Studying the Influence of the Pyrene Intercalator TINA on the Stability of DNA i-Motifs

Abstract

Certain cytosine-rich (C-rich) DNA sequences can fold into secondary structures as four-stranded i-motifs with hemiprotonated base pairs. Here we synthesized C-rich TINA-intercalating oligonucleotides by inserting a nonnucleotide pyrene moiety between two C-rich regions. The stability of their i-motif structures was studied by using UV melting temperature measurements and circular dichroism spectra at different pH values under noncrowding and crowding conditions (20% poly(ethylene glycol)). When TINA ((R)-3-((4-(1-pyrenylethynyl)benzyl)oxy) propane-1,2-diol) is inserted, the oligonucleotides could form an i-motif at a higher pH than observed for the corresponding wildtype oligonucleotide.

Fundamental aspects of the nucleic acid i-motif structures

“…The substitution at the narrow groove results in a faster migration in agarose gel comparing to those at other two wide grooves, suggesting modification at different positions has different extents of influence on the topology 135 . The influence of the insertion of a nonnucleotide pyrene moiety into the loop between two C-rich regions has also been studied 136 . The stability of the i-motif structures was measured at different pH values under non-crowding and crowding conditions (20% poly(ethylene glycol)).…”

i-Clamp phenoxazine for the fine tuning of DNA i-motif stability

“…For example, the insertion of pyrene-attached 2′-deoxyadenosine nucleotide ( Py A) at 5′-end led to prominent increase of T m (+11.4°C) at pH 4.0 that was caused by the stacking interaction between Py A and the terminal hemiprotonated C–C base pair ( 38 ). However other pyrene-containing non-nucleotide inserts, uracil UNA monomer ( 39 ) and TINA ( 40 ), within the loop region were shown to destabilize iM. In turn, different porphyrin-containing nucleotide and non-nucleotide derivatives were placed into the fragment of the sequence that did not participate in iM core formation, and they provoked strong stabilization (average T m was 53°C, whereas T m of the unmodified sequence was <25°C) at pH 5.0 owing to porphyrin–porphyrin interactions ( 41 ).…”

Fluorescent Nucleic Acid Analogues in Research and Clinical Diagnostics

“…Intercalators can be either attached covalently to the nucleic acid sequence or interact with the duplex non-covalently (Rye and Glazer 1995;Karlsen et al 2012). Non-nucleosidic analogues of nucleic acids such as IPN, UNA, and TINA contain a covalently attached intercalating dye within the oligonucleotide probe which is labeled during oligonucleotide synthesis or postsynthetically (Filichev and Pedersen 2005;El-Sayed et al 2012;Stadler et al 2011). The resulting probes were found to be useful in simultaneous targeting and detection of double-stranded DNA in various fashions.…”