title: Invader probes: Harnessing the energy of intercalation to facilitate recognition of chromosomal DNA for diagnostic applications.
abstract: Development of probes capable of recognizing specific regions of chromosomal DNA has been a long-standing goal for chemical biologists. Current strategies such as PNA, triplex-forming oligonucleotides, and polyamides are subject to target choice limitations and/or necessitate non-physiological conditions, leaving a need for alternative approaches. Toward this end, we have recently introduced double-stranded oligonucleotide probes that are energetically activated for DNA recognition through modification with +1 interstrand zippers of intercalator-functionalized nucleotide monomers. Here, probes with different chemistries and architectures - varying in the position, number, and distance between the intercalator zippers - are studied with respect to hybridization energetics and DNA-targeting properties. Experiments with model DNA targets demonstrate that optimized probes enable efficient (C50< 1 μM), fast (t50< 3h), kinetically stable (> 24h), and single nucleotide specific recognition of DNA targets at physiologically relevant ionic strengths. Optimized probes were used in non-denaturing fluorescence in situ hybridization experiments for detection of gender-specific mixed-sequence chromosomal DNA target regions. These probes present themselves as a promising strategy for recognition of chromosomal DNA, which will enable development of new tools for applications in molecular biology, genomic engineering and nanotechnology.
authors.affiliation: Department of Chemistry, University of Idaho, 875 Perimeter Dr, Moscow, ID 83844-2343, USA.
authors.forename: Dale C
authors.initials: DC
authors.lastname: Guenther
authors.affiliation: Department of Chemistry, University of Idaho, 875 Perimeter Dr, Moscow, ID 83844-2343, USA ; Department of Biological Sciences, Montana Tech of the University of Montana, 1300 W Park St, Butte, MT 59701-8997, USA.
authors.forename: Grace H
authors.initials: GH
authors.lastname: Anderson
authors.affiliation: Department of Chemistry, University of Idaho, 875 Perimeter Dr, Moscow, ID 83844-2343, USA.
authors.forename: Saswata
authors.initials: S
authors.lastname: Karmakar
authors.affiliation: Department of Chemistry, University of Idaho, 875 Perimeter Dr, Moscow, ID 83844-2343, USA.
authors.forename: Brooke A
authors.initials: BA
authors.lastname: Anderson
authors.affiliation: MoFA, PO Box 930187, 419 Venture Ct., Verona, WI 53593, USA.
authors.forename: Bradley A
authors.initials: BA
authors.lastname: Didion
authors.affiliation: MoFA, PO Box 930187, 419 Venture Ct., Verona, WI 53593, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Guo
authors.affiliation: MoFA, PO Box 930187, 419 Venture Ct., Verona, WI 53593, USA.
authors.forename: John P
authors.initials: JP
authors.lastname: Verstegen
authors.affiliation: Department of Chemistry, University of Idaho, 875 Perimeter Dr, Moscow, ID 83844-2343, USA.
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Hrdlicka