Abstract
The i-motif is a four-stranded DNA structure formed from the cytosine (C)-rich ssDNA sequence, which is stabilized in slightly acidic pH. Additionally, labeling of a cytosine-rich sequence with a fluorescent molecule may constitute a way to construct a pH-sensitive biosensor. In this paper, we report tC-modified fluorescent probes that contain RET-related sequence C4GC4GC4GC4A. Results of the UV absorption melting experiments, circular dichroism (CD) spectra, and steady-state fluorescence measurements of tC-modified i-motifs are presented and discussed here. Efficient fluorescence quenching of tC fluorophore occurred upon lowering the pH from 8.0 to 5.5. Furthermore, we present and discuss fluorescence spectra of systems containing tC-modified i-motifs and complementary G-rich sequences in the ratios 1:1, 1:2, and 1:3 in response to pH changes. The fluorescence anisotropy was proposed for the study of conformational switching of the i-motif structure for tC-probes in the presence and absence of a complementary sequence. The possibility of using of the sensor for monitoring pH changes was demonstrated.
Highlights
In recent years, there is an increasing interest in developing new aptamers for the detection of any kind of target, both for diagnostic and basic research applications.DNA and RNA are attractive biomaterials for constructing self-secondary structures, such as aptamers and biosensors [1]
The fluorescence anisotropy was proposed for the study of conformational switching of the i-motif structure for tC-probes in the presence and absence of a complementary sequence
We have designed four new pH-sensitive probes based on the d((C4 G)3 C4 A) sequence expected to form i-motif structures
Summary
DNA and RNA are attractive biomaterials for constructing self-secondary structures, such as aptamers and biosensors [1]. I-tetraplexes are formed by C-rich sequences through intercalation of two parallel duplexes with the hemi-protonated base pairs. The building component of the i-motif structure is a base pair C-C+ with one cytosine protonated at the N3 position, which is stabilized in slightly acidic pH [6,7]. The ability of C-rich oligonucleotides to form i-motifs depends on the number of C-C+ base pairs [17,18], the length and nature of loops [19,20,21], the bases at the 50 and 30 ends of C-rich sequences [22,23], etc. The transition midpoint can be shifted as it strictly depends on the sequence and environmental conditions [24]
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