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Updated: Jun 27, 2026

08:04
DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling
Published on: October 8, 2019
Early interrogation and recognition of DNA sequence by indirect readout.
Elizabeth J Little1, Andrea C Babic, Nancy C Horton
1Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA.
Structure (London, England : 1993)
|December 17, 2008
Summary
Proteins find specific DNA sequences through direct or indirect readout. A mutant HincII enzyme, lacking direct DNA contact, surprisingly retained sequence specificity, suggesting indirect readout plays a key role.
Area of Science:
- Molecular Biology
- Biochemistry
- Structural Biology
Background:
- Proteins must recognize specific DNA sequences amidst vast non-specific DNA.
- DNA sequence recognition involves direct readout (base contacts) and indirect readout mechanisms.
Purpose of the Study:
- To investigate the roles of direct and indirect readout in sequence-specific DNA binding.
- To characterize a mutant HincII endonuclease lacking direct DNA contacts.
Main Methods:
- Enzyme characterization of a mutant HincII.
- Three-dimensional crystal structure determination of the mutant enzyme bound to DNA.
Main Results:
- The mutant HincII enzyme, deficient in direct DNA contacts, retained high sequence specificity.
- Crystal structure revealed a loss of most direct readout interactions.
- The structure suggests a mechanism relying heavily on indirect readout for initial site selection.
Conclusions:
- Indirect readout is crucial for sequence-specific DNA recognition by endonucleases like HincII.
- Mutant enzyme structures may capture early stages of DNA target site recognition.
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