Early Interrogation and Recognition of DNA Sequence by Indirect Readout

Elizabeth J. Little, Andrea C. Babic, Nancy C. Horton

Research output: Contribution to journalArticlepeer-review

19 Scopus citations


Control of replication, transcription, recombination and repair requires proteins capable of finding particular DNA sequences in a background of a large excess of nonspecific sequences. Such recognition can involve direct readout, with direct contacts to the bases of DNA, or in some cases through the less well-characterized indirect readout mechanisms. In order to measure the relative contributions of direct and indirect readout by a sequence specific endonuclease, HincII, a mutant enzyme deficient in a direct contact, was characterized, and surprisingly showed no loss of sequence specificity. The three dimensional crystal structure shows the loss of most of the direct readout contacts to the DNA, possibly capturing an early stage in target site recognition using predominately indirect readout to prescreen sites before full sequence interrogation.

Original languageEnglish (US)
Pages (from-to)1828-1837
Number of pages10
Issue number12
StatePublished - Dec 12 2008


  • DNA

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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