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A distinct group of DNA-binding proteins are the DNA-binding proteins that specifically bind single-stranded DNA. In humans, replication protein A is the best-understood member of this family and is used in processes where the double helix is separated, including DNA replication, recombination and DNA repair. [18]
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. A DBD can recognize a specific DNA sequence (a recognition sequence ) or have a general affinity to DNA. [ 1 ]
The authors were able to show that the motif has DNA binding activity. A similar approach is commonly used by modern protein domain databases such as Pfam : human curators would select a pool of sequences known to be related and use computer programs to align them and produce the motif profile (Pfam uses HMMs , which can be used to identify ...
This motif is seen in transcription factors. Zinc finger Two beta strands with an alpha helix end folded over to bind a zinc ion. Important in DNA binding proteins. Helix-turn-helix Two α helices joined by a short strand of amino acids and found in many proteins that regulate gene expression. [12] Nest Extremely common.
All ETS (Erythroblast Transformation Specific) family members are identified through a highly conserved DNA binding domain, the ETS domain, which is a winged helix-turn-helix structure that binds to DNA sites with a central GGA(A/T) DNA sequence. As well as DNA-binding functions, evidence suggests that the ETS domain is also involved in protein ...
The second AT-hook of HMGA1 (black ribbon) bound to the minor-groove of AT-rich DNA. The amino-acid side chains and nucleotides have been hidden. The AT-hook is a DNA-binding motif present in many proteins, including the high mobility group (HMG) proteins, [1] DNA-binding proteins from plants [2] and hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF ...
Recent advances in chromatin immunoprecipitation followed by sequencing have provided powerful ways to identify genome-wide profiling of DNA-binding proteins and histone modifications. [1] [2] The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification sites.
DNA contacts of different types of DNA-binding domains. 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 (1) they are part of a DNA sequence (e.g. a genome) and (2) they are bound by DNA-binding proteins.