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C5‐Functionalized DNA, LNA, and α‐ L ‐LNA: Positional Control of Polarity‐Sensitive Fluorophores Leads to Improved SNP‐Typing
Author(s) -
Østergaard Michael E.,
Kumar Pawan,
Baral Bharat,
Guenther Dale C.,
Anderson Brooke A.,
Ytreberg F. Marty,
Deobald Lee,
Paszczynski Andrzej J.,
Sharma Pawan K.,
Hrdlicka Patrick J.
Publication year - 2011
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.201002109
Subject(s) - nucleobase , locked nucleic acid , chemistry , fluorophore , monomer , fluorescence , dna , circular dichroism , stereochemistry , oligonucleotide , biochemistry , polymer , physics , organic chemistry , quantum mechanics
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.