Spectroscopic Characterization of i-motif Forming c-myc Derived Sequences Double-Labeled with Pyrene

Abstract

In current studies we use the oligonucleotides based on c-myc sequence: CCC CAC CCT CCC CAC CCT CCC C (cmyc22) and CCC CAC CCT CCC CAC CCT CCC CA (cmyc22A) functionalized by pyrene moieties at both termini. Results of the circular dichroism (CD), UV absorption melting experiments, and steady-state fluorescence measurements of pyrene-modified i-motifs as well as their unlabeled precursors are presented and discussed here. The pyrene labels have a remarkable influence on i-motif stability which was deduced from CD spectra and confirmed by UV melting experiments. Both probes emit fluorescence band of pyrene monomer with intensity decreasing upon pH lowering.Electronic supplementary materialThe online version of this article (doi:10.1007/s10895-013-1184-z) contains supplementary material, which is available to authorized users.

Steady-State Fluorescence and Lifetime Emission Study of pH-Sensitive Probes Based on i-motif Forming Oligonucleotides Single and Double Labeled with Pyrene

“…The presented results confirmed our earlier studies [29] with different intramolecular i-motif sequences labeled with pyrene devoted to develop pH indicators working in an excimer/monomerswitching mode. The final conclusion is that elongation of i-motifs ends leading to formation a duplex blunt end should enable arrangement of pyrene moieties that promote formation of fluorescent excimer.…”

“…The presence of flanking bases not engaged into i-motif core was insufficient to help pyrene tags to create fluorescent dimer. These results are consistent with the focus of our previous studies on attempts to examine the capability of c-myc derived sequences double-labeled with pyrene [29]. In the latter case, we supposed that the long loop present in c-myc based i-motif is somehow responsible for lack of excimer emission.…”

“…The transitional pH for Py-RET20-Py is located between 7.0 and 7.5 as the positive maximum begins to shift toward 277 nm at pH 7.0 (Figure 3b). I-motifs formed by dual-pyrene functionalized C-rich oligonucleotides are more stable than unlabeled ones, which is in good agreement with our previous work [29]. Figure 4 shows fluorescence emission spectra of Py-RET21A-Py, Py-RET21-Py and Py-RET20-Py in buffers at pH range 4.0-8.0 (with excitation at 340 nm).…”

“…Therefore, we previously proved that pyrene-modified i-motifs folding c-myc-derived sequences emit fluorescence with intensity decreasing upon pH lowering [29]. In the latter case, we supposed that the long loop present in c-myc-based i-motif is somehow responsible for lack of excimer emission.…”

Pyrene functionalized molecular beacon with pH-sensitive i-motif in a loop

“…The presented design is a consequence of our earlier studies with different intramolecular i-motif sequences labeled with pyrene devoted to develop pH indicators working in an excimer/monomer switching mode. So far, we have obtained several probes based on C-myc as well as RET sequences but in all cases we observed only pH-sensitive monomer emission of pyrene [20,21]. The common feature of these probes was a lack of possibility to form a duplex blunt end.…”