Novel nucleic acid architectures involving locked nucleic acid (LNA) and pyrene residues: Results from an Indo-Danish collaboration

Babu, B. Ravindra; Raunak,; Sørensen, Mads D.; Hrdlicka, Patrick J.; Trikha, Smriti; Prasad, Ashok K.; Parmar, Virinder S.; Wengel, Jesper

doi:10.1351/pac200577010319

Pure Appl. Chem., 2005, Vol. 77, No. 1, pp. 319-326

http://dx.doi.org/10.1351/pac200577010319

Novel nucleic acid architectures involving locked nucleic acid (LNA) and pyrene residues: Results from an Indo-Danish collaboration

B. Ravindra Babu¹, Raunak^2,1, Mads D. Sørensen³, Patrick J. Hrdlicka¹, Smriti Trikha^2,1, Ashok K. Prasad², Virinder S. Parmar² and Jesper Wengel¹

¹ Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
² Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
³ Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark

Abstract: We report herein our results for locked nucleic acid (LNA)-type oligonucleotides containing pyrene residues. Pyrene has a large hydrophobic and planar surface area and is therefore a potential intercalating unit; furthermore, it is interesting as a fluorescent tag when covalently bound to DNA. Synthesis and hybridization of conformationally locked universal base surrogates are described together with efficient interstrand communication as shown by the formation of pyrene excimer bands for duplexes containing 2'-N-(pyren-1-yl)methyl-2'-amino-LNA monomers positioned in a zipper-like manner within a DNA duplex.