Influence of Tetra(ethylene glycol) (EG4) Substitution at the Loop Region on the Intramolecular DNA i-Motif

Advanced Smart Biomaterials for Regenerative Medicine and Drug Delivery Based on Phosphoramidite Chemistry: From Oligonucleotides to Precision Polymers

Over decades of development, while phosphoramidite chemistry has been known as the leading method in commercial synthesis of oligonucleotides, it has also revolutionized the fabrication of sequence-defined polymers (SDPs), offering novel functional materials in polymer science and clinical medicine. This review has introduced the evolution of phosphoramidite chemistry, emphasizing its development from the synthesis of oligonucleotides to the creation of universal SDPs, which have unlocked the potential for designing programmable smart biomaterials with applications in diverse areas including data storage, regenerative medicine and drug delivery. The key methodologies, functions, biomedical applications, and future challenges in SDPs, have also been summarized in this review, underscoring the significance of breakthroughs in precisely synthesized materials.

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.

Rapid Screen of Potential i-Motif Forming Sequences in DNA Repair Gene Promoters

We have studied the in vitro stability of 25 potential i-motif-forming DNA sequences found within the promoter regions of 18 different human DNA repair genes. Three widely available methods of characterization were used to rapidly assess i-motif folding and stability and comprise a simple screen for preliminary identification of physiologically relevant i-motif forming sequences. Four highly pH-stable candidate sequences were identified exhibiting pH transitions (pH at which 50% of the oligodeoxynucleotides in solution are folded) at or above pH 6.6, thermal melting temperatures above 37 °C and isothermal UV difference spectra characteristic of 2'-deoxycytidine imino-nitrogen protonation. These newly identified i-motif forming sequences could represent novel targets for understanding and modulating human DNA repair gene expression.

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.

The importance of loop length on the stability of i-motif structures

I-motif stability is enhanced by short loop lengths compared to long loop lengths.

Using UV and srCD spectroscopy it is found that loop length within the i-motif structure is important for both thermal and pH stability, but in contrast to previous statements, it is the shorter loops that exhibit the highest stability.

Effects of the i-motif DNA loop on the fluorescence of silver nanoclusters

The loop sequences in i-motif DNA templates are well correlated with the fluorescence of the prepared Ag clusters.

DNA nanotechnology based on i-motif structures

CONSPECTUS: Most biological processes happen at the nanometer scale, and understanding the energy transformations and material transportation mechanisms within living organisms has proved challenging. To better understand the secrets of life, researchers have investigated artificial molecular motors and devices over the past decade because such systems can mimic certain biological processes. DNA nanotechnology based on i-motif structures is one system that has played an important role in these investigations. In this Account, we summarize recent advances in functional DNA nanotechnology based on i-motif structures. The i-motif is a DNA quadruplex that occurs as four stretches of cytosine repeat sequences form C·CH(+) base pairs, and their stabilization requires slightly acidic conditions. This unique property has produced the first DNA molecular motor driven by pH changes. The motor is reliable, and studies show that it is capable of millisecond running speeds, comparable to the speed of natural protein motors. With careful design, the output of these types of motors was combined to drive micrometer-sized cantilevers bend. Using established DNA nanostructure assembly and functionalization methods, researchers can easily integrate the motor within other DNA assembled structures and functional units, producing DNA molecular devices with new functions such as suprahydrophobic/suprahydrophilic smart surfaces that switch, intelligent nanopores triggered by pH changes, molecular logic gates, and DNA nanosprings. Recently, researchers have produced motors driven by light and electricity, which have allowed DNA motors to be integrated within silicon-based nanodevices. Moreover, some devices based on i-motif structures have proven useful for investigating processes within living cells. The pH-responsiveness of the i-motif structure also provides a way to control the stepwise assembly of DNA nanostructures. In addition, because of the stability of the i-motif, this structure can serve as the stem of one-dimensional nanowires, and a four-strand stem can provide a new basis for three-dimensional DNA structures such as pillars. By sacrificing some accuracy in assembly, we used these properties to prepare the first fast-responding pure DNA supramolecular hydrogel. This hydrogel does not swell and cannot encapsulate small molecules. These unique properties could lead to new developments in smart materials based on DNA assembly and support important applications in fields such as tissue engineering. We expect that DNA nanotechnology will continue to develop rapidly. At a fundamental level, further studies should lead to greater understanding of the energy transformation and material transportation mechanisms at the nanometer scale. In terms of applications, we expect that many of these elegant molecular devices will soon be used in vivo. These further studies could demonstrate the power of DNA nanotechnology in biology, material science, chemistry, and physics.

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.

pH-Induced conformational change and dimerization of DNA chains investigated by analytical ultracentrifugation

pH-induced conformational change of i-motif DNA has been studied by analytical ultracentrifugation. As pH increases, the hydrodynamic radius of individual DNA chains in aqueous solutions prepared by being heat-treated suddenly increases while the molar mass is constant, indicating that the conformation changes from an i-motif to a random coil. When DNA concentrations are higher than 1.0 μM, relatively stable dimers are formed as pH sharply decreases from 7.5 to 4.5. Moreover, the weight percentage of the dimers increases with the initial DNA concentration. The study can help to understand the functions of the telomeres containing repeated cytosine-rich sequences and to develop DNA-based devices.

Regulation of an enzyme cascade reaction by a DNA machine

A strategy for the regulation of enzyme cascade reaction efficiency by a DNA machine in vitro is presented. Two cascade enzymes (GOx and HRP) are attached to the DNA machine, and the enzyme cascade reaction shows much higher efficiency when the two enzymes are brought closer by the DNA machine than when they are distant.