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.

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.

A conveniently synthesized redox-active fluorescent covalent organic framework for selective detection and adsorption of uranium.

Uranium is a key element in the nuclear industry and also a global environmental contaminant with combined highly toxic and radioactive. Currently, the materials based on post-modification of amidoxime have been developed for uranium detection and adsorption. However, the affinity of amidoxime group for vanadium is stronger than that of uranium, which is the main challenge hindering the practical application of amidoxime-based adsorbents. Herein, we synthesized a fluorescent covalent organic framework (TFPPy-BDOH) through integrating biphenyl diamine and pyrene unit into the π-conjugated framework. TFPPy-BDOH has an excellent selectivity to uranium due to the synergistic effect of nitrogen atom in the imine bond and hydroxyl groups in conjugated framework. It can achieve ultra-fast fluorescence response time (2 s) and ultra-low detection limit (8.8 nM), which may be attributed to its intrinsic regular porous channel structures and excellent hydrophilicity. More excitingly, TFPPy-BDOH can chemically reduce soluble U (VI) to insoluble U (IV), and release the binding site to adsorb additional U (VI), achieving high adsorption capacity of 982.6 ± 49.1 mg g-1. Therefore, TFPPy-BDOH can overcome the challenges faced by current amidoxime-based adsorbents, making it as a potential adsorbent in practical applications.

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.

Direct fluorescence detection of microRNA based on enzymatically engineered primer extension poly-thymine (EPEPT) reaction using copper nanoparticles as nano-dye.

A new strategy based on enzymatically engineered primer extension poly-thymine (EPEPT) and nanomaterials in situ generation technology is reported for direct detection of microRNA (miRNA) in a fluorescence turn-on format using the sequential and complementary reactions catalyzed by Klenow Fragment exo- (KFexo-) and terminal deoxynucleotidyl transferase (TdTase). The short miRNA can be efficiently converted into long poly-thymine (polyT) sequences, which function as template for in situ formation of fluorescence copper nanoparticles (CuNPs) as nano-dye for detecting miRNA. The polyT-CuNPs can effectively form and emit intense red fluorescence under the 340nm excitation. For the proof of concept, microRNA-21 (miR-21) was selected as the model target to testify this strategy as a versatile assay platform. By directly using miR-21 as the primer, the simple, rapid and sensitive miRNA detection was successfully achieved with a good linearity between 1pM and 1nM and a detection limit of 100fM. Thus, the EPEPT strategy holds great potential in biochemical sensing research as an efficient and universal platform.

Computational prediction of species-specific malonylation sites via enhanced characteristic strategy.

MOTIVATION: Protein malonylation is a novel post-translational modification (PTM) which orchestrates a variety of biological processes. Annotation of malonylation in proteomics is the first-crucial step to decipher its physiological roles which are implicated in the pathological processes. Comparing with the expensive and laborious experimental research, computational prediction can provide an accurate and effective approach to the identification of many types of PTMs sites. However, there is still no online predictor for lysine malonylation. RESULTS: By searching from literature and database, a well-prepared up-to-data benchmark datasets were collected in multiple organisms. Data analyses demonstrated that different organisms were preferentially involved in different biological processes and pathways. Meanwhile, unique sequence preferences were observed for each organism. Thus, a novel malonylation site online prediction tool, called MaloPred, which can predict malonylation for three species, was developed by integrating various informative features and via an enhanced feature strategy. On the independent test datasets, AUC (area under the receiver operating characteristic curves) scores are obtained as 0.755, 0.827 and 0.871 for Escherichia coli ( E.coli ), Mus musculus ( M.musculus ) and Homo sapiens ( H.sapiens ), respectively. The satisfying results suggest that MaloPred can provide more instructive guidance for further experimental investigation of protein malonylation. AVAILABILITY AND IMPLEMENTATION: http://bioinfo.ncu.edu.cn/MaloPred.aspx . CONTACT: jdqiu@ncu.edu.cn. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Accurate in silico prediction of species-specific methylation sites based on information gain feature optimization.

As one of the most important reversible types of post-translational modification, protein methylation catalyzed by methyltransferases carries many pivotal biological functions as well as many essential biological processes. Identification of methylation sites is prerequisite for decoding methylation regulatory networks in living cells and understanding their physiological roles. Experimental methods are limitations of labor-intensive and time-consuming. While in silicon approaches are cost-effective and high-throughput manner to predict potential methylation sites, but those previous predictors only have a mixed model and their prediction performances are not fully satisfactory now. Recently, with increasing availability of quantitative methylation datasets in diverse species (especially in eukaryotes), there is a growing need to develop a species-specific predictor. Here, we designed a tool named PSSMe based on information gain (IG) feature optimization method for species-specific methylation site prediction. The IG method was adopted to analyze the importance and contribution of each feature, then select the valuable dimension feature vectors to reconstitute a new orderly feature, which was applied to build the finally prediction model. Finally, our method improves prediction performance of accuracy about 15% comparing with single features. Furthermore, our species-specific model significantly improves the predictive performance compare with other general methylation prediction tools. Hence, our prediction results serve as useful resources to elucidate the mechanism of arginine or lysine methylation and facilitate hypothesis-driven experimental design and validation. AVAILABILITY AND IMPLEMENTATION: The tool online service is implemented by C# language and freely available at http://bioinfo.ncu.edu.cn/PSSMe.aspx CONTACT: jdqiu@ncu.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online.

SuccFind: a novel succinylation sites online prediction tool via enhanced characteristic strategy.

UNLABELLED: Lysine succinylation orchestrates a variety of biological processes. Annotation of succinylation in proteomes is the first-crucial step to decipher physiological roles of succinylation implicated in the pathological processes. In this work, we developed a novel succinylation site online prediction tool, called SuccFind, which is constructed to predict the lysine succinylation sites based on two major categories of characteristics: sequence-derived features and evolutionary-derived information of sequence and via an enhanced feature strategy for further optimizations. The assessment results obtained from cross-validation suggest that SuccFind can provide more instructive guidance for further experimental investigation of protein succinylation. AVAILABILITY AND IMPLEMENTATION: A user-friendly server is freely available on the web at: http://bioinfo.ncu.edu.cn/SuccFind.aspx. CONTACT: jdqiu@ncu.edu.cn. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A norepinephrine coated magnetic molecularly imprinted polymer for simultaneous multiple chiral recognition.

A newly designed molecularly imprinted polymer (MIP) material was developed and successfully used as recognition element for enantioselective recognition by microchip electrophoresis. In this work, molecularly imprinted polymers were facilely prepared employing Fe3O4 nanoparticles (NPs) as the supporting substrate and norepinephrine as the functional monomer in the presence of template molecule in a weak alkaline solution. After extracting the embedded template molecules, the produced imprinted Fe3O4@polynorepinephrine (MIP-Fe3O4@PNE) NPs have cavities complementary to three dimensional shape of template molecules favoring high binding capacity and magnetism property for easy manipulation. The MIP-Fe3O4@PNE NPs prepared with l-tryptophan, l-valine, l-threonine, Gly-l-Phe, S-(-)-ofloxacin or S-(-)-binaphthol as template molecules were packed in the polydimethylsiloxane microchannel via magnetic field as novel stationary phase to successful enantioseparation of corresponding target analysts. The MIP-Fe3O4@PNE NPs-based microchip electrophoresis system exhibited strong recognition ability, excellent high-performance, admirable reproducibility and stability, which provided a powerful protocol for separation enantiomers within a short analytical time and opened up an avenue for multiplex chiral compound assay in various systems.

PredHydroxy: computational prediction of protein hydroxylation site locations based on the primary structure.

Compared to well-known and extensively studied protein phosphorylation, protein hydroxylation attracts much less attention and the molecular mechanism of the hydroxylation is still incompletely understood. And yet annotation of hydroxylation in proteomes is a first-critical step toward decoding protein function and understanding their physiological roles that have been implicated in the pathological processes and providing useful information for the drug designs of various diseases related with hydroxylation. In this work, we present a novel method called PredHydroxy to automate the prediction of the proline and lysine hydroxylation sites based on position weight amino acids composition, 8 high-quality amino acid indices and support vector machines. The PredHydroxy achieved a promising performance with an area under the receiver operating characteristic curve (AUC) of 82.72% and a Matthew's correlation coefficient (MCC) of 69.03% for hydroxyproline as well as an AUC of 87.41% and a MCC of 66.68% for hydroxylysine in jackknife cross-validation. The results obtained from both the cross validation and independent tests suggest that the PredHydroxy might be a powerful and complementary tool for further experimental investigation of protein hydroxylation. Feature analyses demonstrate that hydroxylation and non-hydroxylation have distinct location-specific differences; alpha and turn propensity is of importance for the hydroxylation of proline and lysine residues. A user-friendly server is freely available on the web at: .

Incorporating key position and amino acid residue features to identify general and species-specific Ubiquitin conjugation sites.

MOTIVATION: Systematic dissection of the ubiquitylation proteome is emerging as an appealing but challenging research topic because of the significant roles ubiquitylation play not only in protein degradation but also in many other cellular functions. High-throughput experimental studies using mass spectrometry have identified many ubiquitylation sites, primarily from eukaryotes. However, the vast majority of ubiquitylation sites remain undiscovered, even in well-studied systems. Because mass spectrometry-based experimental approaches for identifying ubiquitylation events are costly, time-consuming and biased toward abundant proteins and proteotypic peptides, in silico prediction of ubiquitylation sites is a potentially useful alternative strategy for whole proteome annotation. Because of various limitations, current ubiquitylation site prediction tools were not well designed to comprehensively assess proteomes. RESULTS: We present a novel tool known as UbiProber, specifically designed for large-scale predictions of both general and species-specific ubiquitylation sites. We collected proteomics data for ubiquitylation from multiple species from several reliable sources and used them to train prediction models by a comprehensive machine-learning approach that integrates the information from key positions and key amino acid residues. Cross-validation tests reveal that UbiProber achieves some improvement over existing tools in predicting species-specific ubiquitylation sites. Moreover, independent tests show that UbiProber improves the areas under receiver operating characteristic curves by ~15% by using the Combined model. AVAILABILITY: The UbiProber server is freely available on the web at http://bioinfo.ncu.edu.cn/UbiProber.aspx. The software system of UbiProber can be downloaded at the same site. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A method to distinguish between lysine acetylation and lysine methylation from protein sequences.

Lysine acetylation and methylation are two major post-translational modifications of lysine residues. They play vital roles in both biological and pathological processes. Specific lysine residues in H3 histone protein tails appear to be targeted for either acetylation or methylation. Hence it is very challenging to distinguish between acetylated and methylated lysine residues using computational methods. This work presents a method that incorporates protein sequence information, secondary structure and amino acid properties to differentiate acetyl-lysine from methyl-lysine. We apply an encoding scheme based on grouped weight and position weight amino acid composition to extract sequence information and physicochemical properties around lysine sites. The proposed method achieves an accuracy of 93.3% using a jackknife test. Feature analysis demonstrates that the prediction model with multiple features can take full advantage of the supplementary information from different features to improve classification performance and prediction robustness. Analysis of the characteristics of lysine residues which can be either methylated or acetylated shows that they are more similar to methyl-lysine than to acetyl-lysine.

Facile synthesis of Fe(3)O(4)@Al(2)O(3) core-shell nanoparticles and their application to the highly specific capture of heme proteins for direct electrochemistry.

In this study, magnetic core-shell Fe(3)O(4)@Al(2)O(3) nanoparticles (NPs) attached to the surface of a magnetic glassy carbon electrode (MGCE) were used as a functional interface to immobilize several heme proteins including hemoglobin (Hb), myoglobin (Mb) and horseradish peroxidase (HRP) for fabricating protein/Fe(3)O(4)@Al(2)O(3) film. Transmission electron microscope, UV-vis spectroscopy, electrochemical impedance spectroscopy, and cyclic voltammetry were used to characterize the films. With the advantages of the magnetism and the excellent biocompatibility of the Fe(3)O(4)@Al(2)O(3) NPs, the protein/Fe(3)O(4)@Al(2)O(3) film could be easily fabricated in the present of external magnetic field, and well retained the bioactivity of the immobilized proteins, hence dramatically facilitated direct electron transfer of heme proteins and excellent electrocatalytic behaviors towards H(2)O(2) were demonstrated. The presented system avoids the complex synthesis for protecting Fe(3)O(4) NPs, supplies a facile, low cost and universal way to immobilize proteins, and is promising for construction of third-generation biosensors and other bio-magnetic induction devices.