A study of the interactions of Hg(II) with T-T mispair containing hairpin loops

A highly parallel DTT/MB-DNA/Au electrochemical biosensor for trace Hg monitoring by using configuration occupation approach and SECM

Environmental pollution and medicine safety have aroused increasing public concerns due to human health. Amongst various contaminants, mercury is of special attention owing to their environmental persistence and biogeochemical recycling and ecological risks. Herein, a simple and highly parallel electrochemical biosensor for Hg determination was designed and investigated. The proposed biosensor was prepared and compared between (1) DTT/MB-DNA/Au with configuration occupation approach and (2) MCH/MB-DNA/Au with passivation approach. According to the combined results of scanning electrochemical microscope (SECM) and Randles-Sevcik equation, the DTT modified electrode exhibited high uniformity on DNA distribution and superb stability on electron transfer in Hg2+ detection. Evidentially, the response value of proposed DTT/MB-DNA/Au was increased from 57.518% to 97.607%, while RSD% between duplicate runs had dropped from 22.658% to 0.223% (n = 3). Moreover, the increased proportion of effective working area was 467.380% compared with general sensors. Besides, DTT concentration, DNA concentration as well as assembly time were optimized, utilizing electrochemical impedance spectroscopy (EIS), Cyclic Voltammetry (CV) and Square Wave Anode Stripping Voltammetry (SWASV). This optimized biosensor exhibited an excellent selectivity toward Hg2+ over Cu2+, As2+, Cd2+, Pb2+, Cr3+, Ni2+ and Zn2+ etc., and the stability of DTT/MB-DNA/Au were at least two times better even after 3 days under room temperature. Also, a linear relation was observed between the peak current and Hg2+concentrations in a range from 0.25 nM to 2.00 μM with a detection limit of 53.00 pM under optimal conditions. Finally, DTT/MB-DNA/Au was applied for plants and medical products analysis. In all, this optimized DTT/MB-DNA/Au with advantages of high repeatability and sensitivity would provide a new insight into the design and application of biosensor for reliable sensing in safeguarding plant protection and medicinal safety.

Novel nucleic acid origami structures and conventional molecular beacon-based platforms: a comparison in biosensing applications

Nucleic acid nanotechnology designs and develops synthetic nucleic acid strands to fabricate nanosized functional systems. Structural properties and the conformational polymorphism of nucleic acid sequences are inherent characteristics that make nucleic acid nanostructures attractive systems in biosensing. This review critically discusses recent advances in biosensing derived from molecular beacon and DNA origami structures. Molecular beacons belong to a conventional class of nucleic acid structures used in biosensing, whereas DNA origami nanostructures are fabricated by fully exploiting possibilities offered by nucleic acid nanotechnology. We present nucleic acid scaffolds divided into conventional hairpin molecular beacons and DNA origami, and discuss some relevant examples by focusing on peculiar aspects exploited in biosensing applications. We also critically evaluate analytical uses of the synthetic nucleic acid structures in biosensing to point out similarities and differences between traditional hairpin nucleic acid sequences and DNA origami.

Role of the backbone of nucleic acids in the stability of Hg2+-mediated canonical base pairs and thymine–thymine mispair: a DFT study

Metal-mediated base pairs have attracted attention in nucleic acid research and molecular devices. Herein, we report a systematic computational study on Hg²⁺-mediated base pairs with canonical and TT mispair dimers. The computed results revealed that the model _DTT_D (thymine–thymine with DNA backbone) mispair is more energetically favored than the canonical base pairs. The _DTTTT_D mispair dimer is more energetically stable by ∼36.0 kcal mol⁻¹ than the corresponding canonical _DATGC_D base pairs. The Hg⋯Hg metallophilic interaction was observed with the _DTTTT_D mispair and not the canonical base pairs. The _DATGC_D (adenine: thymine, guanine: cytosine) base pairs were significantly perturbed upon interaction with the mercury ion; however, the TTTT mispairs were aligned upon interaction with the Hg²⁺ ion. The _DTTTT_D mispair adopts a B-type conformation with proper alignment of its nucleobases along the axis. The MESP calculations showed a larger V_min value for the interacting nitrogen centers of the thymine nucleobase, supporting its stronger binding with the Hg²⁺ ion compared to the other nucleobases. The role of the backbone is crucial in nucleic acids to determine many useful properties, and PNAs have been exploited extensively in the literature. Thus, this study was further extended to metal-mediated PNA-containing dimer mispairs such as _DTTTT_P (thymine–thymine dimer model with hybrid DNA and PNA backbone) and _PTTTT_P (thymine–thymine dimer model with PNA backbone). The calculated results showed that the _PTTTT_P PNA mispair is thermodynamically more stable than the canonical dimers. The enthalpy calculated for _DTTTT_D and _PTTTT_P at the B3LYP-D3/6-31G* level of theory showed that _PTTTT_P is ∼3.0 kcal mol⁻¹ more stable than _DTTTT_D. The metallophilic interaction of Hg²⁺ ions in the _PTTTT_P mispair was not observed; however, the metal ions interact with the nitrogen of the thymine bases, presumably enhancing the stability of this mispair by strong electrostatic interactions. These interactions arise due to the P-type conformations of PNAs, which lack metallophilic interactions between the metal ions and can adopt a wider and more unwounded helix. The interaction of the mispair dimers with the explicit water molecules also showed a similar stability trend to that observed with the implicit solvation model. The metallophilic interaction (Hg⋯Hg) was found to be conserved in _DTTTT_D. The AIM analysis performed for these dimers revealed that the interactions are primarily electrostatic in nature. The UV-vis absorption spectra of the mispair systems calculated at the B3LYP-D3/6-31G* level of theory using the TD-DFT method in the aqueous phase suggested that the absorption maximum is located at a longer wavelength in the case of _PTTTT_P compared to the corresponding _DTTTT_D and can be a signature to identify the formation of metal-mediated nucleic acid systems.

Hg²⁺-mediated PNA–PNA mispair duplex (_PTTTT_P) is more energetically favoured compared to DNA–DNA mispair duplex (_DTTTT_D).

Hg(ii) interactions with T-rich regions in oligonucleotides: effects of positional variations on the electrochemical properties

Hg(ii) binding to thymine-rich oligonucleotides (ODNs) is investigated electrochemically. The focus of this study is to probe the effects of position on the electrochemical response. For this purpose, three oligonucleotides were investigated in which the position of a hexa-thymine repeat is varied within a surface-supported oligonucleotide. The hexa repeats were placed in the top, middle, and bottom positions within the strand with respect to the gold surface. The effects were monitored by electrochemical impedance spectroscopy and scanning electrochemical microscopy. Using charge transfer resistance (RCT) and tip current (I) as a measure, it was possible to monitor the effects of Hg(ii) binding to the ds-oligonucleotide. The extent of film resistance reduces as the T-rich region moves from the bottom to top position within the film. The T-rich region closer to the gold surface probably builds less flexible and more rigid T-Hg(ii)-T basepairs compared to the other two positions and is expected to stay in the upright orientation on the surface. This in turn results in significant differences in the electrochemical readout, demonstrating that the position of T-rich sequences within an oligonucleotide strand matters.

Ultrasensitive electrochemical detection of Hg2+ based on an Hg2+-triggered exonuclease III-assisted target recycling strategy

In the present work, a simple, rapid, isothermal, and ultrasensitive homogeneous electrochemical biosensing platform for target Hg2+ detection was developed on the basis of an exonuclease III (Exo III)-aided target recycling amplification strategy. In the assay, a label-free hairpin probe (HP1) was ingeniously designed, containing a protruding DNA fragment at the 3'-termini as the recognition unit for target Hg2+. Also, the DNA fragment in the loop region and 5'-termini (Helper) could be used when a secondary target analog is introduced, but it is caged in the stem region of HP1 when without such a target. The produced secondary target Helper opened the methylene blue (MB)-labeled hairpin probe (HP2) and triggered the Exo III cleavage process, accompanied with the secondary target recycling. This accordingly resulted in the autonomous reduction of the electroactive material MB on the electrode, inducing a distinct decrease in the electrochemical signal. The current developed homogeneous strategy provides a means for the ultrasensitive electrochemical detection of Hg2+ down to the 227 pM level, with high selectivity. It could be further used as a general autocatalytic and homogeneous strategy toward the detection of a wide spectrum of analytes and may be associated with more analytical techniques.

A Multifunctional Molecular Probe for Detecting Hg2+ and Ag⁺ Based on Ion-Mediated Base Mismatch

In this paper, a multifunctional biosensing platform for sensitively detecting Hg²⁺ and Ag⁺, based on ion-mediated base mismatch, fluorescent labeling, and strand displacement, is introduced. The sensor can also be used as an OR logic gate, the multifunctional design of sensors is realized. Firstly, orthogonal experiments with three factors and three levels were carried out on the designed sensor, and preliminary optimization of conditions was performed for subsequent experiments. Next, the designed sensor was tested the specificity and target selectivity under the optimized conditions, and the application to actual environmental samples further verified the feasibility. Generally, this is a convenient, fast, stable, and low-cost method that provides a variety of ideas and an experimental basis for subsequent research.

Electrochemical biosensor based on Se-doped MWCNTs-graphene and Y-shaped DNA-aided target-triggered amplification strategy

A highly sensitive electrochemical biosensor for detection of platelet-derived growth factor-BB (PDGF-BB) is developed by using Se-doped multi-walled carbon nanotubes (MWCNTs)-graphene hybrids as electrode supporting substrate, hemin/G-quadruplex as trace labels and Y-shaped DNA-aided target recycling as signal magnifier. The aptamer-containing hairpin probes were first immobilized on the electrode. When target PDGF-BB was added, the aptamer binded PDGF-BB to trigger catalytic assembly of two other hairpins to form many G-quadruplex Y-junction DNA structures, which released PDGF-BB to again bind the intact aptamer to initiate another assembly cycle. G-quadruplex/hemin complexes were produced when hemin was added to generate substantially amplified current output. The developed assay showed a linear range toward PDGF-BB from 0.1 pM to 10 nM with a detection limit of 27 fM (S/N = 3). The method showed excellent specificity and repeatability, and could be expediently applied for sensitive detection of other molecules by simply changing the aptamers.