title: High-affinity DNA targeting using readily accessible mimics of N2'-functionalized 2'-amino-α-L-LNA.
abstract: N2'-Pyrene-functionalized 2'-amino-α-L-LNAs (locked nucleic acids) display extraordinary affinity toward complementary DNA targets due to favorable preorganization of the pyrene moieties for hybridization-induced intercalation. Unfortunately, the synthesis of these monomers is challenging (~20 steps, <3% overall yield), which has precluded full characterization of DNA-targeting applications based on these materials. Access to more readily accessible functional mimics would be highly desirable. Here we describe short synthetic routes to a series of O2'-intercalator-functionalized uridine and N2'-intercalator-functionalized 2'-N-methyl-2'-aminouridine monomers and demonstrate, via thermal denaturation, UV-vis absorption and fluorescence spectroscopy experiments, that several of them mimic the DNA-hybridization properties of N2'-pyrene-functionalized 2'-amino-α-L-LNAs. For example, oligodeoxyribonucleotides (ONs) modified with 2'-O-(coronen-1-yl)methyluridine monomer Z, 2'-O-(pyren-1-yl)methyluridine monomer Y, or 2'-N-(pyren-1-ylmethyl)-2'-N-methylaminouridine monomer Q display prominent increases in thermal affinity toward complementary DNA relative to reference strands (average ΔT(m)/mod up to +12 °C), pronounced DNA-selectivity, and higher target specificity than 2'-amino-α-L-LNA benchmark probes. In contrast, ONs modified with 2'-O-(2-napthyl)uridine monomer W, 2'-O-(pyren-1-yl)uridine monomer X or 2'-N-(pyren-1-ylcarbonyl)-2'-N-methylaminouridine monomer S display very low affinity toward DNA targets. This demonstrates that even conservative alterations in linker chemistry, linker length, and surface area of the appended intercalators have marked impact on DNA-hybridization characteristics. Straightforward access to high-affinity building blocks such as Q, Y, and Z is likely to accelerate their use in DNA-targeting applications within nucleic acid based diagnostics, therapeutics, and material science.
authors.affiliation: Department of Chemistry, University of Idaho, Moscow, Idaho 83844, USA.
authors.forename: Saswata
authors.initials: S
authors.lastname: Karmakar
authors.forename: Brooke A
authors.initials: BA
authors.lastname: Anderson
authors.forename: Rie L
authors.initials: RL
authors.lastname: Rathje
authors.forename: Sanne
authors.initials: S
authors.lastname: Andersen
authors.forename: Troels B
authors.initials: TB
authors.lastname: Jensen
authors.forename: Poul
authors.initials: P
authors.lastname: Nielsen
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Hrdlicka
mesh_terms: D032701:Biomimetics; D004247:DNA / Q000737:chemistry*; D016503:Drug Delivery Systems; D007364:Intercalating Agents / Q000737:chemistry; D015394:Molecular Structure; D009841:Oligonucleotides / Q000737:chemistry*
chemical_list: D007364:Intercalating Agents; D009841:Oligonucleotides; C477371:locked nucleic acid; D004247:DNA