Stabilization of Telomeric I-Motif Structures by (2'S)-2'-Deoxy-2'-C-Methylcytidine Residues

i-Motif DNA: identification, formation, and cellular functions

An i-motif (iM) is a four-stranded (quadruplex) DNA structure that folds from cytosine (C)-rich sequences. iMs can fold under many different conditions in vitro, which paves the way for their formation in living cells. iMs are thought to play key roles in various DNA transactions, notably in the regulation of genome stability, gene transcription, mRNA translation, DNA replication, telomere and centromere functions, and human diseases. We summarize the different techniques used to assess the folding of iMs in vitro and provide an overview of the internal and external factors that affect their formation and stability in vivo. We describe the possible biological relevance of iMs and propose directions towards their use as target in biology.

Potentiometric titrations to study ligand interactions with DNA i-motifs

i-Motifs are non-canonical secondary structures of DNA formed by mutual intercalation of hemi-protonated cytosine-cytosine base pairs, most typically in slightly acidic conditions (pH<7.0). These structures are well-studied in vitro and have recently been suggested to exist in cells. Despite nearly a decade of active research, the quest for small-molecule ligands that could selectively bind to and stabilize i-motifs continues, and no reference, bona fide i-motif ligand is currently available. This is, at least in part, due to the lack of robust methods to assess the interaction of ligands with i-motifs, since many techniques well-established for studies of other secondary structures (such as CD-, UV-, and FRET-melting) may generate artifacts when applied to i-motifs. Here, we describe an implementation of automated, potentiometric (pH) titrations as a robust isothermal method to assess the impact of ligands or cosolutes on thermodynamic stability of i-motifs. This approach is validated through the use of a cosolute previously known to stabilize i-motifs (PEG2000) and three small-molecule ligands that are able to stabilize, destabilize, or have no effect on the stability of i-motifs, respectively.

Cytosine-rich oligonucleotides incorporating a non-nucleotide loop: A further step towards the obtainment of physiologically stable i-motif DNA

i-Motifs, also known as i-tetraplexes, are secondary structures of DNA occurring in cytosine-rich oligonucleotides (CROs) that recall increasing interest in the scientific community for their relevance in various biological processes and DNA nanotechnology. This study reports the design of new structurally modified CROs, named Double-Ended-Linker-CROs (DEL-CROs), capable of forming stable i-motif structures. Here, two C-rich strands having sequences d(AC₄A) and d(C₆) have been attached, in a parallel fashion, to the two linker's edges by their 3' or 5' ends. The resulting DEL-CROs have been investigated for their capability to form i-motif structures by circular dichroism, poly-acrylamide gel electrophoresis, HPLC-size-exclusion chromatography, and NMR studies. This investigation established that DEL-CROs could form more stable i-motif structures than the corresponding unmodified CROs. In particular, the i-motif formed by DEL-5'-d(C₆)₂ resulted stable enough to be detected even at near physiological conditions (37 °C, pH 7.0). The results open the way to developing pH-switchable nanocarriers and aptamers based on suitably functionalized DEL-CROs.

Double-Headed 2'-Deoxynucleotides That Hybridize to DNA and RNA Targets via Normal and Reverse Watson-Crick Base Pairs

Through the use of modified nucleotides, synthetic nucleic acids have found several fields of application within biotechnology and in the pharmaceutical industry. We have previously introduced nucleotides with an additional functional nucleobase linked to C2' of arabinonucleotides (B_X). These double-headed nucleotides fit neatly into DNA·DNA duplexes, where they can replace the corresponding natural dinucleotides and thus condense the molecular information. Here, we introduce a 2'-deoxy version of the B_X design with inversion of the C2' stereochemistry (^dSB_X) with the aim of obtaining improved RNA recognition. Specifically, ^dSB_X analogues with cytosine or isocytosine attached to C2' of 2'-deoxyuridine (^dSU_C and ^dSU_iC) were synthesized and evaluated in duplexes. Whereas the ^dSB_X design did not outperform the B_X design in terms of mimicking dinucleotides in nucleic acid duplexes, it was able to engage in reverse Watson-Crick pairing using its 2'-base. This was evident from the ability of the ^dSU_C cytosine to form stable mis-matching base pairs with opposite cytosines identified as hemiprotonated C·C⁺ pairs. Furthermore, specific base-pairing with guanine was only observed for the isocytosine-bearing ^dSU_iC monomer. Very stable duplexes were obtained with ^dSU_C/iC monomers in each strand indicating that fully modified double-headed nucleic acid sequences could be based on the ^dSB_X design.

Stability and context of intercalated motifs (i-motifs) for biological applications

DNA is naturally dynamic and can self-assemble into alternative secondary structures including the intercalated motif (i-motif), a four-stranded structure formed in cytosine-rich DNA sequences. Until recently, i-motifs were thought to be unstable in physiological cellular environments. Studies demonstrating their existence in the human genome and role in gene regulation are now shining light on their biological relevance. Herein, we review the effects of epigenetic modifications on i-motif structure and stability, and biological factors that affect i-motif formation within cells. Furthermore, we highlight recent progress in targeting i-motifs with structure-specific ligands for biotechnology and therapeutic purposes.

Access to a stabilized i-motif DNA structure through four successive ligation reactions on a cyclopeptide scaffold

Four successive chemical ligations were used for the assembly of a sophisticated biomolecular system allowing the formation of a stabilized i-motif DNA at pH 7.

i-Motif DNA: structural features and significance to cell biology

The i-motif represents a paradigmatic example of the wide structural versatility of nucleic acids. In remarkable contrast to duplex DNA, i-motifs are four-stranded DNA structures held together by hemi- protonated and intercalated cytosine base pairs (C:C⁺). First observed 25 years ago, and considered by many as a mere structural oddity, interest in and discussion on the biological role of i-motifs have grown dramatically in recent years. In this review we focus on structural aspects of i-motif formation, the factors leading to its stabilization and recent studies describing the possible role of i-motifs in fundamental biological processes.

Stabilization of an intermolecular i-motif by lipid modification of cytosine-oligodeoxynucleotides

This paper describes the stabilization of an intermolecular i-motif by lipophilic modification on the 3'-terminus of oligonucleotides. The hydrophobic aliphatic chain connected at the 3'-terminus of a trinucleotide (dC)3 promoted the formation of an i-motif and significantly enhanced the quadruplex's stability. The impact of lipophilic modification on i-motif's thermal stability was studied by UV-thermal denaturation melting experiments and isothermal titration calorimetry. We found that alkyl chains containing more than 14 carbon atoms could elevate the i-motif structure's stability in a wide range of pH and concentrations.

Silica nano-channel induced i-motif formation and stabilization at neutral and alkaline pH

Here, we have developed a new strategy to stabilize i-motif DNA in neutral and alkaline media by incorporating C-rich sequences inside silica nano-channels. Subsequently, the reversibility of this conformational transition has been achieved using a positively charged protein. Importantly, this entire conformational transition can be performed in multiple cycles, which offers an alternative way to control i-motif formation other than pH and thermal annealing.