Systematic investigation of sequence requirements for DNA i-motif formation

Development of fluorescence oligonucleotide probes based on cytosine- and guanine-rich sequences

The properties of cytosine- and guanine-rich oligonucleotides contributed to employing them as sensing elements in various biosensors. In this paper, we report our current development of fluorescence oligonucleotide probes based on i-motif or G-quadruplex forming oligonucleotides for cellular measurements or bioimaging applications. Additionally, we also focus on the spectral properties of the new fluorescent silver nanoclusters based system (ChONC12-AgNCs) that is able to anchor at the Langmuir monolayer interface, which is mimicking the surface of living cells membrane.

Tricky Topology: Persistence of Folded Human Telomeric i-Motif DNA at Ambient Temperature and Neutral pH

i-Motifs are four-stranded DNA structures formed from sequences rich in cytosine, held together by hemi-protonated cytosine-cytosine base pairs. These structures have been utilized extensively as pH-switches in DNA-based nanotechnology. Recently there has been an increasing interest in i-motif structures in biology, fuelled by examples of when these can form under neutral conditions. Herein we describe a cautionary tale regarding handling of i-motif samples. Using CD and UV spectroscopy we show that it is important to be consistent in annealing i-motif DNA samples as at neutral pH, i-motif unfolding kinetics is dependent on the time allowed for annealing and equilibration. We describe how the quadruplex structure formed by the human telomeric i-motif sequence can be shown to form and persist in the same conditions of neutral pH and ambient temperature in which, once at thermodynamic equilibrium, it exists predominantly as a random coil. This study has implications not only for work with i-motif DNA structures, but also in the uses and applications of these in nanotechnological devices.

Construction and Characterization of a Mirror-Image l-DNA i-Motif

The first thermally stable and pH-responsive quadruplex intercalated motif (i-motif) structure formed by l-DNA is presented. Although this l-type i-motif exhibits the same physiochemical properties as its d isomer, its inverted chirality and good enzymatic resistance potentially open the way to the development of new DNA materials of pharmaceutical and biological interest.

Access to a stabilized i-motif DNA structure through four successive ligation reactions on a cyclopeptide scaffold

Four successive chemical ligations were used for the assembly of a sophisticated biomolecular system allowing the formation of a stabilized i-motif DNA at pH 7.

Stabilization of Long-Looped i-Motif DNA by Polypyridyl Ruthenium Complexes

A spectroscopic study of the interactions of Λ- and Δ-[Ru(phen)₂(dppz)]²⁺ with i-motif DNA containing thymine loops of various lengths. In the presence of i-motifs, the luminescence of the Λ enantiomer was enhanced much more than the Δ. Despite this, the effect of each enantiomer on i-motif thermal stability was comparable. The sequences most affected by [Ru(phen)₂(dppz)]²⁺ were those with long thymine loops; this suggests that long-looped i-motifs are attractive targets for potential transition metal complex drugs and should be explored further in drug design.

Well-Optimized Conjugated GO-DNA Nanosystem for Sensitive Ratiometric pH Detection in Live Cells

Intracellular pH is a vital parameter which can reflect the physiological process, and the detection of intracellular pH with a high signal-to-noise ratio (SNR) remains a challenge. Compared to pH biosensors based on a single-wavelength signal, it is much easier to obtain better sensitivity and higher SNR from the biosensors by two-wavelength ratiometric signals. In this study, we used DNA-grafted graphene oxide (GO) to ratiometrically detect intracellular pH ranging from basic to acidic. A high SNR with a 35-fold difference in the ratiometric output has been achieved through careful optimization: (1) A high DNA conjugation yield of 45% has been gained through utilizing the partial double-stranded assembly strategy. (2) Herring sperm DNA (HSD) plays an important role in improving the sensitivity of the nanosystem by purifying and passivating the surface of GO; therefore, the concentration of HSD has been optimized to pursue the most sensitive ratiometric response. Apart from the ultrahigh SNR, fabricated GO-AR-Cy5/IFO-Cy3 exhibited excellent stability and biocompatibility in biological environments. Further experiments demonstrated that the nanosystem worked well in live cells in response to pH changes. It is possible to distinguish small pH differences and realize quantitative detection based on ratiometric fluorescence imaging by laser scanning confocal microscope analysis, which makes the nanosystem a promising candidate for further biological study and clinical applications.

Thermodynamically stable and genetically unstable G-quadruplexes are depleted in genomes across species

G-quadruplexes play various roles in multiple biological processes, which can be positive when a G4 is involved in the regulation of gene expression or detrimental when the folding of a stable G4 impairs DNA replication promoting genome instability. This duality interrogates the significance of their presence within genomes. To address the potential biased evolution of G4 motifs, we analyzed their occurrence, features and polymorphisms in a large spectrum of species. We found extreme bias of the short-looped G4 motifs, which are the most thermodynamically stable in vitro and thus carry the highest folding potential in vivo. In the human genome, there is an over-representation of single-nucleotide-loop G4 motifs (G4-L1), which are highly conserved among humans and show a striking excess of the thermodynamically least stable G4-L1A (G3AG3AG3AG3) sequences. Functional assays in yeast showed that G4-L1A caused the lowest levels of both spontaneous and G4-ligand-induced instability. Analyses across 600 species revealed the depletion of the most stable G4-L1C/T quadruplexes in most genomes in favor of G4-L1A in vertebrates or G4-L1G in other eukaryotes. We discuss how these trends might be the result of species-specific mutagenic processes associated to a negative selection against the most stable motifs, thus neutralizing their detrimental effects on genome stability while preserving positive G4-associated biological roles.