title: Sequence-universal recognition of duplex DNA by oligonucleotides via pseudocomplementarity and helix invasion.
abstract: The well-known Watson-Crick complementarity rules, which were discovered 50 years ago, elegantly direct the specific pairing of two DNA single strands. On the contrary, once formed, the double-stranded (ds) DNA lacks such a simple and sequence-universal recognition principle, since most of the characteristic chemical groups of nucleobases are now buried deep inside the double helix, the major DNA form. We report a promising versatile approach for highly selective recognition of designated sites within dsDNA featuring considerable practical potential for a variety of molecular-biological, biotechnological, gene-therapeutic, and diagnostic applications. It may also have implications for prebiotic evolution of genetic machinery at the primordial stages of the origin of life. Our design synergistically employs the robust helix-invasion ability of recently developed DNA mimics and analogs, pseudocomplementary peptide nucleic acids and pseudocomplementary oligonucleotides, thus enabling the sequence-unrestricted recognition of chosen DNA duplexes by nucleobase oligomers. Using this basically general approach, we selectively tagged a unique mixed-base site on the target dsDNA fragment with streptavidin and/or multiply labeled this site with fluorophores via the primer-extension reaction.
authors.affiliation: Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA.
authors.forename: Irina V
authors.initials: IV
authors.lastname: Smolina
authors.forename: Vadim V
authors.initials: VV
authors.lastname: Demidov
mesh_terms: D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D018076:DNA, Complementary / Q000187:drug effects / Q000378:metabolism; D024202:Electrophoretic Mobility Shift Assay; D018390:Gene Targeting; D006824:Hybridization, Genetic; D015345:Oligonucleotide Probes / Q000737:chemistry / Q000378:metabolism*; D011742:Pyrimidine Nucleotides / Q000737:chemistry; D019809:Streptavidin / Q000737:chemistry
chemical_list: D018076:DNA, Complementary; D015345:Oligonucleotide Probes; D011742:Pyrimidine Nucleotides; D004247:DNA; D019809:Streptavidin