i-motif DNA

[1] The structure was originally found only in vitro, usually at a slightly acidic pH, but was recently discovered in the nuclei of human cells.

Found primarily in the G1 phase of the cell cycle and in regulatory regions of the genome, i-motif complexes could potentially affect which gene sequences are read and could play a role in determining which genes are switched on or off[5], and were shown to play a role in determining the direction of transcription at a bi-directional enhancer.

The interactions of the sugar-sugar contacts along the narrow grooves allows for optimal backbone twisting, which ultimately contributes to formation of stacking bases and the stability of the molecule.

These particular i-motif complexes are found under particular conditions, including low temperature (4 °C), molecular crowding, negative super helicity, and the introduction of silver(I) cations.

As a nucleic acid structure, i-motif DNA stability is dependent on the nature of the sequence, temperature, and ionic strength.

This stability is exhibited by the base-pairing energy (BPE) of i-motif being 169.7 kJ/mol, which is relatively high compared to neutral C·C and canonical Watson-Crick G·C, which have BPEs of 68.0 kJ/mol and 96.6 kJ/mol, respectively.

[20] The results of two studies by Waller's group and Mir et al. emphasized the importance of electrostatic interactions contributing to the stability of the C:C+ base pair.

[21] Waller's group wished to determine the effect of 2 - deoxyriboguanylurea (GuaUre-dR), a chemotherapeutic agent, on i-motif DNA formation in human telomeres.

[23] Both studies ultimately found that the existence of positive charges in the core of these structures contributed most to the stability of the C:C+ base pair.

[24] Chemical modifications to the C:C+ base pair in which halogenated analogs (5-fluoro, 5-bromo, and 5-iodo) took the place of cytosine increased i-motif DNA stability in acidic environments.

[26] The minor groove of i-motif DNA consists of a phosphate backbone in which two negatively charged sides repel each other, requiring balance to stabilize the overall structure.

The stability of 3'E and 5'E topologies from the sequence d(CCCC) was observed through molecular dynamic simulations to determine the effect of repulsion between the phosphate backbones.

[27] Mergny and Lacroix determined that the addition of a bulky methyl group had a destabilizing effect on the i-motif formation when they compared phosphorothioate, the natural phosphodiester, methylphosphonate, and peptide linkages and determined that only phosphodiester and phosphorothioate oligodeoxynucleotides were capable of forming stable i-motifs.

[29][32] This result reflects the transcription process in which supercoiled DNA is unwound into single-stranded structures, which causes negative super helicity.

It has been confirmed that motif DNA in vivo can be formed at physiological pH under certain molecular crowding conditions and negative super helicity induced during transcription.

[37] Recent studies have shown that the formation of i-motif DNA by specific genomic sequences can occur at neutral pH.

The study utilized an electrophoretic mobility shift assay (EMSA) by notably not changing the DNA melting temperature.

[44] Smaller macrocycles, penta- (L2H2-5OTD) and tetra-oxazoles (L2H2-4OTD) were developed with amine R-groups to observe stability and binding site locations on i-motif.

Tilorone and Tobramycin are i-motif binding ligands discovered via thiazole orange fluorescence intensity displacement (FID) assay.

It is postulated that i-motifs play roles in gene regulation and expression, telomerase inhibition, and DNA replication and repair.

Once bound with CSWNT, i-motifs were found to interfere with telomerase functions in vitro and in vivo in cancer cells, which was assessed by a TRAP assay.

[56] Like PCBPs, the transcription factor heterogeneous nuclear ribonucleoprotein K (HNPRK) has the ability to selectively modulate the promoter regions of proteins such as KRAS and VGEF, in the presence of C-rich sequences such as i-motifs.

[57][58] C-rich sequences such as i-motifs exist throughout the human genome, acting as targets for a variety of proteins that can regulate gene expression in multiple ways and locations.

Applications of i-motifs are centered around biomedical topics, including bio-sensing, drug delivery systems, and molecular switches.

The development of pH sensitive systems, which includes ligand binding, is a field of great interest to medicine, especially in the treatment and detection of cancer.

The dye of the Poly(24C)-MB system, methylene blue (MB), cannot bind when i-motifs are induced, giving rise to a color change that is easily visible.

[61] This method not only acts as an efficient drug delivery system, but can also be modified to detect cancer cells by including a dye or fluorescent, much like the colormetric sensor.

In a study by Takahashi et al., it was found that by using carboxyl-modified single-walled carbon nanotubes (C-SWNTs), telomerase activity could be inhibited, which could potentially lead to apoptosis of cancer cells.

[51] The binding of fisetin to an i-motif in the promoter region of vascular endothelial growth factor (VEGS), which is a signal protein for angiogenesis, induced a conformational change to a hairpin structure that inhibited it from functioning.

At a pH of 5, these regions contracted to form i-motifs, tightening the ring in a fashion similar to closing a trash bag.