i-Motif folding intermediates with zero-nucleotide loops are trapped by 2'-fluoroarabinocytidine via F···H and O···H hydrogen bonds

Advances in i-motif structures: Stability, gene expression, and therapeutic applications

The i-motif, a cytosine-rich DNA structure formed under acidic conditions, plays a pivotal role in regulating gene expression and holds significant therapeutic potential across various diseases. Found in the promoter regions of oncogenes such as Bcl-2, C-MYC, and KRAS, i-motifs dynamically interact with transcription factors and ligands to modulate oncogene activity. Their pH-sensitive nature enables innovative applications, including cellular pH sensors like the "i-switch" and drug delivery platforms such as DNA hydrogels that release therapeutics in acidic tumor microenvironments. However, challenges remain in developing specific ligands and detection methods. Advances in nanotechnology and multi-target therapies highlight the transformative potential of i-motifs in precision medicine. This review underscores the importance of i-motifs as therapeutic targets and tools, bridging fundamental research with clinical applications in oncology, metabolic disorders, and neurodegenerative diseases.

A controllable DNA: structural features and advanced applications of i-motif

The i-motif consists of two parallel-stranded duplexes, stabilized by intercalated semi-protonated cytosine-cytosine (C·C+) pairing. Initially, the i-motif was thought to be unstable under physiological pH, which limited its biological interest. However, recent studies have demonstrated the presence of i-motifs in regulatory regions of the human genome at neutral pH, making their study biologically relevant. In addition, in the field of nanotechnology, the reversible pH-responsive properties of i-motif structures have been utilized to construct functional nanostructures for biomedical diagnostics and therapeutics. In this review, we present an overview of the structural features of i-motifs, the factors affecting their stability, and detection methods. Furthermore, we focus on summarizing recent advances in the application of i-motif-based functional nanostructures at the cellular level. The challenges and future prospects of i-motifs in nanomedicine are also discussed at the end of this paper.

Early Folding Dynamics of i-Motif DNA Revealed by pH-Jump Time-Resolved X-ray Solution Scattering

The i-motif is a pH-responsive cytosine-rich oligonucleotide sequence that forms, under acidic conditions, a quadruplex structure. This tunable structural switching has made the i-motif a useful platform for designing pH-responsive nanomaterials. Despite the widespread application of i-motif DNA constructs as biomolecular switches, the mechanism of i-motif folding on the atomic scale has yet to be established. We investigate the early folding structural dynamics of i-motif oligonucleotides with laser-pulse-induced pH-jump time-resolved X-ray solution scattering. Following the pH-jump, we observe that the initial random coil ensemble converts into a contracted intermediate state within 113 ns followed by further folding on the 10 ms time scale. We reveal the representative structures of these transient species, hitherto unknown, with molecular dynamics simulations and ensemble fitting. These results pave the way for understanding metastable conformations of i-motif folding and for benchmarking emerging theoretical models for simulating noncanonical nucleic acid structures.

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.

Understanding intercalative modulation of G-rich sequence folding: solution structure of a TINA-conjugated antiparallel DNA triplex

We present here the high-resolution structure of an antiparallel DNA triplex in which a monomer of para-twisted intercalating nucleic acid (para-TINA: (R)-1-O-[4-(1-pyrenylethynyl)phenylmethyl]glycerol) is covalently inserted as a bulge in the third strand of the triplex. TINA is a potent modulator of the hybridization properties of DNA sequences with extremely useful properties when conjugated in G-rich oligonucleotides. The insertion of para-TINA between two guanines of the triplex imparts a high thermal stabilization (ΔTM = 9ºC) to the structure and enhances the quality of NMR spectra by increasing the chemical shift dispersion of proton signals near the TINA location. The structural determination reveals that TINA intercalates between two consecutive triads, causing only local distortions in the structure. The two aromatic moieties of TINA are nearly coplanar, with the phenyl ring intercalating between the flanking guanine bases in the sequence, and the pyrene moiety situated between the Watson-Crick base pair of the two first strands. The precise position of TINA within the triplex structure reveals key TINA-DNA interactions, which explains the high stabilization observed and will aid in the design of new and more efficient binders to DNA.

Dimeric structures of DNA ATTTC repeats promoted by divalent cations

Structural studies of repetitive DNA sequences may provide insights why and how certain repeat instabilities in their number and nucleotide sequence are managed or even required for normal cell physiology, while genomic variability associated with repeat expansions may also be disease-causing. The pentanucleotide ATTTC repeats occur in hundreds of genes important for various cellular processes, while their insertion and expansion in noncoding regions are associated with neurodegeneration, particularly with subtypes of spinocerebellar ataxia and familial adult myoclonic epilepsy. We describe a new striking domain-swapped DNA-DNA interaction triggered by the addition of divalent cations, including Mg2+ and Ca2+. The results of NMR characterization of d(ATTTC)3 in solution show that the oligonucleotide folds into a novel 3D architecture with two central C:C+ base pairs sandwiched between a couple of T:T base pairs. This structural element, referred to here as the TCCTzip, is characterized by intercalative hydrogen-bonding, while the nucleobase moieties are poorly stacked. The 5'- and 3'-ends of TCCTzip motif are connected by stem-loop segments characterized by A:T base pairs and stacking interactions. Insights embodied in the non-canonical DNA structure are expected to advance our understanding of why only certain pyrimidine-rich DNA repeats appear to be pathogenic, while others can occur in the human genome without any harmful consequences.

A beginner's handbook to identify and characterize i-motif DNA

Genomic DNA exhibits an innate ability to manifest diverse sequence-dependent secondary structures, serving crucial functions in gene regulation and cellular equilibrium. While extensive research has confirmed the formation of G-quadruplex structures by guanine-rich sequences in vitro and in cells, recent investigations have turned the quadruplex community's attention to the cytosine (C)-rich complementary strands that can adopt unique tetra-stranded conformation, termed as intercalated motif or i-motif. I-motifs are stabilized by hemi-protonated C:CH+ base pairs under acidic conditions. Initially, the in vivo occurrence of i-motifs was underestimated because their formation is favored at non-physiological pH. However, groundbreaking research utilizing the structure-specific iMab antibody and high-throughput sequencing have recently detected their conserved dispersion throughout the genome, challenging previous assumptions. Given the evolving nature of this research field, it becomes imperative to conduct independent in vitro experiments aimed at identifying potential i-motif formation in C-rich sequences and consolidating the findings to address the properties of i-motifs. This chapter serves as an introductory guide for the swift identification of novel i-motifs, where we present an experimental framework for investigating and characterizing i-motif sequences in vitro. In this chapter, we selected a synthetic oligonucleotide (C7T3) sequence and outlined appropriate methodologies for annealing the i-motif structure into suitable buffers. Then, we validated its formation by CD (Circular Dichroism) and NMR (Nuclear Magnetic Resonance) spectroscopy. Finally, we provided a thorough account of the step-by-step procedures to investigate the effect of i-motif formation on the stalling or retardation of DNA replication using high resolution primer extension assays.

Modulation of the tetrameric I-motif folding of C-rich Tetrahymena telomeric sequences by hexitol nucleic acid (HNA) modifications

I-motifs are non-canonical DNA structures consisting of two parallel strands held together by hemiprotonated cytosine-cytosine+ base pairs, which intercalate to form a ordered column of stacked base pairs. This unique structure covers potential relevance in various fields, including gene regulation and biotechnological applications. A unique structural feature of I-motifs (iM), is the presence of sugar-sugar interactions through their extremely narrow minor grooves. Consistently, oligonucleotides containing pentose derivatives such as ribose, 2'-deoxyribose, arabinose, and 2'-deoxy-2'-fluoroarabinose highlighted a very different attitude to fold into iM. On the other hand, there is significant attention focused on exploring sugar-modifications that can increase nucleic acids resistance to nuclease degradation, a crucial requirement for therapeutic applications. An interesting example, not addressed in the iM field yet, is represented by hexitol nucleic acid (HNA), a metabolically stable six-membered ring analogue compatible with A-like double helix formation. Herein, we selected two DNA C-rich Tetrahymena telomeric sequences whose tetrameric iMs were already resolved by NMR and we investigated the iM folding of related HNA and RNA oligonucleotides by circular dichroism, differential scanning calorimetry and NMR. The comparison of their behaviours vs the DNA counterparts provided interesting insights into the influence of the sugar on iM folding. In particular, ribose and hexitol prevented iM formation. However, by clustering the hexitol-containing residues at the 3'-end, it was possible to modulate the distribution of the different topological species described for the DNA iMs. These data open new avenues for the exploitation of sugar modifications for I-motif characterization and applications.

End-ligation can dramatically stabilize i-motifs at neutral pH

Stabilizing i-motif structures at neutral pH and physiological temperature remains a major challenge. Here, we demonstrate the use of chemical end-ligation to stabilize intramolecular i-motifs at both acidic and neutral pH. We also demonstrate that combining 2'-deoxy-2'-fluoroarabinocytidine substitutions and end-ligation results in an i-motif with an unparalleled thermal stability of 54 °C at neutral pH. Overall, the ligated i-motifs presented herein may be used in screens for selective i-motif ligands and proteins and could find important applications in nanotechnology.