10 |
| GO:0010385 | double-stranded methylated DNA binding | Interacting selectively and non-covalently with double-stranded methylated DNA. Cytosine methylation in DNA is an important mechanism for establishing stable heritable epigenetic marks. | 10 |
| GO:0042162 | telomeric DNA binding | Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end. | 9 |
| GO:0000400 | four-way junction DNA binding | Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. | 9 |
| GO:0001016 | RNA polymerase III regulatory region DNA binding | Interacting selectively and non-covalently with a DNA region that controls the transcription of a gene by RNA polymerase III. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. | 7 |
| GO:0000987 | core promoter proximal region sequence-specific DNA binding | Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon. | 7 |
| GO:0032138 | single base insertion or deletion binding | Interacting selectively and non-covalently with double-stranded DNA containing a single base insertion or deletion. | 7 |
| GO:0000976 | transcription regulatory region sequence-specific DNA binding | Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon. | 6 |
| GO:0001044 | mitochondrial RNA polymerase regulatory region sequence-specific DNA binding | Interacting selectively and non-covalently with a specific sequence of DNA that controls the transcription of a region of DNA by mitochondrial RNA polymerase. | 6 |
| GO:0003681 | bent DNA binding | Interacting selectively and non-covalently with DNA in a bent conformation. | 6 |
| GO:0000401 | open form four-way junction DNA binding | Interacting selectively and non-covalently with DNA containing the open form of a four-way junction, also known as a Holliday junction, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. The open form of a four-way junction can be diagrammed without any of the strands crossing over. | 4 |
| GO:0030983 | mismatched DNA binding | Interacting selectively and non-covalently with double-stranded DNA containing one or more mismatches. | 4 |
| GO:0000402 | crossed form four-way junction DNA binding | Interacting selectively and non-covalently with DNA containing the crossed form of a four-way junction, also known as a Holliday junction, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. The crossed form of a four-way junction cannot be diagrammed without any of the strands crossing over, and instead contains a single crossover between two of the strands. | 4 |
| GO:0000217 | DNA secondary structure binding | Interacting selectively and non-covalently with DNA containing secondary structure elements such as four-way junctions, bubbles, loops, Y-form DNA, or double-strand/single-strand junctions. | 3 |
| GO:0000404 | loop DNA binding | Interacting selectively and non-covalently with DNA containing a loop. A loop occurs when DNA contains a large insertion or deletion that causes a region of unpaired single-stranded DNA to loop out, while the rest of the DNA is in a paired double-stranded configuration. | 3 |
| GO:0000979 | RNA polymerase II core promoter sequence-specific DNA binding | Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery. | 3 |
| GO:0001162 | RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding | Interacting selectively and non-covalently with an RNA polymerase II intronic DNA sequence that regulates the transcription of the transcript it is contained within. | 2 |
| GO:0000403 | Y-form DNA binding | Interacting selectively and non-covalently with segment of DNA shaped like a Y. This shape occurs when DNA contains a region of paired double-stranded DNA on one end and a region of unpaired DNA strands on the opposite end. | 2 |
| GO:0032357 | oxidized purine DNA binding | Interacting selectively and non-covalently with oxidized purine residues in DNA. | 2 |
| GO:0001031 | RNA polymerase III type 2 promoter DNA binding | Interacting selectively and non-covalently with a region of DNA that is a part of a type 2 promoter that controls transcription by RNA polymerase III. Type 2 promoters consist of an A box and a B box downstream of the transcription start site within the sequence within the sequence of the mature RNA. Type 2 promoters are found in many tRNA genes as well as in other small RNAs. | 2 |
| GO:0001032 | RNA polymerase III type 3 promoter DNA binding | Interacting selectively and non-covalently with a region of DNA that is a part of a type 3 promoter that controls transcription by RNA polymerase III. A type 3 Pol III promoter is composed of elements upstream of the transcription start site, including a TATA box. The human U6 snRNA gene has a type 3 promoter. Type 3 Pol III promoters have not been observed in S. cerevisiae. | 2 |
| GO:0032143 | single thymine insertion binding | Interacting selectively and non-covalently with double-stranded DNA containing a single thymine insertion or a deletion that results in an unpaired thymine. | 2 |
| GO:0032181 | dinucleotide repeat insertion binding | Interacting selectively and non-covalently with double-stranded DNA containing a dinucleotide repeat insertion or a deletion resulting in unpaired dinucleotide repeats. | 2 |
| GO:0001012 | RNA polymerase II regulatory region DNA binding | Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by RNA polymerase II. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. | 2 |
| GO:0001030 | RNA polymerase III type 1 promoter DNA binding | Interacting selectively and non-covalently with a region of DNA that is a part of a type 1 promoter that controls transcription by RNA polymerase III. Type 1 promoters are found in 5S rRNA genes, downstream of the transcription start site within the sequence of the mature RNA, and require TFIIIA for recognition. | 2 |
| GO:0000406 | double-strand/single-strand DNA junction binding | Interacting selectively and non-covalently with a region of DNA that contains double-stranded DNA flanked by a region of single-stranded DNA. | 2 |
| GO:0000975 | regulatory region DNA binding | Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair. | 2 |
| GO:0051880 | G-quadruplex DNA binding | Interacting selectively and non-covalently with G-quadruplex DNA structures, in which groups of four guanines adopt a flat, cyclic Hoogsteen hydrogen-bonding arrangement known as a guanine tetrad. The stacking of guanine tetrads results in G-quadruplex DNA structures. G-quadruplex DNA can form under physiological conditions from some G-rich sequences, such as those found in telomeres, immunoglobulin switch regions, gene promoters, fragile X repeats, and the dimerization domain in the human immunodeficiency virus (HIV) genome. | 2 |
| GO:0032142 | single guanine insertion binding | Interacting selectively and non-covalently with double-stranded DNA containing a single guanine insertion or a deletion that results in an unpaired guanine. | 2 |
| GO:0032131 | alkylated DNA binding | Interacting selectively and non-covalently with alkylated residues in DNA. | 1 |
| GO:0035326 | enhancer binding | Interacting selectively and non-covalently with an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter. | 1 |
| GO:0032135 | DNA insertion or deletion binding | Interacting selectively and non-covalently with double-stranded DNA containing insertions or deletions. | 1 |
| GO:0045322 | unmethylated CpG binding | Interacting selectively and non-covalently with unmethylated CpG motifs. Unmethylated CpG dinucleotides are often associated with gene promoters. | 1 |
| GO:0032139 | dinucleotide insertion or deletion binding | Interacting selectively and non-covalently with double-stranded DNA containing a dinucleotide insertion or deletion. | 1 |
| GO:0043035 | chromatin insulator sequence binding | Interacting selectively and non-covalently and stoichiometrically with a chromatin insulator sequence, a DNA sequence that prevents enhancer-mediated activation or repression of transcription. | 1 |
| GO:0080084 | 5S rDNA binding | Interacting selectively and non-covalently with the 5S rDNA sequence encoding ribosomal 5S rRNA, which is individually transcribed by RNA polymerase III, rather than by RNA polymerase I, in species where it exists. | 1 |