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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Sharma, Pawan K. Østergaard, Michael E. Kumar, Pawan Ytreberg, F. Marty Hrdlicka, Patrick J. Paszczynski, Andrzej J. Deobald, Lee Guenther, Dale C. Anderson, Brooke A. Baral, Bharat |
| Description | Author Affiliation: Østergaard ME ( Department of Chemistry, University of Idaho, P.O. Box 442343, Moscow, ID 83844-2343, USA.) |
| 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. |
| ISSN | 09476539 |
| e-ISSN | 15213765 |
| Journal | Chemistry - A European Journal |
| Issue Number | 11 |
| Volume Number | 17 |
| Language | English |
| Publisher | Wiley-VCH;ChemPubSoc Europe |
| Publisher Date | 2011-03-07 |
| Publisher Place | Germany |
| Access Restriction | Open |
| Subject Keyword | DNA Chemistry Oligonucleotides Polymorphism, Single Nucleotide Nucleic Acid Denaturation Nucleic Acid Hybridization Oligodeoxyribonucleotides Spectrometry, Fluorescence Temperature Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. |
| Content Type | Text |
| Resource Type | Article |
| Subject | Organic Chemistry Catalysis |
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