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Methods Mol Biol. 2010;649:365-82. doi: 10.1007/978-1-60761-753-2_23.

Seeing genetic and epigenetic information without DNA denaturation using sequence-enabled reassembly (SEER).

Author information

1
Department of Chemistry, University of Arizona, Tucson, AZ, USA.

Abstract

Virtually all methods for reading the sequence of bases in DNA rely on the ability to denature double-stranded DNA into single strands and then use Watson-Crick base-pairing rules to hybridize the strands with high specificity to another DNA primer or probe. However, nature frequently uses an alternative method, reading the sequence information directly from double-stranded DNA using sequence-specific DNA-binding proteins. Here we describe methods for the construction and testing of sequence probes based on engineered zinc finger DNA-binding proteins. Background is reduced using split-reporter molecules, and signal is amplified using enzymatic reporters. The resulting sequence-enabled reassembly (SEER) probes can be configured to detect DNA sequence (genetic) or DNA methylation (epigenetic) information.

PMID:
20680847
DOI:
10.1007/978-1-60761-753-2_23
[Indexed for MEDLINE]

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