title: C5-functionalized DNA, LNA, and α-L-LNA: positional control of polarity-sensitive fluorophores leads to improved SNP-typing.
abstract: Single nucleotide polymorphisms (SNPs) are important markers in disease genetics and pharmacogenomic studies. Oligodeoxyribonucleotides (ONs) modified with 5-[3-(1-pyrenecarboxamido)propynyl]-2'-deoxyuridine monomer X enable detection of SNPs at non-stringent conditions due to differential fluorescence emission of matched versus mismatched nucleic acid duplexes. Herein, the thermal denaturation and optical spectroscopic characteristics of monomer X are compared to the corresponding locked nucleic acid (LNA) and α-L-LNA monomers Y and Z. ONs modified with monomers Y or Z result in a) larger increases in fluorescence intensity upon hybridization to complementary DNA, b) formation of more brightly fluorescent duplexes due to markedly larger fluorescence emission quantum yields (Φ(F)=0.44-0.80) and pyrene extinction coefficients, and c) improved optical discrimination of SNPs in DNA targets. Optical spectroscopy studies suggest that the nucleobase moieties of monomers X-Z adopt anti and syn conformations upon hybridization with matched and mismatched targets, respectively. The polarity-sensitive 1-pyrenecarboxamido fluorophore is, thereby, either positioned in the polar major groove or in the hydrophobic duplex core close to quenching nucleobases. Calculations suggest that the bicyclic skeletons of LNA and α-L-LNA monomers Y and Z influence the glycosidic torsional angle profile leading to altered positional control and photophysical properties of the C5-fluorophore.
authors.affiliation: Department of Chemistry, University of Idaho, P.O. Box 442343, Moscow, ID 83844-2343, USA.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Østergaard
authors.forename: Pawan
authors.initials: P
authors.lastname: Kumar
authors.forename: Bharat
authors.initials: B
authors.lastname: Baral
authors.forename: Dale C
authors.initials: DC
authors.lastname: Guenther
authors.forename: Brooke A
authors.initials: BA
authors.lastname: Anderson
authors.forename: F Marty
authors.initials: FM
authors.lastname: Ytreberg
authors.forename: Lee
authors.initials: L
authors.lastname: Deobald
authors.forename: Andrzej J
authors.initials: AJ
authors.lastname: Paszczynski
authors.forename: Pawan K
authors.initials: PK
authors.lastname: Sharma
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Hrdlicka
mesh_terms: D004247:DNA / Q000737:chemistry*; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D009841:Oligonucleotides / Q000737:chemistry*; D020641:Polymorphism, Single Nucleotide; D013050:Spectrometry, Fluorescence; D013696:Temperature
chemical_list: D009838:Oligodeoxyribonucleotides; D009841:Oligonucleotides; C477371:locked nucleic acid; D004247:DNA