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Updated: Jun 10, 2026
08:53
Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
Published on: May 2, 2025
Seeing genetic and epigenetic information without DNA denaturation using sequence-enabled reassembly (SEER).
Jason R Porter1, Sarah H Lockwood, David J Segal
1Department of Chemistry, University of Arizona, Tucson, AZ, USA.
Methods in Molecular Biology (Clifton, N.J.)
|August 4, 2010
Summary
Researchers developed novel sequence-enabled reassembly (SEER) probes using engineered zinc finger proteins. These probes detect genetic and epigenetic DNA information directly from double-stranded DNA, offering an alternative to traditional sequencing methods.
Area of Science:
- Molecular Biology
- Biotechnology
- Genomics
Background:
- Traditional DNA sequencing requires denaturation of double-stranded DNA into single strands.
- Nature utilizes sequence-specific DNA-binding proteins to read information directly from double-stranded DNA.
- Existing methods lack the ability to directly interrogate double-stranded DNA sequence information.
Purpose of the Study:
- To develop novel DNA probes capable of detecting sequence information directly from double-stranded DNA.
- To engineer sequence-specific DNA-binding proteins for use as molecular probes.
- To create a method for detecting both genetic and epigenetic DNA information.
Main Methods:
- Construction and testing of sequence probes utilizing engineered zinc finger DNA-binding proteins.
- Implementation of split-reporter molecules to reduce background noise.
- Utilization of enzymatic reporters for signal amplification.
- Development of sequence-enabled reassembly (SEER) probes.
Main Results:
- Engineered zinc finger protein-based probes were successfully constructed and tested.
- SEER probes demonstrated the ability to detect DNA sequence (genetic) information.
- SEER probes were configured to detect DNA methylation (epigenetic) information.
- Background noise was reduced and signal amplified using the described reporter systems.
Conclusions:
- SEER probes offer a novel method for reading DNA sequence information directly from double-stranded DNA.
- Engineered zinc finger proteins provide a versatile platform for developing sequence-specific DNA probes.
- This technology enables the detection of both genetic and epigenetic modifications.
- SEER probes present a promising alternative to traditional DNA sequencing and detection methods.
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