Signatures of Protein-DNA Recognition in Free DNA Binding Sites

Jason W. Locasale, Andrew A. Napoli, Shengfeng Chen, Helen M. Berman, Catherine L. Lawson

Research output: Contribution to journalArticlepeer-review

34 Scopus citations


One obstacle to achieving complete understanding of the principles underlying sequence-dependent recognition of DNA is the paucity of structural data for DNA recognition sequences in their free (unbound) state. Here, we carried out crystallization screening of 50 DNA duplexes containing cognate protein binding sites and obtained new crystal structures of free DNA binding sites for three distinct modes of DNA recognition: anti-parallel β strands (MetR), helix-turn-helix motif + hinge helices (PurR), and zinc fingers (Zif268). Structural changes between free and protein-bound DNA are manifested differently in each case. The new DNA structures reveal that distinctive sequence-dependent DNA geometry dominates recognition by MetR, protein-induced bending of DNA dictates recognition by PurR, and deformability of DNA along the A-B continuum is important in recognition by Zif268. Together, our findings show that crystal structures of free DNA binding sites provide new information about the nature of protein-DNA interactions and thus lend insights towards a structural code for DNA recognition.

Original languageEnglish (US)
Pages (from-to)1054-1065
Number of pages12
JournalJournal of molecular biology
Issue number4
StatePublished - Mar 6 2009

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology


  • DNA structure
  • gene regulation
  • indirect readout
  • protein-DNA interactions
  • transcription factors

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