DNA-conjugated Gold Nanoparticles Research Articles

AuNPs-based lateral flow strip genotoxicity biosensor by sensitive quantification of 8-oxodGuo

Development of rapid and sensitive methods for screening of large number of chemical pollutants with potential genotoxicity is in urgent demands. In this work, we reported a chemical genotoxicity sensor based on the lateral flow strip (LFS) quantification of the 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodGuo). The proposed sensing strategy introduced human 8-oxoguanine DNA glycosylase (hOGG 1) and human apyrimidinic endonuclease (APE 1) to convert 8-oxodGuo to strand break. Then, the DNA conjugated gold nanoparticles (AuNPs) complexes could not be captured on test line (T-line), showing visible red color fading. Additionally, the mean grey value of the optical density in the T-line zone was analyzed by using a mobile phone camera and Image J software to quantify 8-oxodGuo. Under the optimized experimental conditions, the LFS DNA biosensor could detect the lowest concentration of 8-oxodGuo down to 0.2 pmol. To demonstrate its universal applications, in vitro generation of 8-oxodGuo by Rose Bengal under irradiation and Fe2+-mediated Fenton reagent were successfully measured. The detection limit of oxidative DNA damage induced by Rose Bengal or Fenton reagent could be down to 0.01 μM or 1 nM Fe2+/4 nM H2O2, respectively. The 10-fold higher sensitivity for Fenton reagent was attributed to much more severe damage than Rose Bengal, producing both DNA strand break and nucleobases conversion. The results demonstrated that the LFS DNA biosensor could detect oxidative DNA damage for the first time, showing its potential application for assessment of the genotoxicity of abundant chemical pollutants.

Hollow Polyethyleneimine Nanoparticles with Drug Loaded DNA for Chemotherapeutic Applications.

The next generation of anticancer agents are emerging from rationally designed nanostructured materials. This work involved the synthesis and characterization of novel hollow DNA-conjugated gold nanoparticles (DNA-AuNPs) for controlled drug delivery. Polyethyleneimine (PEI) was bound to AuNPs, forming polymer-shell nanoparticles. Dissolution of the gold core via iodine formed hollow core polymeric nanoparticles (HCPNPs) and a high density (85 molecules/particle) of DNA intercalated with daunorubicin was conjugated. Particles were spherical with an average diameter of 105.7±17.3 nm and zeta potential of 20.4±3.54 mV. We hypothesize the DNA backbone electrostatically condensed to the primary amines on the surface of the particle toroidally, weaving itself within the polymer shell. During the DNA intercalation process, increasing the ionic concentration and decreasing the amine/phosphate ratio 10-fold increased drug intercalation 64 % and 61 %, respectively, allowing us to determine the optimal method of particle synthesis. As intercalation sites increased with increasing DNA strand length, drug loading increased. An average of 874±40.1 daunorubicin molecules were loaded per HCPNP. HCPNPs with drug intercalated DNA have strong potential to be clinically efficacious drug delivery vehicles due to the versatility of DNA and high drug loading capacities.

Comparison of DNA-Gold Nanoparticle Conjugation Methods: Application in Lateral Flow Nucleic Acid Biosensors.

Lateral flow nucleic acid biosensors (LFNABs) have attracted extensive attention due to their rapid turnaround time, low cost, and results that are visible to the naked eye. One of the key steps to develop LFNABs is to prepare DNA-gold nanoparticle (DNA-AuNP) conjugates, which affect the sensitivity of LFNABs significantly. To date, various conjugation methods-including the salt-aging method, microwave-assisted dry heating method, freeze-thaw method, low-pH method, and butanol dehydration method-have been reported to prepare DNA-AuNP conjugates. In this study, we conducted a comparative analysis of the analytical performances of LFNABs prepared with the above five conjugation methods, and we found that the butanol dehydration method gave the lowest detection limit. After systematic optimization, the LFNAB prepared with the butanol dehydration method had a detection limit of 5 pM for single-strand DNA, which is 100 times lower than that of the salt-aging method. The as-prepared LFNAB was applied to detect miRNA-21 in human serum, with satisfactory results. The butanol dehydration method thus offers a rapid conjugation approach to prepare DNA-AuNP conjugates for LFNABs, and it can also be extended to other types of DNA biosensors and biomedical applications.

A microchamber-free and enzyme-free digital assay based on ultrabright fluorescent microspheres

Digital analysis is an effective single-molecule detection method and has attracted extensive attention in the field of bioassays. However, most digital assays require microchambers for signal compartmentalization. Herein, we developed a microchamber-free and enzyme-free digital assay by labeling paramagnetic beads directly with ultrabright fluorescent microspheres. In this assay, a DNA sandwich analysis was firstly performed on the bead to label a fluorescent microsphere. Then, the beads were loaded on the glass slide to form a monolayer film for signal readout. The whole analysis process does not require the participation of enzymes and the preparation of microchambers, which greatly simplifies the experimental steps and saves the costs. Furthermore, by introducing non-enzymatic hybridization chain reaction (HCR) and biotinylated DNA-conjugated gold nanoparticles (Au NPs-Bio), the capture efficiency and analytical sensitivity were improved. As a proof of concept, single-stranded DNA (ssDNA) of SARS-CoV-2 fragment was chosen as a model, and a detection limit of 1.5 fM was achieved. Spiked and recovery experiments on human serum and saliva samples validated the good performance of the proposed digital assay in real biological samples. The proposed assay provides a facile way of signal generation and readout for digital analysis.

Aggregation of DNA-Grafted Nanoparticles in Water: The Critical Role of Sequence-Dependent Conformation of DNA Coating.

Aggregation behavior of nanoparticles in water, particularly in the presence of surface coating, is a fundamental behavior to understand as it closely relates to the material function, reactivity, and toxicity. Engineered DNA, an important type of surface coating, is essentially different from conventional polymeric coatings with homogeneous repeating units. The heterogeneous nature of DNA with numerous combinations of the four nucleotides poses a challenge to understand the aggregation of nanoparticles coated with them. In this study, we use both experimental and computational approaches to study how DNA properties influence the aggregation of DNA-conjugated gold nanoparticles (DNA-AuNPs). Aggregation kinetics under different pH values and in three salts (NaCl, CaCl2, and MgCl2) were investigated. Overall, DNA-AuNPs demonstrated similar aggregation behavior of electrosterically stabilized nanoparticles, where the surface coating layer thickness played a determining role. The underlying interactions between DNA-AuNPs were analyzed by an extended DLVO model, and the excluded volume repulsion, which varied as a function of layer thickness, was the dominant stabilizing repulsion. Interestingly, the DNA sequence was found to cause different layer thicknesses and thus profoundly different aggregation behaviors in the presence of cations. The interactions between DNA strands with different sequences and surrounding counterions were investigated via molecular dynamics simulations. The simulation results were consistent with experimental observations and supported the sequence-dependent conformational change of DNA coating. Our study provides new molecular-level insights into aggregation of nanoparticles with heterogeneous surface coating such as DNA.

Detection of Hg(II) at Part-Per-Quadrillion Levels by Fiber Optic Plasmonic Absorption Using DNA Hairpin and DNA-Gold Nanoparticle Conjugates

Mercury ion (Hg2+) is extremely toxic even at very low concentrations and its detection mainly relies on bulky and high-cost analytical instruments. Here, we introduce a fast and ultrasensitive biosensing method developed by the integration of fiber optic particle plasmon resonance and a highly selective molecular beacon with a stem-loop DNA structure immobilized on the unclad surface of an optical fiber. In the presence of Hg2+ ions and a free assisting DNA probe, the stem-loop opens and forms thymine–Hg2+–thymine complexes. A DNA reporting probe conjugated to gold nanoparticles is used as a label to interrogate the recognition event by binding with the terminal DNA binding domain of the opened stem-loop. The method provides a wide linear range of at least 5 orders from 10–14 to 10–9 M and an extremely low detection limit of 4.37 fM (0.876 ppq). It takes less than 15 min to analyze the concentration of Hg2+ ions in aqueous samples. The method is desirable for point-of-use applications because of its low-cost instrumentation and sensor chips, easy operation, and portability.

DNA Gold Nanoparticle Motors Demonstrate Processive Motion with Bursts of Speed Up to 50 nm Per Second.

Synthetic motors that consume chemical energy to produce mechanical work offer potential applications in many fields that span from computing to drug delivery and diagnostics. Among the various synthetic motors studied thus far, DNA-based machines offer the greatest programmability and have shown the ability to translocate micrometer-distances in an autonomous manner. DNA motors move by employing a burnt-bridge Brownian ratchet mechanism, where the DNA "legs" hybridize and then destroy complementary nucleic acids immobilized on a surface. We have previously shown that highly multivalent DNA motors that roll offer improved performance compared to bipedal walkers. Here, we use DNA-gold nanoparticle conjugates to investigate and enhance DNA nanomotor performance. Specifically, we tune structural parameters such as DNA leg density, leg span, and nanoparticle anisotropy as well as buffer conditions to enhance motor performance. Both modeling and experiments demonstrate that increasing DNA leg density boosts the speed and processivity of motors, whereas DNA leg span increases processivity and directionality. By taking advantage of label-free imaging of nanomotors, we also uncover Lévy-type motion where motors exhibit bursts of translocation that are punctuated with transient stalling. Dimerized particles also demonstrate more ballistic trajectories confirming a rolling mechanism. Our work shows the fundamental properties that control DNA motor performance and demonstrates optimized motors that can travel multiple micrometers within minutes with speeds of up to 50 nm/s. The performance of these nanoscale motors approaches that of motor proteins that travel at speeds of 100-1000 nm/s, and hence this work can be important in developing protocellular systems as well next generation sensors and diagnostics.

Facile construction of targeted pH-responsive DNA-conjugated gold nanoparticles for synergistic photothermal-chemotherapy

Recently, stimuli-responsive DNA nanostructure-based nanodevices have been applied for cancer therapy. In this study, pH-responsive i-motif DNA was modified on gold nanoparticles (AuNPs) via a facile, time-saving freeze-thaw method and utilized to construct stimuli-responsive drug nanocarriers. When the environment pH changes from 7.4 to 5.0, the i-motif DNA would be folded into four-stranded (C-quadruplex) that could be characterized by circular dichroism, and the characteristic of acid stimulate was verified by fluorescence resonance energy transfer (FRET). To enhance specifical cellular uptake, MUC1 aptamer was employed as the targeting moiety. Doxorubicin (Dox) is an anticancer drug that can be efficiently intercalated into GC base pairs of DNA nanostructure to form drug-loaded nanovehicles (Dox@AuNP-MUC1). Additionally, owing to the excellent photothermal conversion efficiency of AuNPs, the synergistic effect between chemotherapy and PTT can be readily achieved by 808 nm near-infrared (NIR) irradiation, which exhibits specifically and efficiently anticancer efficiency. Hence, this multifunctional drug carrier shows the potential for synergistic photothermal-chemotherapy.

Colorimetric sensing strategy for multiplexed detection of proteins based on three DNA-gold nanoparticle conjugates sensors

Proteins play important roles in mediating various forms of life activities. The development of convenient and reliable strategies for simultaneous recognition of multiple proteins is meaningful for early diagnostics of diseases. Herein, we develop a differential colorimetric sensor array, which is made of nonspecific single-stranded DNA (ssDNA) as receptors and gold nanoparticles (AuNPs) as colorimetric probes for multiple identification of the nine proteins. Upon the addition of analyte proteins, different interactions between various proteins and ssDNA lead to the desorption of different amounts of ssDNA from the AuNP surface, thus resulting in AuNP aggregation to varying degrees in salt environment, which in turn leads to the colorimetric signal change of AuNPs. On the basis of the principle, nine proteins (i.e., bovine serum albumin (BSA), horseradish peroxidase (HRP), pepsin (Pep), hemoglobin (Hem), egg white albumin (EA), trypsin (Try), myoglobin (Myo), cytochrome C (Cyt-C), and concanavalin (Con)) at low concentration (20 nM) were well discriminated by the sensor array.

Stabilization of DNA by sodium and magnesium ions during the synthesis of DNA-bridged gold nanoparticles

Nanostructures synthesized using DNA-conjugated gold nanoparticles have a wide range of applications in the field of biosensorics. The stability of the DNA duplex plays a critical role as it determines the final geometry of these nanostructures. The main way to control DNA stability is to maintain a high ionic strength of the buffer solution; at the same time, high salt concentrations lead to an aggregation of nanoparticles. In this study, by means of the instrumentality of DNA-bridged seeds using tris(hydroxymethyl)aminomethane as a soft reducing agent the dumbbell-like gold nanoparticles up to 35 nm were synthesized with a high concentration of sodium ions of up to 100 mM and magnesium ions up to 1 mM. We also examined at the atomic level the details of the effect of the gold nanoparticle surface, as well as Na+ and Mg2+ ions, on the stability of nucleotide pairs located in close proximity to the grafting site.

Biodistribution of Graphene Oxide Determined through Postadministration Labeling with DNA-Conjugated Gold Nanoparticles and ICPMS.

Recent research has revealed the use of graphene oxide (GO) and its derivatives as a potential biomaterial because of their attractive physicochemical characteristics and functional properties. However, if GO and related derivatives are to become useful materials for biomedical applications, it will be necessary to evaluate their biodistribution for health and safety considerations. To obtain a more accurate biodistribution for GO, we (i) developed a postadministration labeling strategy employing DNA-conjugated gold nanoparticles (DNA-AuNPs) to selectively label administered GO in Solvable-treated tissue samples and (ii) constructed an automatic sample pretreatment scheme (using a C18-packed minicolumn) to effectively separate the DNA-AuNP-labeled GO from the unbound DNA-AuNPs and the dissolved tissue matrices, thereby enabling ultrasensitive, interference-free quantification of GO through measurement (inductively coupled plasma mass spectrometry) of the Au signal intensities. The DNA-AuNPs can bind to GO in a concentration- and time-dependent manner. After optimizing the labeling conditions (DNA length, incubation pH, DNA-AuNP concentration, and incubation time) and the separation scheme (sample loading flow rate, rinsing volume, and eluent composition), we found that A20R20-AuNPs (R20: random DNA sequence including A, T, C, and G) had the strongest binding affinity for labeling of the administered GO (dissociation constant: 36.0 fM) and that the method's detection limit reached 9.3 ag L-1 with a calibration curve having a working range from 10-1 to 1010 fg L-1. Moreover, this approach revealed that the intravenously administered GO accumulated predominantly in the liver and spleen at 1 and 12 h post administration, with apparent discrepancies in the concentrations measured using pre- and postadministration labeling strategies.

An aptasensor strip-based colorimetric determination methodfor kanamycin using cellulose acetate nanofibers decorated DNA-gold nanoparticle bioconjugates.

The preparation ofportable colorimetric biosensor strips is describedby combining aptamer-immobilized electrospun nanofiber membranes (A-NFMs) with signal probes (DNA-conjugated gold nanoparticles (AuNPs)) for determination of kanamycin (KMC) as a model analyte. The A-NFMs were decorated with complementary single-stranded DNA (cDNA) of KMC aptamer-conjugated AuNPs (cDNA@Au) to get the colorimetric biosensor strips. The constructed biosensor strips showed a significant absorbance decreasing band at 510nm which induce a visual color change from pink to white when exposed to KMC, with a low detection limit of 2.5nM (at S/N = 3). The effect is due to disassembling of cDNA@Au from NFMs in the presence of KMC because the aptamer has a higher affinity to KMC than its complementary DNA, which resulted in replacing cDNA@Au with KMC. Satisfactory performance was observed in real sample (drinking water and milk) analysis with a recovery of 98.9-102.2%. The constructed colorimetric biosensor test strips hold great application promise for food safety control. Graphical abstract Schematic representation of biosensor strips for kanamycin detection prepared with the cDNA@Au immobilized aptamer-based cellulose acetate nanofibers.

DNA-Conjugated Gold Nanoparticles as High-Mass Probes in Imaging Mass Cytometry.

We employ imaging mass cytometry (IMC) to investigate in vitro uptake and cellular distribution of DNA-functionalized gold nanoparticles (AuNPs). IMC enables the multiparametric imaging of cell components and allows for the detection of AuNPs in cells with >100 times higher sensitivity than conventional confocal fluorescence imaging, as each nanoparticle contains thousands of atoms for signal amplification. Changes in the accumulation of nanoparticles in cells due to oligonucleotide sequence-dependent interactions are exploited to examine a model biomarker for hypoxia-microRNA-210. We find that AuNPs functionalized with microRNA-210-targeting sequence accumulate in hypoxic cells 3 to 4-fold compared to normoxic cells. The work examines the potential use of DNA-AuNP as high-mass probes for the analysis of nonabundant nucleic acids.

MRNA Guided Intracellular Self-Assembly of DNA-Gold Nanoparticle Conjugates as a Precise Trigger to Up-Regulate Cell Apoptosis and Activate Photothermal Therapy.

The size of nanoparticles was generally accepted to have a close relationship with the penetration and retention properties among tumor sites, which is one of the most significant issues during nanomedicine delivery. Despite the outstanding stealth property when circulating and the penetration ability in tumor tissue, small nanoparticles still have the problem of inadequate retention time. Taking advantage of the precise self-assembly of DNA-nanoparticle conjugates, we developed an intracellular assembly system to realize the change of nanoparticle size from small to large as well as activation of therapeutic function inside cancer cells. A duplex sequence of cancer-cell-specific mRNA, survivin, was selected to hybridize with complementary sequence of gold nanoparticle-DNA (AuNP-DNA) conjugates in cancer cell cytoplasm, resulting in the specific and precise formation of intracellular assemblies. Enhanced retention behavior of AuNPs inside cancer cells was shown to be achieved because of the increased nanoparticle size. Meanwhile, an up-regulation effect of cell apoptosis and an activated photothermal therapy function were also created by the formation of AuNP aggregations, and eventually contributed to a high rate of cancer cells death up to 93.33%. In contrast, it exhibited almost no toxicity toward normal cells because of the absence of survivin-induced assembly. Therefore, this mRNA guided intracellular assembly system exhibited its potential as a new precise cancer therapy strategy, and also broadened the application field of DNA-conjugated nanoparticle assembly.

Polymer Pen Lithography-Fabricated DNA Arrays for Highly Sensitive and Selective Detection of Unamplified Ganoderma Boninense DNA.

There is an increasing demand for lithography methods to enable the fabrication of diagnostic devices for the biomedical and agri-food sectors. In this regard, scanning probe lithography methods have emerged as a possible approach for this purpose, as they are not only convenient, robust and accessible, but also enable the deposition of “soft” materials such as complex organic molecules and biomolecules. In this report, the use of polymer pen lithography for the fabrication of DNA oligonucleotide arrays is described, together with the application of the arrays for the sensitive and selective detection of Ganoderma boninense, a fungal pathogen of the oil palm. When used in a sandwich assay format with DNA-conjugated gold nanoparticles, this system is able to generate a visually observable result in the presence of the target DNA. This assay is able to detect as little as 30 ng of Ganoderma-derived DNA without any pre-amplification and without the need for specialist laboratory equipment or training.

Colorimetric sensor assay for discrimination of proteins based on exonuclease I-triggered aggregation of DNA-functionalized gold nanoparticles.

Proteins play a key role in disease diagnosis, and protein discrimination is an important but difficult issue. Here, we report a novel strategy for improving protein discrimination through a facile colorimetric sensor array, which is based on DNA-gold nanoparticle (AuNP) conjugates manipulated by exonuclease I (Exo I). Different proteins exhibit diverse affinities toward the three DNAs, and the DNA-protein binding is resistant to the digestion of Exo I and protects the AuNPs from aggregation in high concentrations of NaCl media, forming distinct response patterns of the array. These response patterns as "fingerprints" can be acquired on the sensor array and then identified by linear discriminant analysis (LDA). The sensor array achieved the correct discrimination of 15 proteins at a 10 nM level in buffer solution and real serum samples. Also, the sensor array had the capability to discriminate individual proteins and the mixtures of them. Remarkably, the practicability of the sensor array was further confirmed by the identification of 35 unknown protein samples with 100% accuracy.

Universal mRNA Translation Enhancement with Gold Nanoparticles Conjugated to Oligonucleotides with a Poly(T) Sequence.

DNA-conjugated gold nanoparticles (AuNPs) have been shown to enhance the translation of mRNA. However, the specific sequence on the DNA dictates the specific mRNA to be enhanced. This study describes poly(thymine)-functionalized AuNPs (AuNP-p(T)DNA) capable of enhancing the translation of any mRNA template that is incorporated into pcDNA6 vector with bovine growth hormone (BGH) polyadenylation signal (P(A)). We demonstrated this by incorporating four genes: green fluorescence protein (GFP), general control nonderepressible 5 (GCN5), cAMP-responsive element binding protein 1 (CREB1), and X-box-binding protein 1-spliced (XBP-1S) separately into pcDNA6 vector with BGH P(A) before their expression in HeLa lysate. The addition of AuNP-p(T)DNA to HeLa lysate containing GFP, GCN5, CREB1, and XBP-1S mRNA increased protein synthesis 1.80, 1.99, 1.95, and 2.20 times, respectively. Similar translation enhancement was also observed in a multiplex reaction containing the mRNA of three genes together in the lysate. Complementary p(T)DNA hybridization to the poly(A) tail of the mRNA was critical as the removal of either p(T)DNA or BGH P(A) in XBP-1S mRNA or the replacement of p(T)DNA with p(A)DNA reduced the translation back to baseline level. Finally, an optimum length of 25 nucleotides for the DNA oligomer and a AuNP-p(T)DNA:mRNA ratio of 0.658 achieved a 3.08-fold translation enhancement. The AuNP-p(T)DNA nanoconstruct could be incorporated into commercial cell-free protein synthesis kits as a universal translation enhancer.

Sequence-Modulated Interactions between Single Multivalent DNA-Conjugated Gold Nanoparticles.

DNA-conjugated gold nanoparticle (AuNP) is an attractive building block to construct elegant plasmonic nanomaterials by self-assembly but the complicated interaction between multivalent nanoconjugates governing the assembly process and the properties of assembled structures remains poorly understood. Herein, with an in situ kinetic single-particle imaging method, we report the dynamic interaction between single multivalent DNA-conjugated AuNPs quantitatively depends on the nucleic acid sequence in nanoconjugates. From the binding dynamics analysis, it was found that the binding of nanoconjugates with DNA length longer than nine bases is kinetically irreversible and the binding rate is dependent on both the sequence length and GC content, enabling us to predict the rational modulation of binding rates of individual building blocks for stepwise assembly. Moreover, the reversibility for the multivalent interaction between single nanoconjugates at constant temperature can be reinstated by adopting the DNA sequence with single-nucleotide mismatch and the lifetime for nanoconjugates at bound state can be tailored by changing the mismatch positions in DNA strands, providing new opportunity to create active nanostructures with controlled dynamic properties. All these findings provide new insights for understanding the multivalent interaction during the assembly process at the single-nanoconjugate level and predicting the programmable self-assembly of engineered nanoconjugates for the fabrication of dynamic nanomaterials.

DNA-conjugated gold nanoparticles based colorimetric assay to assess helicase activity: a novel route to screen potential helicase inhibitors

Helicase are essential enzymes which are widespread in all life-forms. Due to their central role in nucleic acid metabolism, they are emerging as important targets for anti-viral, antibacterial and anti-cancer drugs. The development of easy, cheap, fast and robust biochemical assays to measure helicase activity, overcoming the limitations of the current methods, is a pre-requisite for the discovery of helicase inhibitors through high-throughput screenings. We have developed a method which exploits the optical properties of DNA-conjugated gold nanoparticles (AuNP) and meets the required criteria. The method was tested with the catalytic domain of the human RecQ4 helicase and compared with a conventional FRET-based assay. The AuNP-based assay produced similar results but is simpler, more robust and cheaper than FRET. Therefore, our nanotechnology-based platform shows the potential to provide a useful alternative to the existing conventional methods for following helicase activity and to screen small-molecule libraries as potential helicase inhibitors.

Model-Guided Interface Probe Arrangement for Sensitive Protein Detection.

A wide range of analytical techniques in bioanalysis relies on surface-based biomolecular detection, which requires the confinement of probes onto a heterogeneous surface to react with targets. Probe arrangement on the interface is critical for target recognition and determines assay performance. Much effort has been devoted to screen the optimized probe arrangement according to experimental tests. Such a data-driven posteriori pattern faces low efficiency, ambiguous orientation, and possible deviated tested ranges from the best case. Herein, we demonstrate that a model can effectively guide probe arrangement onto the interface to facilitate probe-target recognition, embodied by the assay of human telomerase activity with DNA-conjugated gold nanoparticles (AuNPs). Both theoretical calculation and experimental results indicate that telomerase activity is maximized on the AuNP surface under guidance of the model. The detection limit is at least 1 order of magnitude lower than that of AuNP bearing densely packed DNA, comparable to that of the telomeric repeat amplification protocol (TRAP). The model-guided interface probe arrangement is proved to be highly useful in regulating interface recognition and may offer a new paradigm to promote surface-based biomolecular detection.