A fluorescence-quencher pair for DNA hybridization studies based on hydrophobic base surrogates

• Published in: Tetrahedron Vol. 63; no. 17; pp. 3440 - 3449
• Main Authors: Stoop, Matthias, Zahn, Alain, Leumann, Christian J.
• Format: Journal Article
• Language: English
• Published: Elsevier Ltd 23-04-2007
• Subjects: Biphenyl DNA; DNA analogues; Fluorescence quenching; Hydrophobic base pairs; Biphenyl DNA; DNA analogues; Hydrophobic base pairs; Fluorescence quenching
• ISSN: 0040-4020; 1464-5416
• DOI: 10.1016/j.tet.2006.12.095

The synthesis of the novel, fluorescent 3-aminobiphenyl-C-nucleoside
M as well as the corresponding building block for oligodeoxynucleotide synthesis is described.
M was incorporated into oligodeoxynucleotides via standard phosphoramidite chemistry and the thermal stabilities of duplexes with one and three consecutive
M–
M,
M–
P, and
M–
O pairs, where
P denotes an unmodified biphenyl C-nucleoside and
O a 3,5-dinitrobiphenyl-C-nucleoside, were determined. It was found that duplexes containing three consecutive
M–
O pairs were the most stable in the series, notably more stable than a duplex with one additional natural G–C pair instead of the modified residues. Furthermore it was found that the fluorescence of
M is efficiently quenched in a duplex when placed opposite to the dinitrophenyl unit
O. Thus
M and
O constitute a novel fluorophore/quencher pair that is orthogonal to natural base pairs in its recognition properties enabling its use as highly specific tags with reporting properties.
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