Investigation of the interactions between methylene blue and intramolecular G-quadruplexes: an explicit distinction in electrochemical behavior.

G-quadruplex sequences exist in eukaryotic organisms and prokaryotes, and the investigation of the interactions between G-quadruplexes and small molecule ligands is important for gene therapy, biosensor fabrication, fluorescence imaging and so on. Here, we investigated the behaviour of methylene blue (MB), an electroactive molecule, in the presence of different intramolecular G-quadruplexes by an electrochemical method using a miniaturized electrochemical device based on its intrinsic electrochemical properties. Although the effects of MB on different intramolecular G-quadruplex structures are not obvious by circular dichroism spectroscopy, distinct differences in the binding affinities of MB with different intramolecular G-quadruplexes were quickly and easily observed by an electrochemical technique. At the same time, for the human telomerase G-rich sequence (HT), the diffusion current of MB changed sensitively under different ionic conditions due to the formation of different conformations of HT, which indicated that our electrochemical method has the potential to study the influence of metal ions on the conformations of the G-quadruplexes with simplicity, rapid response and low cost. From all these, a new stacking mechanism and rule were obtained, which were also validated by docking studies and isothermal titration calorimetry (ITC).

A cupric ion triggered DNA diode based on a tandem linkage-cleavage reaction.

Based on click chemistry and DNAzyme, we constructed for the first time a cupric ion triggered DNA diode using a tandem linkage-cleavage process, which could occur in order in a programmable and autonomous manner. This DNA diode is a new DNA functional element and can precisely control the translation direction of information.

A smart tailor-made G-clip reporter for sensitive detection of G-triplet-containing sequences.

Taking advantage of the intrinsic characteristics of G-triplet-containing sequences, a pioneering tailor-made clip-like reporter containing three-fourths of a G-quadruplex is established. The reporter can clip the G triplet in the target sequence through a recognition process to form a complete G-quadruplex structure.

DNA cross-triggered cascading self-amplification artificial biochemical circuit.

The construction of compact and robust artificial biochemical circuits based on nucleic acids can help researchers to understand the essential mechanisms of complex biological systems, and design sophisticated strategies for various requirements. In this study, a novel DNA cross-triggered cascading self-amplification artificial biochemical circuit was developed. Once triggered by trace amounts (as low as 2 amol) of either of two fully independent oligonucleotide factors under homogeneous isothermal conditions, the circuit simultaneously amplified both factors by 105-107 fold, which was proved using mass spectrometry. The compact and robust circuit was successfully used to construct a multi-input Boolean logic operation and a sensitive DNA biosensor based on the dual-amplification of both the target and reporter. The circuit showed great potential for signal gain in complicated molecular programming, and flexible control of nucleic acid nanomachines in biochemical network systems and nanotechnology.

A G-quadruplex based platform for label-free monitoring of DNA reaction kinetics.

Research on the kinetic characteristics and mechanisms of DNA reactions is crucial for bioengineering and biosensing. A G-quadruplex, which can form a peroxidase-mimicking DNAzyme with hemin, was for the first time used to establish a versatile platform for kinetic investigations on DNA reactions. G-quadruplex sequence EAD2 was incorporated into the corresponding nucleic acid reaction as product. The kinetic curves can be obtained rapidly and simply via the quantification of created DNAzyme. In this paper, the kinetics of isothermal linear strand displacement amplification reactions with different DNA lengths and isothermal exponential amplification reactions were successfully elucidated via the G-quadruplex based monitoring platform. As a safe and accessible alternative to the traditional methods, this robust, label-free, time-saving and high-throughput platform shows great potential for the exploration of more novel DNA reactions or circuits in an ingenious manner.