Solution conformation of d(C4ACAC4TGT)2; an intramolecularly folded i-motif from the insulin minisatellite

Structural insights into i-motif DNA structures in sequences from the insulin-linked polymorphic region

The insulin-linked polymorphic region is a variable number of tandem repeats region of DNA in the promoter of the insulin gene that regulates transcription of insulin. This region is known to form the alternative DNA structures, i-motifs and G-quadruplexes. Individuals have different sequence variants of tandem repeats and although previous work investigated the effects of some variants on G-quadruplex formation, there is not a clear picture of the relationship between the sequence diversity, the DNA structures formed, and the functional effects on insulin gene expression. Here we show that different sequence variants of the insulin linked polymorphic region form different DNA structures in vitro. Additionally, reporter genes in cellulo indicate that insulin expression may change depending on which DNA structures form. We report the crystal structure and dynamics of an intramolecular i-motif, which reveal sequences within the loop regions forming additional stabilising interactions that are critical to formation of stable i-motif structures. The outcomes of this work reveal the detail in formation of stable i-motif DNA structures, with potential for rational based drug design for compounds to target i-motif DNA.

Emerging roles of i-motif in gene expression and disease treatment

As non-canonical nucleic acid secondary structures consisting of cytosine-rich nucleic acids, i-motifs can form under certain conditions. Several i-motif sequences have been identified in the human genome and play important roles in biological regulatory functions. Due to their physicochemical properties, these i-motif structures have attracted attention and are new targets for drug development. Herein, we reviewed the characteristics and mechanisms of i-motifs located in gene promoters (including c-myc, Bcl-2, VEGF, and telomeres), summarized various small molecule ligands that interact with them, and the possible binding modes between ligands and i-motifs, and described their effects on gene expression. Furthermore, we discussed diseases closely associated with i-motifs. Among these, cancer is closely associated with i-motifs since i-motifs can form in some regions of most oncogenes. Finally, we introduced recent advances in the applications of i-motifs in multiple areas.

Probing the hras-1Y i-motif with small molecules

Non-B DNA structures represent intriguing and challenging targets for small molecules. For example, the promoter of the HRAS oncogene contains multiple G-quadruplex and i-motif structures, atypical globular folds that serve as molecular switches for gene expression. Of the two, i-motif structures are far less studied. Here, we report the first example of small organic compounds that directly interact with the hras-1Y i-motif. We use a small molecule microarray screen to identify drug-like small molecules that bind to the hras-1Y i-motif but not to several other DNA or RNA secondary structures. Two different lead compounds, 1 and 2, were discovered to have 7.4 ± 5.3 μM and 5.9 ± 3.7 μM binding affinity by surface plasmon resonance and similar affinity by fluorescence titration. A structure-activity relationship (SAR) was developed and two improved analogues of 2 demonstrated submicromolar binding affinities. Both compounds display pH-dependent binding, indicating that they interact with the DNA only when the i-motif is properly folded. Chemical shift perturbation shows that 1 alters the structure of the i-motif, while 2 has no effect on the i-motif conformation, indicating different modes of interaction.

Detection of protonated non-Watson-Crick base pairs using electrospray ionization mass spectrometry

Many studies have shown that protonated nucleic acid base pairs are involved in a wide variety of nucleic acid structures. However, little information is available on relative stability of hemiprotonated self- and non-self-dimers at monomer level. We used electrospray ionization mass spectrometry (ESI-MS) to evaluate the relative stability under various concentrations of hydrogen ion. These enable conjecture of the formation of protonated non-Watson-Crick base pairs based on DNA and RNA base sequence. In the present study, we observed that ESI-MS peaks corresponded to respective self-dimers for all examined nucleosides except for adenosine. Peak heights depended on the concentration of hydrogen ion. The ESI-MS peak heights of the hemiprotonated cytidine dimers and the hemiprotonated thymidine dimer sharply increased with increased concentration of hydrogen ion, suggesting direct participation of hydrogen ion in dimer formations. In ESI-MS measurements of the solutions containing adenosine, cytidine, thymidine and guanosine, we observed protonated cytidine-guanosine dimer (CH+-G) and protonated cytidine-thymidine dimer (CH+-T) in addition to hemiprotonated cytidine-cytidine dimer (CH+-C) with following relative peak height, (CH+-C) > (CH+-G) ≈ (CH+-T) > (CH+-A). Additionally, in the ESI-MS measurements of solutions containing adenosine, thymidine and guanosine, we observed a considerable amount of protonated adenosine-guanosine (AH+-G) and protonated adenosine-thymidine (AH+-T).

The formation and characteristics of the i-motif structure within the promoter of the c-myb proto-oncogene

C-myb proto-oncogene is a potential therapeutic target for some human solid tumors and leukemias. A long cytosine-rich sequence, which locates the downstream of the transcription initiation site, is demonstrated to fold into an intramolecular i-motif DNA using electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy. Effects of factors, including the pH value, the number of C:C(+) dimers, the concentration of buffer, the molecular crowding condition, and the coexistence of the complementary DNA, on the formation and the structural stability of the i-motif DNA are systematically studied. We have demonstrated that the i-motif folding in the c-myb promoter could be accelerated upon synergistic physiological stimuli including intracellular molecular crowding and low pH values, as well as the large number of the i-motif C:C(+) dimers. Meanwhile, various inputs, such as acids/bases and metal ions, have exhibited their abilities in controlling the conformational switch of the c-myb GC-rich DNA. Acidic pH values and the presence of K(+) ions can induce the dissociation of the double helix. Our present strategy can greatly extend the potential usages of i-motif DNA molecules with specific sequences as conformational switch-controlled devices. Moreover, this work demonstrates the superiority of CD spectroscopy associated with ESI-MS as a rapid, more cost-effective and sensitive structural change responsive method in the research of DNA conformational switching.

Reversible DNA i-motif to hairpin switching induced by copper(II) cations

i-Motif DNA structures have previously been utilised for many different nanotechnological applications, but all have used changes in pH to fold the DNA. Herein we describe how copper(II) cations can alter the conformation of i-motif DNA into an alternative hairpin structure which is reversible by chelation with EDTA.

The analytical and biomedical potential of cytosine-rich oligonucleotides: A review

Polycytosine DNA strands are often found among natural sequences, including the ends of telomeres, centromeres, and introns or in the regulatory regions of genes. A characteristic feature of oligonucleotides that are rich in cytosine (C-rich) is their ability to associate under acidic conditions to form a tetraplex i-motif consisting of two parallel stranded cytosine-hemiprotonated cytosine (C·C+) base-paired duplexes that are mutually intercalated in an antiparallel orientation. Nanotechnology has been exploiting the advantages of i-motif pH-dependent formation to fabricate nanomachines, nanoswitches, electrodes and intelligent nanosurfaces or nanomaterials. Although a few reviews regarding the structure, properties and applications of i-motifs have been published, this review focuses on recently developed biosensors (e.g., to detect pH, glucose or silver ions) and drug-delivery biomaterials. Furthermore, we have included examples of sensors based on parallel C-rich triplexes and silver nanoclusters (AgNCs) fabricated on cytosine-rich DNA strands. The potential diagnostic and therapeutic applications of this type of material are discussed.

i-Motif DNA: structure, stability and targeting with ligands

i-Motifs are four-stranded DNA secondary structures which can form in sequences rich in cytosine. Stabilised by acidic conditions, they are comprised of two parallel-stranded DNA duplexes held together in an antiparallel orientation by intercalated, cytosine-cytosine(+) base pairs. By virtue of their pH dependent folding, i-motif forming DNA sequences have been used extensively as pH switches for applications in nanotechnology. Initially, i-motifs were thought to be unstable at physiological pH, which precluded substantial biological investigation. However, recent advances have shown that this is not always the case and that i-motif stability is highly dependent on factors such as sequence and environmental conditions. In this review, we discuss some of the different i-motif structures investigated to date and the factors which affect their topology, stability and dynamics. Ligands which can interact with these structures are necessary to aid investigations into the potential biological functions of i-motif DNA and herein we review the existing i-motif ligands and give our perspective on the associated challenges with targeting this structure.

Fundamental aspects of the nucleic acid i-motif structures

The latest research on fundamental aspects of i-motif structures is reviewed with special attention to their hypothetical rolein vivo.

G-quadruplex and i-motif are mutually exclusive in ILPR double-stranded DNA

G-quadruplex has demonstrated its biological functions in vivo. Although G-quadruplex in single-stranded DNA (ssDNA) has been well characterized, investigation of this species in double-stranded DNA (dsDNA) lags behind. Here we use chemical footprinting and laser-tweezers-based single-molecule approaches to demonstrate that a dsDNA fragment found in the insulin-linked polymorphic region (ILPR), 5'-(ACA GGGG TGT GGGG)2 TGT, can fold into a G-quadruplex at pH 7.4 with 100 mM K+, and an i-motif at pH 5.5 with 100 mM Li+. Surprisingly, under a condition that favors the formation of both G-quadruplex and i-motif (pH 5.5, 100 mM K+), a unique determination of change in the free energy of unfolding (ΔGunfold) by laser-tweezers experiments provides compelling evidence that only one species is present in each dsDNA. Under this condition, molecules containing G-quadruplex are more stable than those with i-motif. These two species have mechanical stabilities (rupture force≥17 pN) comparable to the stall force of RNA polymerases, which, from a mechanical perspective alone, could justify a regulatory mechanism for tetraplex structures in the expression of human insulin.

Synthesis and characterization of circular structures of i-motif tagged with fluoresceins

Synthesis of a fluorescein-tagged circular structure of i-motif was accomplished during our investigations. The backbone circularity of this molecular probe and the presence of the fluorescent moiety within its structure were also confirmed through exonuclease hydrolysis and fluorescence spectroscopy.

The energetics of i-DNA tetraplex structures formed intermolecularly by d(TC5) and intramolecularly by d[(C5T3)3C5]

Cytosine-rich DNA at low pH adopts an antiparallel tetraplex structure via the intercalation of two partially protonated, parallel stranded duplexes. This intriguing structural motif has been named i-DNA. We have used a combination of spectroscopic and calorimetric techniques to characterize the properties of an intermolecular i-DNA formed by d(TC(5)) and an intramolecular i-DNA formed by d[(C(5)T(3))(3)C(5)]. Our measurements reveal that both i-DNA complexes are enthalpically stabilized by 6.5-7.0 kcal/mol(base) and entropically destabilized by 20 cal/mol(base)/K. These values are about 50% larger than the corresponding enthalpy and entropy values per base for Watson and Crick duplexes and for Hoogsteen triplexes, while being similar to per base enthalpy and entropy values reported for G-quadruplexes. Our data also reveal a positive heat capacity change between 20 and 30 cal/mol(base)/K, values similar to that reported for polymeric Watson & Crick DNA duplexes. Solution-dependent studies reveal the overall thermal and thermodynamic stability of i-DNA complexes to be dictated by an interplay between pH and ionic strength. Based on the thermodynamic data measured, we discuss the feasibility of i-DNA formation in the context of conventional DNA sequences, while commenting on potential roles for this structural motif in biological regulatory mechanisms.