Direct detection of double-stranded DNA: Molecular methods and applications for DNA diagnostics.
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.
Ghosh
Indraneel
I
Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA. ghosh@email.arizona.edu
Stains
Cliff I
CI
Ooi
Aik T
AT
Segal
David J
DJ
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
D003432:Cross-Linking Reagents; D004268:DNA-Binding Proteins; D015226:Dinucleoside Phosphates; D009757:Nylons; C051802:triplex DNA; C018309:guanylyl-(3'-5')-guanosine; D004247:DNA