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Issue 14, 2015
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Fluorescence probing of metal-ion-mediated hybridization of oligonucleotides

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Abstract

The sensitivity of fluorescence of pyrrolocytosine-containing oligonucleotides to changes in their secondary structure has been harnessed to monitor the hybridization of modified metal-ion-chelating oligonucleotides with their unmodified counterparts. With short double-helical oligonucleotides, quenching of fluorescence correlated well with the length and, hence, Tm of the duplex provided that the pyrrolo-dC residue was incorporated within the duplex. Furthermore, hybridization of the metal-ion-chelating oligonucleotides was greatly enhanced on addition of 1 eq. of Cu2+, as evidenced by both Tm and fluorometric measurements. As an example of a case where interpretation of a conventional UV-melting profile is challenging, application of the fluorometric method was extended to probing hybridization of short metal-ion-carrying oligonucleotides with the trinucleotide bulge motif of TAR RNA models. In this case the results were more ambiguous, presumably due to weak hybridization with the short target sequence.

Graphical abstract: Fluorescence probing of metal-ion-mediated hybridization of oligonucleotides

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Supplementary files

Article information


Submitted
24 Nov 2014
Accepted
22 Dec 2014
First published
05 Jan 2015

RSC Adv., 2015,5, 10837-10844
Article type
Paper

Fluorescence probing of metal-ion-mediated hybridization of oligonucleotides

S. Taherpour and T. Lönnberg, RSC Adv., 2015, 5, 10837
DOI: 10.1039/C4RA15136D

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