title: Identification and characterization of second-generation invader locked nucleic acids (LNAs) for mixed-sequence recognition of double-stranded DNA.
abstract: The development of synthetic agents that recognize double-stranded DNA (dsDNA) is a long-standing goal that is inspired by the promise for tools that detect, regulate, and modify genes. Progress has been made with triplex-forming oligonucleotides, peptide nucleic acids, and polyamides, but substantial efforts are currently devoted to the development of alternative strategies that overcome the limitations observed with the classic approaches. In 2005, we introduced Invader locked nucleic acids (LNAs), i.e., double-stranded probes that are activated for mixed-sequence recognition of dsDNA through modification with "+1 interstrand zippers" of 2'-N-(pyren-1-yl)methyl-2'-amino-α-l-LNA monomers. Despite promising preliminary results, progress has been slow because of the synthetic complexity of the building blocks. Here we describe a study that led to the identification of two simpler classes of Invader monomers. We compare the thermal denaturation characteristics of double-stranded probes featuring different interstrand zippers of pyrene-functionalized monomers based on 2'-amino-α-l-LNA, 2'-N-methyl-2'-amino-DNA, and RNA scaffolds. Insights from fluorescence spectroscopy, molecular modeling, and NMR spectroscopy are used to elucidate the structural factors that govern probe activation. We demonstrate that probes with +1 zippers of 2'-O-(pyren-1-yl)methyl-RNA or 2'-N-methyl-2'-N-(pyren-1-yl)methyl-2'-amino-DNA monomers recognize DNA hairpins with similar efficiency as original Invader LNAs. Access to synthetically simple monomers will accelerate the use of Invader-mediated dsDNA recognition for applications in molecular biology and nucleic acid diagnostics.
authors.affiliation: Department of Chemistry, University of Idaho , Moscow, Idaho 83844, United States.
authors.forename: Sujay P
authors.initials: SP
authors.lastname: Sau
authors.forename: Andreas S
authors.initials: AS
authors.lastname: Madsen
authors.forename: Peter
authors.initials: P
authors.lastname: Podbevsek
authors.forename: Nicolai K
authors.initials: NK
authors.lastname: Andersen
authors.forename: T Santhosh
authors.initials: TS
authors.lastname: Kumar
authors.forename: Sanne
authors.initials: S
authors.lastname: Andersen
authors.forename: Rie L
authors.initials: RL
authors.lastname: Rathje
authors.forename: Brooke A
authors.initials: BA
authors.lastname: Anderson
authors.forename: Dale C
authors.initials: DC
authors.lastname: Guenther
authors.forename: Saswata
authors.initials: S
authors.lastname: Karmakar
authors.forename: Pawan
authors.initials: P
authors.lastname: Kumar
authors.forename: Janez
authors.initials: J
authors.lastname: Plavec
authors.forename: Jesper
authors.initials: J
authors.lastname: Wengel
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Hrdlicka
mesh_terms: D004247:DNA / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides; D011721:Pyrenes / Q000737:chemistry*; D013050:Spectrometry, Fluorescence; D013938:Thymidine Monophosphate / Q000031:analogs & derivatives* / Q000737:chemistry
chemical_list: C520121:7-(2-cyanoethoxy(diisopropylamino)phosphinoxy)-1-(4,4'-dimethoxytrityloxymethyl)-5-(9'-fluorenylmethoxycarbonyl)-3-(thymin-1-yl)-2-oxa-5-azabicyclo(2.2.1)heptane; D009841:Oligonucleotides; D011721:Pyrenes; C477371:locked nucleic acid; D013938:Thymidine Monophosphate; D004247:DNA; C030984:pyrene
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