Metal ions are essential to many chemical, biological, and environmental processes. In the past two decades, many DNA-based metal sensors have emerged. While the main biological role of DNA is to store genetic information, its chemical structure is ideal for metal binding via both the phosphate backbone and nucleobases. DNA is highly stable, cost-effective, easy to modify, and amenable to combinatorial selection. Two main classes of functional DNA were developed for metal sensing: aptamers and DNAzymes. While a few metal binding aptamers are known, it is generally quite difficult to isolate such aptamers. On the other hand, DNAzymes are powerful tools for metal sensing since they are selected based on catalytic activity, thus bypassing the need for metal immobilization. In the last five years, a new surge of development has been made on isolating new metal-sensing DNA sequences. To date, many important metals can be selectively detected by DNA often down to the low parts-per-billion level. Herein, each me...

Metal Sensing by DNA

Detection of analytes by means of field-effect transistors bearing ligand-specific receptors is fundamentally limited by the shielding created by the electrical double layer (the "Debye length" limitation). We detected small molecules under physiological high-ionic strength conditions by modifying printed ultrathin metal-oxide field-effect transistor arrays with deoxyribonucleotide aptamers selected to bind their targets adaptively. Target-induced conformational changes of negatively charged aptamer phosphodiester backbones in close proximity to semiconductor channels gated conductance in physiological buffers, resulting in highly sensitive detection. Sensing of charged and electroneutral targets (serotonin, dopamine, glucose, and sphingosine-1-phosphate) was enabled by specifically isolated aptameric stem-loop receptors.

/pdf/aptamer-field-effect-transistors-overcome-debye-length-4iykjic6nx.pdf

Aptamer–field-effect transistors overcome Debye length limitations for small-molecule sensing

This review is focused on the structural and physico-chemical aspects of metal cation coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G-Quadruplex structures are non-canonical secondary structures formed by both DNA and RNA. G-quadruplexes regulate a wide range of important biochemical processes. Besides the sequence requirements, the coordination of monovalent cations in the GQ is essential for its formation and determines the stability and polymorphism of GQ structures. The nature, location and dynamics of the cation coordination and their impact on the overall GQ stability are dependent on several factors such as the ionic radii, hydration energy and the bonding strength to the O6 of guanines. The intracellular monovalent cation concentration and the localized ion concentrations determine the formation of GQs and can potentially dictate their regulatory roles. A wide range of biochemical and biophysical studies on an array of GQ enabling sequences have generated at a minimum the knowledge base that allows us to often predict the stability of GQs in presence of the physiologically relevant metal ions, however, prediction of conformation of such GQs is still out of the realm.

/pdf/metal-cations-in-g-quadruplex-folding-and-stability-1ynzpd3at7.pdf

Metal Cations in G-Quadruplex Folding and Stability

RNA G-Quadruplexes in Biology: Principles and Molecular Mechanisms.

Development of biosensing platforms plays a key role in research settings for identification of biomarkers and in clinical applications for diagnostics. Biosensors based on nucleic acids have taken many forms, from simple duplex-based constructs to stimuli-responsive nucleic acid nanostructures. In this review, we look at various nucleic acid-based biosensors, the different read-out strategies employed, and their use in chemical and biological sensing. We also look at current developments in DNA nanotechnology-based biosensors and how rational design of such constructs leads to more efficient biosensing platforms.

Rationally Engineered Nucleic Acid Architectures for Biosensing Applications.

DNA sequences with guanine repeats can form G-quartets that adopt G-quadruplex structures in the presence of specific metal ions. Using circular dichroism (CD) and ultraviolet-visible (UV-Vis) spectroscopy, we determined the spectral characteristics and the overall conformation of a G-quadruplex of PS2.M with an oligonucleotide sequence, d(GTG(3)TAG(3)CG(3)TTG(2)). UV-melting curves demonstrate that the Pb(2+)-induced G-quadruplex formed unimolecularly and the highest melting temperature (T(m)) is 72°C. The analysis of the UV titration results reveals that the binding stoichiometry of Pb(2+) ions to PS2.M is two, suggesting that the Pb(2+) ions coordinate between adjacent G-quartets. Binding of ions to G-rich DNA is a complex multiple-pathway process, which is strongly affected by the type of the cations. Kinetic studies suggest that the Pb(2+)-induced folding of PS2.M to G-quadruplex probably proceeds through a three-step pathway involving two intermediates. Structural transition occurs after adding Pb(NO(3))(2) to the Na(+)- or K(+)-induced G-quadruplexes, which may be attributed to the replacement of Na(+) or K(+) by Pb(2+) ions and the generation of a more compact Pb(2+)-PS2.M structure. Comparison of the relaxation times shows that the Na(+)→Pb(2+) exchange is more facile than the K(+)→Pb(2+) exchange process, and the mechanisms for these processes are proposed.

/pdf/kinetics-and-mechanism-of-g-quadruplex-formation-and-46o270l2va.pdf

Kinetics and mechanism of G-quadruplex formation and conformational switch in a G-quadruplex of PS2.M induced by Pb2+

The lead-induced folding into G-quadruplex structures for three guanine-rich oligonucleotides, two model human telomeric oligomers (HTG/T2) and thrombin-binding aptamer (TBA), was characterized by equilibrium titrations, rapid mixing techniques and stopped-flow kinetics. The analysis of optical titration data reveals that the saturated Pb2+–DNA binding stoichiometries are 1 : 1, 2 : 1 and 3 : 1 for TBA, HTG and T2, respectively. Thermal denaturation experiments were performed to determine the structural stability. The overall results are consistent with the higher stability of T2 that contains four G-quartets, as opposed to HTG and TBA that have only three and two quartets, respectively. We also present kinetic studies of the formation of G-quadruplexes of G-rich DNA induced by Pb2+ ions. The binding of Pb2+ ions to G-DNA is a complex multiple pathway process, which is affected by the sequence of the G-DNA. The studies show that the connecting loops of the DNA play an important role in modulating the structures.

G-quadruplex formation and sequence effect on the assembly of G-rich oligonucleotides induced by Pb2+ ions

DNA sequences with guanine repeats can form G-quartets that adopt G-quadruplex structures in the presence of specific metal ions. Using circular dichroism (CD) and ultraviolet-visible (UV–Vis) spectroscopy, we determined the spectral characteristics and the overall conformation of a G-quadruplex of PS2.M with an oligonucleotide sequence, d(GTG3TAG3CG3TTG2). UV-melting curves demonstrate that the Pb 2+ -induced G-quadruplex formed unimolecularly and the highest melting temperature (Tm )i s 72 � C. The analysis of the UV titration results reveals that the binding stoichiometry of Pb 2+ ions to PS2.M is two, suggesting that the Pb 2+ ions coordinate between adjacent G-quartets. Binding of ions to G-rich DNA is a complex multiple-pathway process, which is strongly affected by the type of the cations. Kinetic studies suggest that the Pb 2+ -induced folding of PS2.M to G-quadruplex probably proceeds through a three-step pathway involving two intermediates. Structural transition occurs after adding Pb(NO3)2 to the Na + -o r K + -induced G-quadruplexes, which may be attributed to the replacement of Na + or K + by Pb 2+ ions and the generation of a more compact Pb 2+ –PS2.M structure. Comparison of the relaxation times shows that the Na + !Pb 2+ exchange is more facile than the K + !Pb 2+ exchange process, and the

Kinetics and mechanism of G-quadruplex formation and conformational switch in a G-quadruplex

It has been shown that guanine-rich DNA can fold into a G-quadruplex with certain metal cations. The spectral characteristics, thermostability, and kinetics for the formation of a Pb2+-driven G-quadruplex of thrombin-binding aptamer (TBA) were measured in the current work using a combination of ultraviolet (UV) and circular dichroism (CD) spectroscopy along with stopped-flow technique. CD spectra demonstrated that TBA could fold into a unique G-quadruplex with a strong positive peak at 312 nm. Analysis of the titration data reveals that the binding stoichiometry is 1:1 for the titration of TBA with Pb(NO3)2, which is in accordance with the localization of the Pb2+ ion between the adjacent G-quartets. Thermal denaturation profiles indicate that the Pb2+-induced intramolecular G-quadruplex is more stable than those driven by Na+ or K+ ions. Kinetic studies suggest that the Pb2+-induced folding G-quadruplex of TBA probably proceeds through the rapid formation of an intermediate Pb2+–TBA complex, which then i...

Kinetics and mechanism of conformational changes in a G-quadruplex of thrombin-binding aptamer induced by Pb2+.

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Kinetics and mechanism of G-quadruplex formation and conformational switch in a G-quadruplex of PS2.M induced by Pb2+

G-quadruplex formation and sequence effect on the assembly of G-rich oligonucleotides induced by Pb2+ ions

Kinetics and mechanism of G-quadruplex formation and conformational switch in a G-quadruplex

Kinetics and mechanism of conformational changes in a G-quadruplex of thrombin-binding aptamer induced by Pb2+.