title: Direct detection of double-stranded DNA: Molecular methods and applications for DNA diagnostics.
abstract: Methodologies to detect DNA sequences with high sensitivity and specificity have tremendous potential as molecular diagnostic agents. Most current methods exploit the ability of single-stranded DNA (ssDNA) to base pair with high specificity to a complementary molecule. However, recent advances in robust techniques for recognition of DNA in the major and minor groove have made possible the direct detection of double-stranded DNA (dsDNA), without the need for denaturation, renaturation, or hybridization. This review will describe the progress in adapting polyamides, triplex DNA, and engineered zinc finger DNA-binding proteins as dsDNA diagnostic systems. In particular, the sequence-enabled reassembly (SEER) method, involving the use of custom zinc finger proteins, offers the potential for direct detection of dsDNA in cells, with implications for cell-based diagnostics and therapeutics.
authors.affiliation: Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA. ghosh@email.arizona.edu
authors.forename: Indraneel
authors.initials: I
authors.lastname: Ghosh
authors.forename: Cliff I
authors.initials: CI
authors.lastname: Stains
authors.forename: Aik T
authors.initials: AT
authors.lastname: Ooi
authors.forename: David J
authors.initials: DJ
authors.lastname: Segal
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D020029:Base Pairing; D003432:Cross-Linking Reagents; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics; D015226:Dinucleoside Phosphates; D006801:Humans; D008969:Molecular Sequence Data; D009757:Nylons / Q000737:chemistry*; D015202:Protein Engineering / Q000379:methods*; D017434:Protein Structure, Tertiary; D013329:Structure-Activity Relationship; D016335:Zinc Fingers
chemical_list: D003432:Cross-Linking Reagents; D004268:DNA-Binding Proteins; D015226:Dinucleoside Phosphates; D009757:Nylons; C051802:triplex DNA; C018309:guanylyl-(3'-5')-guanosine; D004247:DNA