New fluorescent nucleobases derived From 5-alkynylpyrimidines

Robert H. E. Hudson; Andrew K. Dambenieks; Joanne M. Moszynski

doi:10.1117/12.629808

12 October 2005 New fluorescent nucleobases derived from 5-alkynylpyrimidines

Robert H. E. Hudson, Andrew K. Dambenieks, Joanne M. Moszynski

Proceedings Volume 5969, Photonic Applications in Biosensing and Imaging; 59690J (2005) https://doi.org/10.1117/12.629808
Event: Photonics North, 2005, Toronto, Canada

Abstract

Fluorescent reporter groups are widely used in many areas of macromolecular science. In nucleic acid chemistry, fluorescently labeled oligonucleotides find use in the study of nucleic acid conformations, as reporters of the state of hybridization and as probes of nucleic acid-protein interactions, as well as, probes and primers for the detection and quantification of desired sequences. Often, the fluorophore is a separate and independent entity covalently attached to an otherwise unmodified oligonucleotide. Another class of fluorophore is the nucleobase analog - a chemically modified nucleobase that is unable to base pair properly. Recently, we have become interested in pyrrolocytosine (pC) as an intrinsically fluorescent, pairing-competent nucleobase. It has previously been shown that incorporation of pyrrolocytidine into oligonucleotides gives a fluorescent molecule that responds to the state of hybridization. We have refined the syntheses of pyrrolocytosine derivatives and the related modified uracil derivatives, furanouracil (fU), from cytosine and uracil respectively via three sequential steps: iodination of the nucleobase; Pd-catalyzed cross-coupling with a terminal alkyne; and metal-catalyzed cyclization. The fluorescence properties of the 5-alkynyl nucleobases and the bicyclic pC and fU analogs have been characterized and depend on: 1) the nature of the substituent on the alkyne, 2) whether the nucleobase is 5-alkynyl or cyclized, and 3) the presence of a substituent on the N¹-position of the nucleobase. The chemistry and properties of peptide nucleic acid oligomers incorporating these types of base modifications and their possible use in point-mutation detection is presented.

Citation Download Citation

Robert H. E. Hudson, Andrew K. Dambenieks, and Joanne M. Moszynski "New fluorescent nucleobases derived from 5-alkynylpyrimidines", Proc. SPIE 5969, Photonic Applications in Biosensing and Imaging, 59690J (12 October 2005); https://doi.org/10.1117/12.629808

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