Full Paper

C5-Functionalized DNA, LNA, and α-L-LNA: Positional Control of Polarity-Sensitive Fluorophores Leads to Improved SNP-Typing†

  1. Dr. Michael E. Østergaard1,
  2. Dr. Pawan Kumar1,2,
  3. Bharat Baral1,
  4. Dale C. Guenther1,
  5. Brooke A. Anderson1,
  6. Prof. F. Marty Ytreberg3,
  7. Dr. Lee Deobald4,
  8. Prof. Andrzej J. Paszczynski4,
  9. Prof. Pawan K. Sharma2,
  10. Prof. Patrick J. Hrdlicka1,*

Article first published online: 15 FEB 2011

DOI: 10.1002/chem.201002109

Issue

Chemistry - A European Journal

Chemistry - A European Journal

Volume 17, Issue 11, pages 3157–3165, March 7, 2011

Additional Information

How to Cite

Østergaard, M. E., Kumar, P., Baral, B., Guenther, D. C., Anderson, B. A., Ytreberg, F. M., Deobald, L., Paszczynski, A. J., Sharma, P. K. and Hrdlicka, P. J. (2011), C5-Functionalized DNA, LNA, and α-L-LNA: Positional Control of Polarity-Sensitive Fluorophores Leads to Improved SNP-Typing. Chem. Eur. J., 17: 3157–3165. doi: 10.1002/chem.201002109

Author Information

  1. 1

    Department of Chemistry, University of Idaho, P.O. Box 442343, Moscow, ID 83844-2343 (USA), Fax: (+1) 208-885-6173

  2. 2

    Department of Chemistry, Kurukshetra University, Kurukshetra 136119 (India)

  3. 3

    Department of Physics, University of Idaho, P. O. Box 440903, Moscow, ID 83844-0903 (USA)

  4. 4

    Environmental Biotechnology Institute, University of Idaho, P. O. Box 441052, Moscow, ID 83844-1052 (USA)

*Department of Chemistry, University of Idaho, P.O. Box 442343, Moscow, ID 83844-2343 (USA), Fax: (+1) 208-885-6173

  1. †

    LNA=locked nucleic acid; SNP=single nucleotide polymorphism.

Publication History

  1. Issue published online: 25 FEB 2011
  2. Article first published online: 15 FEB 2011
  3. Manuscript Revised: 16 NOV 2010
  4. Manuscript Received: 23 JUL 2010

Funded by

  • NSF
  • EPSCoR

SEARCH

SEARCH BY CITATION

ARTICLE TOOLS

View Full Article with Supporting Information (HTML) Get PDF (551K)

Keywords:

  • bicyclic nucleotides;
  • BNA;
  • DNA targeting;
  • pyrene;
  • single nucleotide polymorphisms

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 (ΦF=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.

View Full Article with Supporting Information (HTML) Get PDF (551K)