Specific recognition of AT-rich DNA sequences by the mammalian high mobility group protein AT-hook 2: a SELEX study

Biochemistry. 2007 Nov 13;46(45):13059-66. doi: 10.1021/bi701269s. Epub 2007 Oct 23.


The mammalian high mobility group protein AT-hook 2 (HMGA2) is a transcriptional factor involved in cell differentiation and transformation. Disruption of its normal expression pattern is directly linked to oncogenesis and obesity. HMGA2 contains three "AT-hook" DNA binding domains, which specifically bind to the minor groove of AT-rich sequences. Using a PCR-based systematic evolution of ligands by exponential enrichment (SELEX) procedure, we have identified two consensus sequences for HMGA2, 5'-ATATTCGCGAWWATT-3' and 5'-ATATTGCGCAWWATT-3', where W represents A or T. These two consensus sequences have a unique and interesting feature: the first five base pairs are AT-rich, the middle four base pairs are GC-rich, and the last six base pairs are AT-rich. Our results showed that all three of these segments are critical for high-affinity binding of HMGA2 to DNA. For example, if one of the AT-rich sequences is mutated to a non-AT-rich sequence, the DNA binding affinity of HMGA2 is reduced at least 100-fold. Intriguingly, if the GC-segment is replaced by an AT-rich segment, the binding affinity of HMGA2 is reduced approximately 5-fold. Identification of the consensus sequences for HMGA2 represents an important step toward finding its binding sites within the genome.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Consensus Sequence
  • Electrophoretic Mobility Shift Assay
  • HMGA2 Protein / chemistry*
  • Oligodeoxyribonucleotides / chemistry*
  • SELEX Aptamer Technique


  • HMGA2 Protein
  • Oligodeoxyribonucleotides