Comparative Electrochemical and Spectroscopic Studies of I‐Motif‐forming DNA Nonamers

Abstract

The paper shows the structural diversity of cytosine (C)‐rich oligodeoxynucleotides (ODNs) arising from their detail nucleotide sequence and experimental conditions. In slightly acidic solutions, the ODN nonamers with different adenine (A) and cytosine (C) sequences can adopt non‐canonical structures involving protonated bases. A distinct secondary structure formed in (C)‐rich sequences, called i‐motif (iM), consists of hemiprotonated and intercalated cytosine base pairs (C.C+). Folding and unfolding of particular structures in solutions were monitored by 1H NMR and CD spectroscopies and native polyacrylamide gel electrophoresis (PAGE), which are capable to determine their structural characteristics. Effects of sequences and their proclivity to formation of the iM on electrochemical behaviour of the ODN nonamers were studied by electrochemical methods. The LSV signals of A and C obtained from the reductive dissolution of ODN adsorption layers on a hanging mercury drop electrode were processed by elimination voltammetry with linear scan (EVLS), which revealed complex effects of the nonamer properties (namely their primary and secondary structure confirmed in solution) on their adsorption and reduction activity.

Fractionation of Single-stranded DNAs with/without Stable Preorganized Structures Using Capillary Sieving Electrophoresis for Aptamer Selection

“…In the previous studies, it was reported that the DNAs with different tertiary structures show different apparent migration velocities for almost the same length in native polyacrylamide gel electrophoresis (native-PAGE). [38][39][40][41] In other words, these results indicated that DNAs with different tertiary structures can be separated by molecular sieving effect. Thus, the DNAs with different migration times detected as peaks in CSE are expected to have different three-dimensional structures.…”