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

Protein Condensation at Nanopore Entrances as Studied by Differential Scanning Calorimetry and Small-Angle Neutron Scattering

The condensation of globular myoglobin (Mb) at the pore entrances of mesoporous silica (MPS) with a series of pore diameters (4.2, 6.4, 7.7, and 9.0 nm) was examined by differential scanning calorimetry (DSC) and contrast-matching small-angle neutron scattering (CM-SANS) experiments. The DSC measurements were performed to estimate the amount of Mb adsorbed at two different adsorption sites, namely, the pore interior and the pore entrance regions. The CM-SANS measurements were conducted to observe condensation of Mb molecules at the pore entrance regions. Notably, the nanopore entrance with a diameter close to twice that of the Mb diameter was found to be the specific cavity to facilitate the condensation of globular Mb. The Mb condensation occurred at the entrances of the 6.4 nm pore during the adsorption uptake from concentrated Mb solutions, whereas the adsorption uptake from diluted Mb solutions induced the condensation of Mb at the entrances of the 7.7 nm pore.

In Situ Monitoring of DNA-Hg2+ Binding Reaction within Confined Nanospace of Metamaterial Nanochannel by Plasmon-Enhanced Raman Scattering

Nanochannel-based plasmon-enhanced Raman scattering (PERS) substrates can simulate biological environments, revealing the recognition and conformation information on biomolecules in confined spaces. In this work, a metamaterial nanochannel-based PERS platform was constructed for highly sensitive analysis of DNA recognition to Hg²⁺ with the lowest Hg²⁺ concentration down to 1.0 pM. The established platform enables in situ monitoring of the thermodynamics and kinetics of DNA-Hg²⁺ recognition reaction in a confined nanospace. The recognition reaction in a nanospace shows good reversibility and specificity, and the isotherm follows well the Freundlich adsorption model. Compared to its folding on a rough Au nanofilm, the folding time of ssDNA-Rox decorated in nanochannels is remarkably increased, and the folding process can be tuned through varying the pore size and ionic strength. The presented PERS platform is promising for studying biomolecule-ion binding events and biomolecule conformation change under nanochannel-confined conditions.

A DNA nanosensor for monitoring ligand-induced i-motif formation

A GNP-based DNA nanosensor has been developed that identifies i-motif inducing ligands at physiological pH from a chemical library.

Opposite salt-dependent stability of i-motif and duplex reflected in a single DNA hairpin nanomachine

We herein report a DNA hairpin structure containing a polycytosine loop region, and this hairpin can operate like a nanomachine allowing independently controlled stability of the i-motif loop and duplex stem region. This was made possible by the opposite salt-dependent stability of DNA duplex and hairpin, thus providing a new method for designing molecular devices or switches design. A singly-labeled fluorescent method was used to measure the stability of an i-motif DNA in the presence of various metal ions. Salt in general destabilizes the i-motif but stabilizes duplex DNA, allowing us to engineer an i-motif containing hairpin for modulating the stability of each secondary structure independently.

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.

Chemical Regulation of DNA i-Motifs for Nanobiotechnology and Therapeutics

DNA sequences rich in cytosine have the propensity, under acidic pH, to fold into four-stranded intercalated DNA structures called i-motifs. Recent studies have provided significant breakthroughs that demonstrate how chemists can manipulate these structures for nanobiotechnology and therapeutics. The first section of this Minireview discusses the development of advanced functional nanostructures by synthetic conjugation of i-motifs with organic scaffolds and metal nanoparticles and their role in therapeutics. The second section highlights the therapeutic targeting of i-motifs with chemical scaffolds and their significance in biology. For this, first we shed light on the long-lasting debate regarding the stability of i-motifs under physiological conditions. Next, we present a comparative analysis of recently reported small molecules for specifically targeting i-motifs over other abundant DNA structures and modulating their function in cellular systems. These advances provide new insights into i-motif-targeted regulation of gene expression, telomere maintenance, and therapeutic applications.

DNA Quadruple Helices in Nanotechnology

DNA has played an early and powerful role in the development of bottom-up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs. However, in addition to the above components underlying the iconic double helix, a number of alternative pairing schemes of nucleobases are known. This review focuses on two of these noncanonical classes of DNA helices: G-quadruplexes and the i-motif. The unique properties of these two classes of DNA helix have been utilized toward some remarkable constructions and applications: G-wires; nanostructures such as DNA origami; reconfigurable structures and nanodevices; the formation and utilization of hemin-utilizing DNAzymes, capable of generating varied outputs from biosensing nanostructures; composite nanostructures made up of DNA as well as inorganic materials; and the construction of nanocarriers that show promise for the therapeutics of diseases.