Probing Biomolecular Interactions with Dual Polarization Interferometry: Real-Time and Label-Free Coralyne Detection by Use of Homoadenine DNA Oligonucleotide

Oligo-Adenine Derived Secondary Nucleic Acid Frameworks: From Structural Characteristics to Applications

Oligo-adenine (polyA) is primarily known for its critical role in mRNA stability, translational status, and gene regulation. Beyond its biological functions, extensive research has unveiled the diverse applications of polyA. In response to environmental stimuli, single polyA strands undergo distinctive structural transitions into diverse secondary configurations, which are reversible upon the introduction of appropriate counter-triggers. In this review, we systematically summarize recent advances of noncanonical structures derived from polyA, including A-motif duplex, A-cyanuric acid triplex, A-coralyne-A duplex, and T ⋅ A-T triplex. The structural characteristics and mechanisms underlying these conformations under specific external stimuli are addressed, followed by examples of their applications in stimuli-responsive DNA hydrogels, supramolecular fibre assembly, molecular electronics and switches, biosensing and bioengineering, payloads encapsulation and release, and others. A detailed comparison of these polyA-derived noncanonical structures is provided, highlighting their distinctive features. Furthermore, by integrating their stimuli-responsiveness and conformational characteristics, advanced material development, such as pH-cascaded DNA hydrogels and supramolecular fibres exhibiting dynamic structural transitions adapting environmental cues, are introduced. An outlook for future developments is also discussed. These polyA derived, stimuli-responsive, noncanonical structures enrich the arsenal of DNA "toolbox", offering dynamic DNA frameworks for diverse future applications.

Real-time analysis of the biomolecular interaction between gelsolin and Aβ1-42 monomer and its implication for Alzheimer's disease

Biomolecular interaction acts a pivotal part in understanding the mechanisms underlying the development of Alzheimer's disease (AD). Herein, we built a biosensing platform to explore the interaction between gelsolin (GSN) and different β-amyloid protein 1-42 (Aβ1-42) species, including Aβ1-42 monomer (m-Aβ), Aβ1-42 oligomers with both low and high levels of aggregation (LLo-Aβ and HLo-Aβ) via dual polarization interferometry (DPI). Real-time molecular interaction process and kinetic analysis showed that m-Aβ had the strongest affinity and specificity with GSN compared with LLo-Aβ and HLo-Aβ. The impact of GSN on inhibiting aggregation of Aβ1-42 and solubilizing Aβ1-42 aggregates was evaluated by circular dichroism (CD) spectroscopy. The maintenance of random coil structure of m-Aβ and the reversal of β-sheet structure in HLo-Aβ were observed, demonstrating the beneficial effects of GSN on preventing Aβ from aggregation. In addition, the structure of m-Aβ/GSN complex was analyzed in detail by molecular dynamics (MD) simulation and molecular docking. The specific binding sites and crucial intermolecular forces were identified, which are believed to stabilize m-Aβ in its soluble state and to inhibit the fibrilization of Aβ1-42. Combined theoretical simulations and experiment results, we speculate that the success of GSN sequestration mechanism and the balance of GSN levels in cerebrospinal fluid and plasma of AD subjects may contribute to a delay in AD progression. This research not only unveils the molecular basis of the interaction between GSN and Aβ1-42, but also provides clues to understanding the crucial functions of GSN in AD and drives the development of AD drugs and therapeutic approaches.

Insights into Zwitterionic Surfactant Interactions at the Oil-Water Interface by Interferometry Experiments and MDS Calculations

In this work, the interaction performance of zwitterionic surfactant [dodecyl dimethyl sulfopropyl betaine (DSB-12) and hexadecyl dimethyl sulfopropyl betaine (DSB-16)] at the n-octadecane oil surface is investigated from experimental and simulation insights. For a macroscopic experiment, interfacial interferometry technology was developed for real-time monitor interaction performances and to obtain the quantitative interfacial thickness and mass results. The Langmuir model was characterized by thermodynamic analysis, deducing the aggregation spontaneity of DSB-16 > DSB-12 with ΔGagg(DSB-16) = -5.94 kJ mol-1 < ΔGagg(DSB-12) = 24.08 kJ mol-1. A three-step dynamic model (adsorption, arrangement, and aggregation) was characterized by kinetic analysis, indicating arrangement process as slow-limiting step with k2(arr) < k1(ads), k3(agg). For microscopic simulation, and molecular dynamic (MD) method was utilized to theoretically investigate interaction performances and obtain the interfacial configuration and energy results. The interaction stability and interaction strength were indicated to be DSB-16 > DSB-12 with differences of final energy ΔEfin = 48-88 kcal mol-1. The interaction mechanism was explained by proposing the model of "response enhancement" and "deposition activity" for DSB-16 interactions, and "response decrease" and "elution activity" for DSB-12 interactions. The different performances can be attributed to the different interaction forms and forces of surfactants. This work provided a platform for performance and mechanism investigation between the surfactant molecule and oil surface, which is of great significance in reservoir exploitation and enhanced oil recovery (EOR).

Selectivity of natural isoquinoline alkaloid assembler in programming poly(dA) into parallel duplex by polyvalent synergy

Ligand-induced assembly of disordered DNAs attracts much attention due to its potential action in transcription regulation and molecular switches-based sensors. Among natural isoquinoline alkaloids (NIAs), we screened out nitidine (NIT) as polyvalent-binding assembler to program poly(dA) into a parallel duplex assembly at neutral pH. The molecule planarity of NIAs was believed to be a determinant factor in programming the parallel poly(dA) assembly. Poly(dA) with more than six adenines can initiate the synergistic binding of NIT to generate the parallel assembly. It is expected that one A-A pair in duplex can bind one NIT molecule provided that poly(dA) is long enough, suggesting the pivotal role of the polyvalent synergy of NIT in programming the parallel poly(dA) assembly. A gold nanoparticles-based colorimetric method was also developed to screen NIT out of NIAs having the potential to construct the poly(dA) assembly. Our work will inspire more interest in developing polyadenine-based switches and sensors by concentrating NIT within the polyadenine parallel assembly.

Coumarin 6H-fused fluorescent probe for highly sensitive detection of coralyne using oligonucleotide-modified silver nanoparticles

In this study, a novel, rapid, and sensitive fluorescence sensing platform was developed for the detection of coralyne (COR) by the conjugation of coumarin 6H (C6H) fluorescent dye with oligonucleotide-modified silver nanoparticles [(dT)₃₂-AgNPs]. In the presence of COR, a remarkable and rapid decrease in the fluorescence signal of the probe with a quenching efficiency of around 62% was observed. The quenching response of the system towards COR was possibly due to the displacement of thymidine-rich deoxyoligonucleotides by COR on the surface of AgNPs. The complementary experiments with an adenine-rich single strand as well as with two different secondary structures (i.e., duplex and triplex) revealed a favorable sequence specificity of the sensing platform. The influence of key parameters including the incubation time and temperature was evaluated and optimized to achieve the highest performance. The linear range of 10-183 nM with a correlation coefficient of R = 0.9982 and a limit of detection of 5.24 nM were obtained under the optimized conditions. The selectivity of the proposed probe towards COR was revealed by the evaluation of its response to other small molecules that have molecular structures similar to COR. Finally, the successful applicability of the system was shown with the obtained average recoveries in the range of 87.28-104.52% in human urine samples.

Recent advancements in coralyne (COR)-based biosensors: Basic principles, various strategies and future perspectives

As a kind of protoberberine alkaloid heterocyclic analogues, coralyne (COR) has been reported to exhibit superior antileukemic ability and used as anticancer drug agent. While, the severe hazards and side effects caused by unreasonable use have made its accurate detection more and more important. Although scientists have explored various methods to sense COR and other related targets, a systematical review which could not only elaborate recent developments and analyze current challenges of COR-based biosensors, but also present future perspective has not been reported and is urgently needed. In this review, we attempt to summarize latest advancements in COR-based biosensors in recent decade. Firstly, the operating principles, advantages and disadvantages of various strategies for COR detection (colorimetric, fluorescent, electrochemical and other ones) are comprehensively demonstrated and reviewed. Secondly, COR-assisted biosensors for detection of different non-COR targets (heparin, toxins, nucleic acids and other small molecules) are further discussed. Finally, we analyze current challenges and also suggest potential perspectives for this area.

The hot-wire concept: Towards a one-element thermal biosensor platform

In this work, the 3ω hot-wire concept is explored as a prospective biosensing platform with a single sensing element that can detect analytes based on a change in the thermal interface conductance. A uniform receptor layer such as single-stranded DNA is immobilized on a thin aluminium wire, which serves not only as an immobilization platform but also as a heating element and temperature sensor together. The wire is heated periodically with an alternating current (angular frequency ω) and the third harmonic (frequency 3ω) of the voltage across the wire renders the efficiency of heat transfer from the wire to the surrounding medium. The amplitude of the 3ω voltage depends sensitively on the composition and conformation of the biofunctional interface layer. We illustrate this with a model system that includes blank aluminium wires, wires with silanes bound covalently to the native surface oxide, and with single-, respectively double-stranded DNA tethered to the silanes. The difference in heat-transfer due to these coatings is significant and measurable not only in a liquid but also in air. Based on this proof-of-concept, various applications come in sight such as mutation analysis and analyte detection with aptamers or molecularly-imprinted polymers as receptors. Wire materials other than aluminium are possible as well and the concept is suitable for miniaturization and parallelization.

Real-Time Analysis of Specific Binding between Apolipoprotein E Isoforms and Amyloid β-Peptide by Dual Polarization Interferometry

One of the pathogenesis hypotheses of Alzheimer's disease (AD) is amyloid depositions and neurofibrillary tangles. Apolipoprotein E (Apo E) acts a vital part in the development of AD by affecting the aggregation and clearance of amyloid-β (Aβ). In this paper, a dual polarization interferometry (DPI) technique was employed for a real-time investigation toward the binding events of Apo E isoforms, for instance, Apo E2, Apo E3, and Apo E4, with Aβ_1-40. By evaluation of detailed binding information provided by DPI, the affinities between Apo E isoforms and Aβ_1-40 follow the order of E4 > E3 > E2, and the dissociation constants (K_D) of Aβ_1-40 with Apo E2, Apo E3, and Apo E4 were determined to be 251 ± 37, 40 ± 0.65, and 24.6 ± 2.42 nM, respectively. Our findings reveal the isoform-specific binding behaviors from a kinetics perspective, which can help us understand that Apo E4 has a higher risk of causing AD because of its promoting effect on Aβ aggregation and fibrillation and inefficient clearance of Aβ. Remarkably, this work provides a promising method for exploring the dynamics of interactions between biomolecules and expectantly contributes to the development of AD drugs and therapies targeting Apo E and Aβ.

Label-Free and Regenerable Aptasensor for Real-Time Detection of Cadmium(II) by Dual Polarization Interferometry

Recently, numerous aptamer-based biosensors have been developed to detect heavy metal ions. Most of aptamer-based biosensors only can be used to get some quantitative information. The mechanism of the interaction between aptamer and metal ions, however, is rarely studied. In this work, a label-free and regenerable aptamer-based biosensor was constructed using dual polarization interferometry (DPI). This aptasensor was used to investigate the real-time interaction process between cadmium(II) and its aptamer. According to the information on mass, thickness, and density obtained by DPI, a Cd²⁺ concentration-dependent interaction mechanism and conformation of aptamer was proposed. At low Cd²⁺ concentration, Cd²⁺ mainly interacted with phosphate groups on aptamer, resulting in the stretched ssDNA and a few vertical hairpin structures. When adding the high concentration of Cd²⁺, Cd²⁺ primarily bound with bases of DNA by coordination interaction and the conformation of aptamer transferred to a tight and short hairpin structure. In addition, the association rate constant (k_a), dissociation rate constant (k_d) and disassociation constant (K_D) between Cd²⁺ and its aptamer were calculated to be 96 M^-1 S^-1, 2.11 × 10^-5 S^-1, and 220 nM, respectively. The proposed aptasensor showed high sensitivity for Cd²⁺ detection with the detection limit of 0.61 μg/L, which was far below the 5.0 μg/L ranked by the U.S. Environmental Protection Agency. The biosensor also exhibited excellent regenerability and could be used for three cycles without obvious change in response signal. Therefore, the developed method could not only provide quantitative information, but also offered the information on conformation and kinetics for molecular interaction. This method can facilely extend to study the interaction of DNA with other ions, small molecules, or biomacromolecules.

Detection of coralyne and heparin by polymerase extension reaction using SYBR Green I

Polydeoxyadenosine (poly (dA)) has been extensively applied for detecting many drug molecules. Herein, we developed a sensitive method for detecting coralyne and heparin using a modified DNA probe with poly (dA) at one end. In the absence of coralyne, the DNA probe was digested by the Exonuclease I (Exo I), and therefore the SYBR Green I (SG I) emitted an extremely low fluorescent signal. While coralyne specifically binding to poly (dA) with strong propensity could remarkably restrain the disintegration of the DNA probe, through which as a template the second strand of DNA sequence was formed with the introduction of DNA polymerase. Therefore, the fluorescent signal of SG I was intensified to quantify coralyne. Based on this method, heparin can be determined due to its strong affinity towards coralyne. This method showed a linear range from 2 to 500 nM for coralyne with a low detection limit of 0.98 nM, and the linear range of heparin was from 1 to 100 nM when 1.25 nm was the detection limit. The proposed method was also implemented successfully in biological samples and showed a potential application for screening potential therapeutic molecules.

Optical Biosensors for Label-Free Detection of Small Molecules

Label-free optical biosensors are an intriguing option for the analyses of many analytes, as they offer several advantages such as high sensitivity, direct and real-time measurement in addition to multiplexing capabilities. However, development of label-free optical biosensors for small molecules can be challenging as most of them are not naturally chromogenic or fluorescent, and in some cases, the sensor response is related to the size of the analyte. To overcome some of the limitations associated with the analysis of biologically, pharmacologically, or environmentally relevant compounds of low molecular weight, recent advances in the field have improved the detection of these analytes using outstanding methodology, instrumentation, recognition elements, or immobilization strategies. In this review, we aim to introduce some of the latest developments in the field of label-free optical biosensors with the focus on applications with novel innovations to overcome the challenges related to small molecule detection. Optical label-free methods with different transduction schemes, including evanescent wave and optical fiber sensors, surface plasmon resonance, surface-enhanced Raman spectroscopy, and interferometry, using various biorecognition elements, such as antibodies, aptamers, enzymes, and bioinspired molecularly imprinted polymers, are reviewed.

Real-time and label-free detection of bisphenol A by an ssDNA aptamer sensor combined with dual polarization interferometry

DPI is an efficient and reliable platform for detection of organic pollutants and toxicants.

An interferometric imaging biosensor using weighted spectrum analysis to confirm DNA monolayer films with attogram sensitivity

Interferometric imaging biosensors are powerful and convenient tools for confirming the existence of DNA monolayer films on silicon microarray platforms. However, their accuracy and sensitivity need further improvement because DNA molecules contribute to an inconspicuous interferometric signal both in thickness and size. Such weaknesses result in poor performance of these biosensors for low DNA content analyses and point mutation tests. In this paper, an interferometric imaging biosensor with weighted spectrum analysis is presented to confirm DNA monolayer films. The interferometric signal of DNA molecules can be extracted and then quantitative detection results for DNA microarrays can be reconstructed. With the proposed strategy, the relative error of thickness detection was reduced from 88.94% to merely 4.15%. The mass sensitivity per unit area of the proposed biosensor reached 20 attograms (ag). Therefore, the sample consumption per unit area of the target DNA content was only 62.5 zeptomoles (zm), with the volume of 0.25 picolitres (pL). Compared with the fluorescence resonance energy transfer (FRET), the measurement veracity of the interferometric imaging biosensor with weighted spectrum analysis is free to the changes in spotting concentration and DNA length. The detection range was more than 1µm. Moreover, single nucleotide mismatch could be pointed out combined with specific DNA ligation. A mutation experiment for lung cancer detection proved the high selectivity and accurate analysis capability of the presented biosensor.

Real-Time Study of the Interaction between G-Rich DNA Oligonucleotides and Lead Ion on DNA Tetrahedron-Functionalized Sensing Platform by Dual Polarization Interferometry

G-quadruplex plays roles in numerous physiological and pathological processes of organisms. Due to the unique properties of G-quadruplex (e.g., forming G4/hemin complexes with catalytic activity and electron acceptability, binding with metal ions, proteins, fluorescent ligands, and so on), it has been widely applied in biosensing. But the formation process of G-quadruplex is not yet fully understood. Here, a DNA tetrahedron platform with higher reproducibility, regenerative ability, and time-saving building process was coupled with dual polarization interferometry technique for the real-time and label-free investigation of the specific interaction process of guanine-rich singled-stranded DNA (G-rich ssDNA) and Pb²⁺. The oriented immobilization of probes greatly decreased the spatial hindrance effect and improved the accessibility of the probes to the Pb²⁺ ions. Through real-time monitoring of the whole formation process of the G-quadruplex, we speculated that the probes on the tetrahedron platform initially stood on the sensing surface with a random coil conformation, then the G-rich ssDNA preliminarily formed unstable G-quartets by H-bonding and cation binding, subsequently forming a completely folded and stable quadruplex structure through relatively slow strand rearrangements. On the basis of these studies, we also developed a novel sensing platform for the specific and sensitive determination of Pb²⁺ and its chelating agent ethylenediaminetetraacetic acid. This study not only provides a proof-of-concept for conformational dynamics of G-quadruplex-related drugs and pathogenes, but also enriches the biosensor tools by combining nanomaterial with interfaces technique.

One-step purification and concentration of DNA in porous membranes for point-of-care applications

The emergence of rapid, user-friendly, point-of-care (POC) diagnostic systems is paving the way for better disease diagnosis and control. Lately, there has been a strong emphasis on developing molecular-based diagnostics due to their potential for greatly increased sensitivity and specificity. One of the most critical steps in developing practical diagnostic systems is the ability to perform sample preparation, especially the purification of nucleic acids (NA), at the POC. As such, we have developed a simple-to-use, inexpensive, and disposable sample preparation system for in-membrane purification and concentration of NAs. This system couples lateral flow in a porous membrane with chitosan, a linear polysaccharide that captures NAs via anion exchange chromatography. The system can also substantially concentrate the NAs. The combination of these capabilities can be used on a wide range of sample types, which are prepared for use in downstream processes, such as qPCR, without further purification.

Sensitive detection for coralyne and mercury ions based on homo-A/T DNA by exonuclease signal amplification

Based on specific homo-A/T DNA binding properties, a strategy for coralyne and mercury ions detection was realised by exonuclease-aided signal amplification. Coralyne could specifically bind homo-A DNA and protect it from the hydrolysis of exonuclease I. The coralyne-protected DNA was subsequently used as a trigger strand to hydrolyze DNA2 in exonuclease-aided signal amplification process. Thiazole orange was used to quantify the remainder DNA2. Under the optimal condition, the fluorescence intensity was linearly proportional to the concentration of coralyne in the range of 0.2-100 nM with a limit of detection (LOD) of 0.31 nM, which presented the lowest LOD for coralyne among all reported. With homo-T and Hg(2+) taking the place of homo-A DNA and coralyne, respectively, the system could also be used for Hg(2+) detection. The experiments in real samples also showed good results. This method was label-free, low-cost, easy-operating and highly repeatable for the detection of coralyne and mercury ions. It could also be extended to detect various analytes, such as other metal ions, proteins and small molecules by using appropriate aptamers.

A simple, sensitive colorimetric assay for coralyne based on target induced split G-quadruplex formation

The screening of potential drugs specifically binding to polydeoxyadenosine (poly(dA)) has been of great interest in recent studies. We have developed a simple colorimetric strategy through the mechanism of target induced split G-quadruplex formation for detecting coralyne, a poly(dA)-binding drug with noticeable antitumor activity. Two DNA oligonucleotides containing a split G-quadruplex sequence and an adenine-rich sequence are used in our strategy. In the presence of coralyne, the adenine-rich sequences of two oligonucleotides are drawn into close proximity, resulting in the formation of a split G-quadruplex DNAzyme that catalyzes the generation of a colored product. The DNAzyme-based colorimetric assay for coralyne has a linear range of from 0.033 to 1.667 μM with a low detection limit of 16 nM. The developed method is simple, cost-effective and visible; it holds great potential for applications in drug screening.

Unexpected complex formation between coralyne and cyclic diadenosine monophosphate providing a simple fluorescent turn-on assay to detect this bacterial second messenger

Cyclic diadenosine monophosphate (c-di-AMP) has emerged as an important dinucleotide that is involved in several processes in bacteria, including cell wall remodeling (and therefore resistance to antibiotics that target bacterial cell wall). Small molecules that target c-di-AMP metabolism enzymes have the potential to be used as antibiotics. Coralyne is known to form strong complexes with polyadenine containing eight or more adenine stretches but not with short polyadenine oligonucleotides. Using a panel of techniques (UV, both steady state fluorescence and fluorescence lifetime measurements, circular dichroism (CD), NMR, and Job plots), we demonstrate that c-di-AMP, which contains only two adenine bases is an exception to this rule and that it can form complexes with coralyne, even at low micromolar concentrations. Interestingly, pApA (the linear analog of c-di-AMP that also contains two adenines) or cyclic diguanylate (c-di-GMP, another nucleotide second messenger in bacteria) did not form any complex with coralyne. Unlike polyadenine, which forms a 2:1 complex with coralyne, c-di-AMP forms a higher order complex with coralyne (≥6:1). Additionally, whereas polyadenine reduces the fluorescence of coralyne when bound, c-di-AMP enhances the fluorescence of coralyne. We use the quenching property of halides to selectively quench the fluorescence of unbound coralyne but not that of coralyne bound to c-di-AMP. Using this simple selective quenching strategy, the assay could be used to monitor the synthesis of c-di-AMP by DisA or the degradation of c-di-AMP by YybT. Apart from the practical utility of this assay for c-di-AMP research, this work also demonstrates that, when administered to cells, intercalators might not only associate with polynucleotides, such as DNA or RNA, but also could associate with cyclic dinucleotides to disrupt or modulate signal transduction processes mediated by these nucleotides.

Chemical surface modifications for the development of silicon-based label-free integrated optical (IO) biosensors: a review

Increasing interest has been paid to label-free biosensors in recent years. Among them, refractive index (RI) optical biosensors enable high density and the chip-scale integration of optical components. This makes them more appealing to help develop lab-on-a-chip devices. Today, many RI integrated optical (IO) devices are made using silicon-based materials. A key issue in their development is the biofunctionalization of sensing surfaces because they provide a specific, sensitive response to the analyte of interest. This review critically discusses the biofunctionalization procedures, assay formats and characterization techniques employed in setting up IO biosensors. In addition, it provides the most relevant results obtained from using these devices for real sample biosensing. Finally, an overview of the most promising future developments in the fields of chemical surface modification and capture agent attachment for IO biosensors follows.