Photosensitized covalent organic framework as a light-induced oxidase mimic for colorimetric detection of uric acid.

As large numbers of people are suffering from gout, an accurate, rapid, and sensitive method for the detection of gout biomarker, uric acid, is important for its effective control, diagnosis, and therapy. Although colorimetric detection methods based on uricase have been considered, they still have limitations as they produce toxic H2O2 and are expensive and not stable. Here, a novel uricase-free colorimetric method was developed for the sensitive and selective detection of uric acid based on the light-induced oxidase-mimicking activity of a new photosensitized covalent organic framework (COF) (2,4,6-trimethylpyridine-3,5-dicarbonitrile-4-[2-(4-formylphenyl)ethynyl]benzaldehyde COF [DCTP-EDA COF]). DCTP-EDA COF has a strong ability to harvest visible light, and it could catalyze the oxidation of 1,4-dioxane, 3,3',5,5'-tetramethylbenzidine under visible light irradiation to produce obvious color changes. With the addition of uric acid, however, the significant inhibition of the oxidase-mimicking activity of DCTP-EDA COF remarkably faded the color, and thus uric acid could be colorimetrically detected in the range of 2.0-150 µM with a limit of detection of 0.62 µM (3σ/K). Moreover, the present colorimetric method exhibited high selectivity; uric acid level in serum samples was successfully determined, and the recoveries ranged from 96.5% to 105.64%, suggesting the high accuracy of the present colorimetric method, which demonstrates great promise in clinical analysis.

DNAzyme-Derived Aptamer Reversely Regulates the Two Types of Enzymatic Activities of Covalent-Organic Frameworks for the Colorimetric Analysis of Uranium.

Nanozymes are nanomaterials with enzyme-mimetic activity. It is known that DNA can interact with various nanozymes in different ways, enhancing or inhibiting the activity of nanozymes, which can be used to develop various biosensors. In this work, we synthesized a photosensitive covalent-organic framework (Tph-BT) as a nanozyme, and its oxidase and peroxidase activities could be reversely regulated by surface modification of single-stranded DNA (ssDNA) for the colorimetric detection of UO22+. Tph-BT exhibits excellent oxidase activity and weak peroxidase activity, and it is surprising to find that the UO22+-specific DNA aptamer can significantly inhibit the oxidase activity while greatly enhancing the peroxidase activity. The present UO22+ interacts with the DNA aptamer to form secondary structures and detaches from the surface of Tph-BT, thereby restoring the enzymatic activity of Tph-BT. Based on the reversed regulation effects of the DNA aptamer on the two types of enzymatic activities of Tph-BT, a novel "off-on" and "on-off" sensing platform can be constructed for the colorimetric analysis of UO22+. This research demonstrates that ssDNA can effectively regulate the different types of enzymatic activities of single COFs and achieve the sensitive and selective colorimetric analysis of radionuclides by the naked eye.

Reversed Regulation Effects of ssDNA on the Mimetic Oxidase and Peroxidase Activities of Covalent Organic Frameworks.

Nanomaterials with enzyme mimetic activity have attracted extensive attention, especially in the regulation of their catalytic activities by biomolecules or other polymers. Here, a covalent organic framework (Tph-BT COF) with excellent photocatalytic activity is constructed by Schiff base reaction, and its mimetic oxidase activity and peroxidase activity is inversely regulated via single-stranded DNA (ssDNA). Under light-emitting diode (LED) light irradiation, Tph-BT exhibited outstanding oxidase activity, which efficiently catalyzed oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) to produce blue oxTMB, and ssDNA, especially those with poly-thymidine (T) sequences, can significantly inhibit its oxidase activity. On the contrary, Tph-BT showed weak peroxidase activity, and the presence of ssDNA, particularly poly-cytosine (C) sequences, can remarkably enhance the peroxidase activity. The influence of base type, base length, and other factors on the activities of two enzymes is also studied, and the results reveal that the adsorption of ssDNA on the surface of Tph-BT prevented intersystem crossing (ISC) and energy transfer processes to reduce 1 O2 generation, while the electrostatic interaction between ssDNA and TMB enhanced Tph-BT's affinity for TMB to facilitate the electron transfer from TMB to • OH. This study investigates multitype mimetic enzyme activities of nonmetallic D-A conjugated COFs and demonstrates their feasibility of regulation by ssDNA.

Construction of Two-Dimensional Fluorescent Covalent Organic Framework Nanosheets for the Detection and Removal of Nitrophenols.

In this work, we synthesized a two-dimensional fluorescent covalent-organic framework (TFPB-TTA COF) nanosheet by selecting and designing reactive monomers to realize the dual-functional processing of nitrophenols. The staggered benzene ring, triazine structure, and imine bond (C═N) of the TFPB-TTA COF can capture free nitrophenols through hydrogen bonding and conjugation interaction, and then, the photoinduced electron transfer and fluorescence resonance energy transfer (FRET) between the TFPB-TTA COF and nitrophenols affects the fluorescence emission of the TFPB-TTA COF, realizing the fluorescence sensing of nitrophenols. The large Ksv values and the low detection limit suggest that the TFPB-TTA COF can serve as sensitive and selective fluorescence sensors for nitrophenol detection in an aqueous system. At the same time, the strong interaction combined with the porous network structure of the TFPB-TTA COF facilitates the efficient adsorption and removal of nitrophenols. Especially for 2,4,6-trinitrophenol, the maximum adsorption capacity can reach 1045.53 mg/g with good recyclability and high structural stability of the TFPB-TTA COF. This work proposed a simple synthetic method for the construction of a fluorescent COF platform for the sensitive determination and efficient adsorption of nitrophenols.

Ultrasensitive detection of UO2 2+ based on dopamine-functionalized MoOx quantum dots.

Uranium is an important nuclear fuel and the risk of human exposure to uranium increases as increasing amounts of uranium-containing waste enter the environment due to the rapid growth of nuclear power. Therefore, rapid, sensitive, and portable uranium detection is a promising approach to effectively control and monitor uranium contamination. To achieve this goal, abundant oxygen- and nitrogen-containing groups were introduced to molybdenum oxide quantum dot (MoOx QDs) surfaces with dopamine (DA) modification. Due to the excellent coordination ability of oxygen- and nitrogen-containing groups with uranium, the obtained DA-functionalized MoOx QDs (DA-MoOx QDs) showed a strong binding affinity for uranium and sensitivity was increased nearly 1000-fold compared with MoOx QDs alone. The limit of detection was 3.85 nM, which is higher than most of the reported nanomaterials. Moreover, the DA-MoOx QD-based method showed high selectivity and uranium could be clearly detected under masking with ethylenediaminetetraacetic acid even when the concentration of other metal ions was 100-fold higher than that of uranium, showing a very promising method for uranium contamination control and monitoring.

Facile Construction of Covalent Organic Framework Nanozyme for Colorimetric Detection of Uranium.

2D covalent organic frameworks (2D COFs) have been recognized as a novel class of photoactive materials owing to their extended π-electron conjugation and high chemical stabilities. Herein, a new covalent organic framework (Tph-BDP) is facilely synthesized by using a porphyrin derivative and an organic dye BODIPY derivative (5,5-difluoro-2,8-diformyl-1,3,7,9-tetramethyl-10-phenyl-5H-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazabori-nin-4-ium-5-uide) as monomers for the first time, and their unique photosensitive properties endow them excellent simulated oxidase activity under 635 nm laser irradiation that can catalyze the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB). Further findings demonstrate that the presence of uranium (UO22+ ) can coordinate with imines of the oxidation products of TMB, thus modulating the charge transfer process of the colored products accompanied with intensive aggregation and remarkable color fading. This research provides a preparation strategy for COFs with excellent photocatalytic properties and nanozyme activity, and broadens the applications of the simple colorimetric methods for sensitive and selective radionuclide detection.

Rapid and sensitive detection of Mycobacterium tuberculosis based on strand displacement amplification and magnetic beads.

Tuberculosis is one of the main infectious diseases threatening public health, and the development of simple, rapid, and cost-saving methods for tuberculosis diagnosis is of profound importance for tuberculosis prevention and treatment. The bacterium Mycobacterium tuberculosis (MTB) is the pathogen that causes tuberculosis, and assaying for MTB is the only criterion for tuberculosis diagnosis. A new enzyme-free method based on strand displacement amplification and magnetic beads was developed for simple, rapid, and cost-saving MTB detection. Under optimum conditions, a good linear relationship could be observed between fluorescence and MTB specific DNA concentration ranging from 0.05 to 150 nM with a correlation coefficient of 0.993 (n = 8) and a detection limit of 47 pM (3σ/K). The present method also distinguished a one base mismatch from MTB specific DNA, showing great promise for MTB genome single base polymorphism analysis. MTB specific DNA content in polymerase chain reaction samples was successfully detected using the new method, and recoveries were 97.8-100.8%, indicating that the present method had high accuracy and shows good potential for the early diagnosis of tuberculosis.

[Label-Free and Rapid Detection of Histidine-Rich Peptides in Saliva].

Siliva as a kind of biomarker containing a variety of bioactive components can be used to help disease diagnosis. Compared with the urine and blood, the collection of saliva is more simple and convenient while the collection process is completely non-invasive. Therefore, saliva detection attracts more and more attention in non-invasive disease diagnosis. Histatins are a family of small, cationic, histidine-rich peptides, which secreted by salivary bringing innate defense of the oral cavity. It has been reported that histatins are related to many other diseases, such as HIV and AIDs. Thus the detection of histatins in saliva is significantly important for oral healthy monitoring and disease diagnosis. In this paper, a new label free method for rapid detection of histidine-rich peptides was developed based on the fact that histidine-rich peptides can interact with 3-azidocoumarin through hydrogen bonds which decreases the electron-donating ability of the azido group and results in fluorescence enhancement of the system. The results showed that the fluorescence intensities were dramatically increased when histatin 5 were incubation with 3-azidocoumarin. There is a good relationship with the linear co r of 0.994 between the enhanced fluorescence and histatin 5 concentration ranging from 0.23 to 31.05 µmol·L-1, and the limit of detection is 72 nmol·L-1 (3σ/k). Moreover, the detection of histidine-rich peptides in saliva was successfully achieved by the new developed label free method since amino acids and proteins in saliva will not be interfered with the detection with the recoveries between 96.7%~111.6%. Compared with the existing saliva analysis methods, this method has the advantage of simple, fast and low cost. It might be applied in non-invasive disease diagnosis.

Advanced "turn-on" colorimetric uranium platform based on the enhanced nanozyme activity of a donor-acceptor structured covalent organic framework.

BACKGROUND: The increasing uranium containing wastes generated during uranium mining and finishing pose a huge threat to the environment and human health, and thus robust strategies for on-site monitoring of uranium pollutant are of great significance for environmental protection around uranium tailings. RESULTS: Herein, a facile "turn-on" colorimetric platform that can achieve uranium detection by spectrometry and naked eyes was developed based on the uranium-enhanced nanozyme activity of covalent organic framework (JUC-505). Thanks to the extended π-conjugated skeleton and donor-acceptor (D-A) structure, JUC-505 exhibited superior photo-activated nanozyme activity, which would be prohibited when the cyano group in JUC-505 skeleton was transformed to the amidoxime group. Further results elucidated that the coordination of uranium with amidoxime groups led to the electron transfer between uranium and the JUC-505-AO skeleton, and thus significantly restored the nanozymatic activity of JUC-505-AO with the subsequent remarkable color changes. Moreover, the uranium concentrations in uranium tailing wastewater detected by the present "turn-on" colorimetric method were well agreed with those by ICP-MS, demonstrating a high accuracy of the present method in real samples. SIGNIFICANCE: The D-A structured JUC-505 with superior photocatalytic property and nanozymatic activity was applied to facilitate colorimetric detection of uranium, which displays the advantages of low detection limit, excellent selectivity, fast response and simple operation for uranium detection in real samples, and shows a great potential in on-site monitoring of uranium pollutant around uranium tailings as well as nuclear power plant.

The construction of a stable hydrogen-bonded organic framework for the photocatalytic reduction and removal of uranium.

An imidazolyl hydrogen-bonded organic framework (HOF-T) with outstanding thermal and water stability was constructed by C-H⋯N hydrogen bonding and C-H⋯π interactions. UO22+ can be selectively captured by the imidazole group of HOF-T and rapidly reduced to UO2 under visible light irradiation, realizing exceptional uranium removal with high capacity and fast kinetics.

Efficient capture of iodine in steam and water media by hydrogen bond-driven charge transfer complexes.

Untreated radioactive iodine (129I and 131I) released from nuclear power plants poses a significant threat to humans and the environment, so the development of materials to capture iodine from water media and steam is critical. Here, we report a charge transfer complex (TCNQ-MA CTC) with abundant nitrogen atoms and π-conjugated system for adsorption of I2 vapor and I3- from aqueous solutions. Due to the synergistic binding mechanism of benzene/triazine rings and N-containing groups with iodine, special I-π and charge transfer interaction can be formed between the guest and the host, and thus efficient removal of I2 and I3- can be realized by TCNQ-MA CTC with the adsorption capacity up to 2.42 g/g and 800 mg/g, respectively. TCNQ-MA CTC can capture 92% of I3- within 2.5 min, showing extremely fast kinetics, excellent selectivity and high affinity (Kd = 5.68 × 106 mL/g). Finally, the TCNQ-MA CTC was successfully applied in the removal of iodine from seawater with the efficiency of 93.71%. This work provides new insights in the construction of charge transfer complexes and lays the foundation for its environmental applications.

Simultaneous detection and separation of uranium based on a fluorescent amidoxime-functionalized covalent organic polymer.

To ensure the long-term sustainable development of nuclear energy as well as the prevention and control of uranium pollution, new materials that can simultaneously detect and separate uranium are still urgently needed. Herein, a new fluorescent covalent organic polymer (COP), namely HT-COP-AO, was synthesized andemployed as both the fluorescent probe and absorbent for simultaneous uranium detection and separationconsidering its excellent fluorescence property and strong uranium coordination ability. The results showed that the fluorescence of HT-COP-AO was quickly quenched by uranium within 2 min, and the limit of detection was 0.23 µM (3σ/K). Further studies implied that uranium was coordinated with the amidoxime groups of HT-COP-AO through U-N and O = U = O bonds, which resulted in electron transfer from uranium to HT-COP-AO and quenching the fluorescence of HT-COP-AO consequently. Meanwhile, HT-COP-AO exhibited excellent absorption ability towards uranium, and the maximum absorption capacity (qmax = 401.3 mg/g) was higher than most reported amidoxime modified materials. The HT-COP-AO also showed high selectivity for both uranium detection and separation which makes it a great promising for uranium monitoring in real water samples.

Construction of covalent organic framework nanozymes with photo-enhanced hydrolase activities for colorimetric sensing of organophosphorus nerve agents.

Construction of covalent organic frameworks (COFs)-based nanozymes is of great importance for the extensive applications in catalysis and sensing fields. In this work, a two-dimensional COF (DAFB-DCTP COF) was fabricated via Knoevenagel condensation reaction. The integration of catalytically active sites of pyridine groups into the donor-acceptor (D-A) conjugated skeleton endows DAFB-DCTP COF with both hydrolytic and photosensitive properties. The DAFB-DCTP COF can be utilized as an artificial enzyme with selective and photo-enhanced catalytic efficiency, facilitating its application in photocatalytic degradation of hydrolase substrates (p-nitrophenyl acetate, pNPA) by nucleophilic reaction and further realizing colorimetric detection of the nanozyme inhibitor of organophosphorus nerve agent (diethyl cyanophosphonate, DCNP). The distinct color changes could be distinguished by naked eyes even at a low DCNP concentration, and the versatile smartphone analysis featured with reliability and simplicity. For the first time, the COFs' intrinsic hydrolase activity depending on their structural characteristics was investigated in synergy with the photosensitive performance originating from their photoelectric features. The present contribution provides a promising direction towards construction of colorimetric sensing platform based on the regulation of COFs' non-oxidoreductase activity under visible light irradiation.

An in-situ strategy to construct uracil-conjugated covalent organic frameworks with tunable fluorescence/recognition characteristics for sensitive and selective Mercury(II) detection.

Previous researches of covalent organic frameworks (COFs) have shown their potential as fluorescent probes, but the regulation of their optical properties and recognition characteristics still remains a challenge, and most of reports required complicated post-decoration to improve the sensing performance. In this context, we propose a novel in-situ strategy to construct uracil-conjugated COFs and modulate their fluorescence properties for sensitive and selective mercury(II) detection. By using 1,3,6,8-tetrakis(4-formylphenyl)pyrene (TFPPy) and 1,3,6,8-tetrakis(4-aminophenyl)pyrene (TAPPy) as fundamental blocks and 5-aminouraci (5-AU) as the functional monomer, a series of COFs (Py-COFs and Py-U-COFs-1 to Py-U-COFs-5) with tunable fluorescence were solvothermally synthesized through an in-situ Schiff base reaction. The π-conjugated framework serves as a signal reporter, the evenly and densely distributed uracil acts as a mercury(II) receptor, and the regular pores (channels) make the rapid and sensitive detection of the mercury(II) possible. In this research, we manage to regulate the crystalline structure, the fluorescence properties, and the sensing performance of COFs by simply changing the molar ratio of precursors. We expect this research to open up a new strategy for effective and controllable construction of functionalized COFs for environmental analysis.

Aptamer-mediated nanoparticle-based protein labeling platform for intracellular imaging and tracking endocytosis dynamics.

Although nanoparticles have been widely used as optical contrasts for cell imaging, the complicated prefunctionalized steps and low labeling efficiency of nanoprobes greatly inhibit their applications in cellular protein imaging. In this study, we developed a novel and general strategy that employs an aptamer not only as a recognizer for protein recognition but also as a linker for nanoreporter targeting to specifically label membrane proteins of interest and track their endocytic pathway. With this strategy, three kinds of nanoparticles, including gold nanoparticles, silver nanoparticles, and quantum dots (QDs), have been successfully targeted to the membrane proteins of interest, such as nucleolin or prion protein (PrP(C)). The following investigations on the subcellular distribution with fluorescent immunocolocalization assay indicated that PrP(C)-aptamer-QD complexes most likely internalized into cytoplasm through a classical clathrin-dependent/receptor-mediated pathway. Further single-particle tracking and trajectory analysis demonstrated that PrP(C)-aptamer-QD complexes exhibited a complex dynamic process, which involved three types of movements, including membrane diffusion, vesicle transportation, and confined diffusion, and all types of these movements were associated with distinct phases of PrP(C) endocytosis. Compared with traditional multilayer methods, our proposed aptamer-mediated strategy is simple in procedure, avoiding any complicated probe premodification and purification. In particular, the new double-color labeling strategy is unique and significant due to its superior advantages of targeting two signal reporters simultaneously in a single protein using only one aptamer. What is more important, we have constructed a general and versatile aptamer-mediated protein labeling nanoplatform that has shown great promise for future biomedical labeling and intracellular protein dynamic analysis.

[Detection of trace uranium in air with field spectrometry].

As a natural radioactive element, uranium and its compounds exist as aerosol and transfer in air. In gas phase, uranium can cause various kinds of radioactive damage to human body. The change in its concentration in a local area is related to the exploration and utilization of nuclear energy. Therefore, the development of field method for rapid uranium detection in air sample is very important. In this contribution, the air samples over uranium ores collected by a general pump was absorbed with 2.0 mol x L(-1) nitrate and then reacted with solid reagent kit. When the reaction between trace uranium and chromogenic reagent was finished, the homemade portable photometer was used to measure the absorbance. The results showed that the concentration of uranium in air samples over low grade uranium ores can be successfully determined by the present method and the values agree with that obtained by ICP-MS. The RSD measured by the new method was 1.72%. The application of the new field spectrometry in discriminating uranium ores from other ores has the potential advantages of easy operation, cost-saving and high accuracy.

Construction of D-A-Conjugated Covalent Organic Frameworks with Enhanced Photodynamic, Photothermal, and Nanozymatic Activities for Efficient Bacterial Inhibition.

Bacterial infection causes serious threats to human life, especially with the appearance of antibiotic-resistant bacteria. Phototherapeutic approaches have become promising due to their noninvasiveness, few adverse effects, and high efficiency. Herein, a covalent organic framework (TAPP-BDP) with a conjugated donor-acceptor (D-A) structure has been constructed for efficient photoinduced bacteriostasis. Under the irradiation with a single near-infrared (NIR) light (λ = 808 nm), TAPP-BDP alone involves triple and synergistic bacterial inhibition based on the integration of photodynamic, photothermal, and peroxidase-like enzymatic activities. The unique D-A structure endows TAPP-BDP with a narrow energy band gap, improving its photodynamic and nanozyme activities to generate reactive oxygen species (ROS) to realize the broad-spectrum bactericidal activity. The extended π-conjugated skeleton of TAPP-BDP results in enhanced absorption in NIR, and the remarkable photothermal activity can increase the temperature up to 65 °C to cause efficient bacterial degeneration. TAPP-BDP shows excellent antibacterial efficiency against both Gram-negative and Gram-positive bacteria. Animal experiments further suggest that TAPP-BDP can effectively heal wounds infected with Staphylococcus aureus in living systems.

Carbon nanotubes as a low background signal platform for a molecular aptamer beacon on the basis of long-range resonance energy transfer.

Although holding the advantages of both an aptamer and a molecular beacon (MB), a molecular aptamer beacon (MAB) needs complicated and expensive modifications at both of its ends and usually has a high background signal because of the low energy transfer efficiency between the donor and the acceptor. To overcome these shortcomings, in this study, we develop a long-range resonance energy transfer (LrRET) system by separating the donor from the acceptor, wherein only one end of the MAB is fluorescently labeled and acts as the energy donor and multiwalled carbon nanotubes (MWCNTs) are introduced as the energy acceptor. To test the feasibility of the newly designed MAB system, adenosine triphosphate (ATP) has been employed as a proof-of-concept target. It is found that the fluorescence of the designed MAB is completely quenched by MWCNTs, supplying a very low background signal. Then the quenched fluorescence is recovered significantly with the addition of ATP, so that ATP can be detected in the range of 0.8-80 µM with a limit of detection of 0.5 µM (3σ). Compared with the conventional fluorescence resonance energy transfer, the efficiency of LrRET between the dye and MWCNTs is much higher. Since only one end of the MAB needs the modification, the present strategy is simple and cost-effective. Furthermore, the use of MWCNTs can greatly reduce the fluorescence background of the MAB and supply a high sensitivity, showing its generality for detection of a variety of targets.

Sensitive discrimination and detection of prion disease-associated isoform with a dual-aptamer strategy by developing a sandwich structure of magnetic microparticles and quantum dots.

The major challenge of prion disease diagnosis at the presymptomatic stage is how to sensitively or selectively discriminate and detect the minute quantity of disease-associated prion protein isoform (PrP(Res)) in complex biological systems such as serum and brain homogenate. In this contribution, we developed a dual-aptamer strategy by taking the advantages of aptamers, the excellent separation ability of magnetic microparticles (MMPs), and the high fluorescence emission features of quantum dots (QDs). Two aptamers (Apt1 and Apt2), which can recognize their two corresponding distinct epitopes of prion proteins (PrP), were coupled to the surfaces of MMPs and QDs, respectively, to make MMPs-Apt1 and QDs-Apt2 ready at first, which then could be coassociated together through the specific recognitions of the two aptamers with their two corresponding distinct epitopes of PrP, forming a sandwich structure of MMPs-Apt1-PrP-Apt2-QDs and displaying the strong fluorescence of QDs. Owing to the different binding affinities of the two aptamers with PrP(Res) and cellular prion protein (PrP(C)), both of which have distinct denaturing detergent resistance, our dual-aptamer strategy could be applied to discriminate PrP(Res) and PrP(C) successfully in serum. Further identifications showed that the present dual-aptamer assay could be successfully applied to the detection of PrP in 0.01% brain homogenate, about 1000-fold lower than that of commonly applied antibody-mediated assays, which can detect PrP just in 10% brain homogenate, indicating that the present designed dual-aptamer assay is highly sensitive and adequate for clinical diagnosis without isolation of target protein prior to assay.

Tetrakis(4-sulfonatophenyl)porphyrin-directed assembly of gold nanocrystals: tailoring the plasmon coupling through controllable gap distances.

It is known that universality and controllability over nanocrystal orientation must be accomplished to facilitate the potential applications of metal nanocrystals in the areas of photonics, electronics, and optics. The facile fabrication of linear chains of Au nanorods and bifurcated junctions of nanorods/nanospheres is achieved via the crosslinking of H-type tetrakis(4-sulfonatophenyl)porphyrin aggregates in solution. The tuning of the plasmon coupling between the Au nanocrystals is demonstrated by varying the porphyrin concentration and thus the interparticle gap distances. Finite-difference time-domain calculations show that the red shift of the plasmon band exhibits a nearly exponential decay with increasing interparticle gap distances, thus giving rise to a "plasmon ruler equation." The gap distances determined according to this equation agree well with the experimental observations and further confirm the porphyrin-directed assembly process. The interaction mechanism between the Au nanorods and porphyrins is further investigated by a biological procedure using the dark-field light scattering technique.