DNA-binding properties of ARID family proteins

Nucleic Acids Res. 2005 Jan 7;33(1):66-80. doi: 10.1093/nar/gki145. Print 2005.


The ARID (A-T Rich Interaction Domain) is a helix-turn-helix motif-based DNA-binding domain, conserved in all eukaryotes and diagnostic of a family that includes 15 distinct human proteins with important roles in development, tissue-specific gene expression and proliferation control. The 15 human ARID family proteins can be divided into seven subfamilies based on the degree of sequence identity between individual members. Most ARID family members have not been characterized with respect to their DNA-binding behavior, but it is already apparent that not all ARIDs conform to the pattern of binding AT-rich sequences. To understand better the divergent characteristics of the ARID proteins, we undertook a survey of DNA-binding properties across the entire ARID family. The results indicate that the majority of ARID subfamilies (i.e. five out of seven) bind DNA without obvious sequence preference. DNA-binding affinity also varies somewhat between subfamilies. Site-specific mutagenesis does not support suggestions made from structure analysis that specific amino acids in Loop 2 or Helix 5 are the main determinants of sequence specificity. Most probably, this is determined by multiple interacting differences across the entire ARID structure.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Amino Acids, Aromatic / genetics
  • Binding Sites
  • DNA / chemistry
  • DNA / metabolism*
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / classification
  • DNA-Binding Proteins / metabolism*
  • Drosophila Proteins / chemistry
  • Drosophila Proteins / genetics
  • Helix-Turn-Helix Motifs
  • Homeodomain Proteins / chemistry
  • Homeodomain Proteins / genetics
  • Humans
  • Molecular Sequence Data
  • Mutation
  • Nuclear Proteins / chemistry
  • Nuclear Proteins / genetics
  • Nucleic Acid Conformation
  • Protein Structure, Tertiary
  • Sequence Alignment
  • Transcription Factors / chemistry
  • Transcription Factors / genetics


  • ARID1A protein, human
  • Amino Acids, Aromatic
  • DNA-Binding Proteins
  • Drosophila Proteins
  • Homeodomain Proteins
  • Nuclear Proteins
  • Retn protein, Drosophila
  • Transcription Factors
  • DNA