Large flanking sequence effects in single nucleotide mismatch detection using fluorescent nucleoside C(f)

Bioorganic & Medicinal Chemistry
Haraldur Gardarsson, Snorri Th Sigurdsson

Abstract

The first systematic study of flanking sequence effects on mismatch detection by a fluorescent nucleotide is described, using fluoroside C(f). Although a high degree of variance was observed in fluorescence intensity of mismatched duplexes between different flanking sequences, C(f) was able to distinguish a mismatch from the fully base-paired duplex in 13 out of 16 sequences, and even identify each mismatch in 10 of those flanking sequences. For the flanking sequences where fluoroside C(f) did not unambiguously determine its base-pairing partner, the experimental conditions were varied in an attempt to facilitate mismatch identification. No beneficial effect on the relative fluorescence intensities was achieved by changing the temperature, adding organic co-solvents or potassium iodide. In contrast, mercuric ions selectively quenched the fluorescence intensity of the C(f).T mismatch, effectively resolving the overlap of all emission spectra and thereby facilitating identification of all base-pairing partners in any flanking sequence by C(f). This is the first time mercuric ions have been used to selectively quench the fluorescence of a single mismatch. A noticeable characteristic of C(f) is that, unlike most fluorosides, the fl...Continue Reading

References

Nov 9, 2004·Chembiochem : a European Journal of Chemical Biology·Kazuhiko Nakatani
Apr 27, 2005·Chembiochem : a European Journal of Chemical Biology·Chikara Dohno, Isao Saito

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Citations

Jan 22, 2011·Nucleic Acids Research·Thomas E EdwardsSnorri Th Sigurdsson
Mar 28, 2012·Biochemical and Biophysical Research Communications·Pavol Cekan, Snorri Th Sigurdsson
Sep 22, 2017·Physical Chemistry Chemical Physics : PCCP·Henrik GustmannJosef Wachtveitl
Mar 31, 2015·Beilstein Journal of Organic Chemistry·Dnyaneshwar B Gophane, Snorri Th Sigurdsson
Feb 16, 2011·Chembiochem : a European Journal of Chemical Biology·Haraldur GardarssonSnorri Th Sigurdsson
Nov 2, 2012·Organic & Biomolecular Chemistry·Kristmann GislasonSnorri Th Sigurdsson
May 7, 2021·Chemical Society Reviews·Dmytro DziubaYves Mély

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