Li-Juan Tang

Homogeneous Label-Free Genotyping of Single Nucleotide Polymorphism Using Ligation-Mediated Strand Displacement Amplification with DNAzyme-Based Chemiluminescence Detection

Genotyping of single nucleotide polymorphisms (SNPs) is a central challenge in disease diagnostics and personalized medicine. A novel label-free homogeneous SNP genotyping technique is developed on the basis of ligation-mediated strand displacement amplification (SDA) with DNAzyme-based chemiluminescence detection. Discrimination of single-base mismatches is first accomplished using DNA ligase to generate a ligation product between a discriminant probe and a common probe. The ligated product then initiates two consecutive SDA reactions to produce a great abundance of aptamer sequences against hemin, which can be probed by chemiluminscence detection. The developed strategy is demonstrated using a model SNP target of cytochrome P450 monooxygenase CYP2C19*2, a molecular marker for personalized medicines. The results reveal that the developed technique displays superb selectivity in discriminating single-base mismatches, very low detection limit as low as 0.1 fM, a wide dynamic range from 1 fM to 1 nM, and a high signal-to-background ratio of 150. Due to its label-free, homogeneous, and chemiluminescence-based detection format, this technique can be greatly robust, cost-efficient, readily automated, and scalable for parallel assays of hundreds of samples. The developed genotyping strategy might provide a robust, highly sensitive, and specific genotyping platform for genetic analysis and molecular diagnostics.

Activity-based DNA-gold nanoparticle probe as colorimetric biosensor for DNA methyltransferase/glycosylase assay.

We have developed a novel biosensor platform for colorimetric detection of active DNA methyltransferase/glycosylase based on terminal protection of the DNA-gold nanoparticle (AuNP) probes by mechanistically covalent trapping of target enzymes. This biosensor relied on covalent capture of target enzymes by activity-based DNA probes which created terminal protection of the DNA probes tethered on AuNPs from degradation by Exo I and III. This biosensor has the advantages of having highly sensitive, rapid, and convenient detection due to its use of the homogeneous assay format and strong surface plasmon absorption. Because the activity-based probes (ABPs) are mechanistically specific to target enzymes, this strategy also offers improved selectivity and can achieve the information about both abundance and activity of the enzymes. We have demonstrated this strategy using a human DNA (cytosine-5) methyltransferase (Dnmt 1) and a human 8-oxoguanine glycosylase (hOGG 1). The results reveal that the colorimetric response increases dynamically with increasing activity of the enzymes, implying a great potential of this strategy for DNA methyltransferase/glycosylase detection and molecular diagnostics and drug screening. Our strategy can also be used as a promising and convenient approach for visualized screening of ABPs for DNA modifying enzymes.

Terminal protection of small molecule-linked DNA: A versatile biosensor platform for protein binding and gene typing assay.

Assays of small molecule-protein interactions are of tremendous importance in chemical genetics, molecular diagnostics, and drug development. This work reports a new finding of generalized terminal protection that small molecule-DNA chimeras are protected from degradation by various DNA exonucleases, when the small molecule moieties are bound to their protein targets. This generalization converts small molecule-protein interaction assays into the detection of DNA of various structures, affording a useful mechanism for the analytics of small molecules. On the basis of this mechanism, a label-free biosensor strategy has been developed for a homogeneous assay of protein-small molecule interactions based on the fluorescence staining detection. Also, a label-free SNP genotyping technique is proposed based on polymerase extension of a single nucleotide with a small molecule label. The developed techniques are demonstrated using a model protein-small molecule system of biotin/streptavidin and a model SNP system of human β-globin gene around the position of codon 39. The results revealed that the protein-small molecule interaction assay strategy shows dynamic responses in the concentration range from 0.5 to 100 nM with a detection limit of 0.1 nM, and the SNP typing technique gives dynamic responses in the concentration range from 0.1 to 200 nM with a detection limit of 0.02 nM. Besides desirable sensitivity, the developed strategies also offer high selectivity, excellent reproducibility, low cost, and simplified operations, implying that these techniques may hold considerable potential for molecular diagnostics and genomic research.

Surface-enhanced Raman spectroscopy-based, homogeneous, multiplexed immunoassay with antibody-fragments-decorated gold nanoparticles.

We report the development of a novel single-step, multiplexed, homogeneous immunoassay platform for sensitive detection of protein targets based on our realization of high surface-enhanced raman spectroscopy (SERS) signal enhancement by controlled assembly of SERS nanoparticles. An essential design of this platform is the use of gold nanoparticles or nanorods codecorated with specially reduced antibody half-fragments, nonfluorescent Raman-active dyes, and passivating proteins as the SERS nanoparticles. These nanoparticles offer a facile approach to accomplish orientational immobilization of antibodies, minimized interparticle distance, multicolor Raman fingerprint coding, low fluorescence background, as well as excellent biocompatibility and stability. Through sandwiched antibody-antigen interactions, controlled assembly of SERS nanoparticles is realized with a strong SERS signal achieved via plasmonic coupling, creating an immunoassay platform for rapid, sensitive, multiplexed quantification of proteins. This platform is demonstrated for reproducible quantification of three cytokines, interferon gamma, interleukin-2, and tumor necrosis factor alpha, with large signal-to-noise ratio. It is also successfully applied to multiplexed cytokine analysis for T cell secretion studies in complicated biological samples. The developed SERS immunoassay platform may create a simple but valuable tool for facilitating accurate validation and early detection of disease biomarkers as well as for point-of-care tests in clinical diagnostics.

Ensemble preprocessing of near-infrared (NIR) spectra for multivariate calibration.

Preprocessing of raw near-infrared (NIR) spectral data is indispensable in multivariate calibration when the measured spectra are subject to significant noises, baselines and other undesirable factors. However, due to the lack of sufficient prior information and an incomplete knowledge of the raw data, NIR spectra preprocessing in multivariate calibration is still trial and error. How to select a proper method depends largely on both the nature of the data and the expertise and experience of the practitioners. This might limit the applications of multivariate calibration in many fields, where researchers are not very familiar with the characteristics of many preprocessing methods unique in chemometrics and have difficulties to select the most suitable methods. Another problem is many preprocessing methods, when used alone, might degrade the data in certain aspects or lose some useful information while improving certain qualities of the data. In order to tackle these problems, this paper proposes a new concept of data preprocessing, ensemble preprocessing method, where partial least squares (PLSs) models built on differently preprocessed data are combined by Monte Carlo cross validation (MCCV) stacked regression. Little or no prior information of the data and expertise are required. Moreover, fusion of complementary information obtained by different preprocessing methods often leads to a more stable and accurate calibration model. The investigation of two real data sets has demonstrated the advantages of the proposed method.

Graphene oxide-hairpin probe nanocomposite as a homogeneous assay platform for DNA base excision repair screening.

Uracil-DNA glycosylase (UDG) as one of the most important base excision repair enzymes plays a crucial role in protecting the genome from endogenous DNA damage and sustaining the genome integrity. Quantitative activity analysis of UDG is a central challenge and of fundamental importance in bioanalysis. Here, we proposed a novel biosensor constituted by adsorbing a fluorophore-labeled hairpin probe onto the surface of graphene oxide (GO) as a homogeneous assay platform for sensitive UDG activity assay. Active UDG could excise the uracil base in the hairpin probe, and further hydrolysis of the leaving abasic site gave rise to high fluorescence. Thus, it provided a convenient approach for UDG activity quantification. Because of the unique ability of GO in universal fluorescence quenching, a low background fluorescence signal can be obtained for the efficient fluorescence resonant energy transfer from the fluorophore-labeled on the hairpin probe to GO sheet. A quite wide dynamic range from 0.0017 U/mL to 0.8 U/mL was achieved for UDG assay and the detection limit was estimated to be 0.0008 U/mL. The results indicated that this strategy offers a simple, cost-effective, highly sensitive and selective homogeneous detection platform for UDG activity assay related biochemical studies.

Phospholipid–Graphene Nanoassembly as a Fluorescence Biosensor for Sensitive Detection of Phospholipase D Activity

A novel phospholipid-graphene nanoassembly is developed based on self-assembly of phospholipids on nonoxidative graphene surfaces. The nanoassembly can be prepared easily through noncovalent hydrophobic interactions between the lipid tails and the graphene without destroying the electronic conjugation within the graphene sheet. This imparts the nanoassembly with desired electrical and optical properties with nonoxidative graphene. The phospholipid coating offers excellent biocompatibility, facile solubilization, and controlled surface modification for graphene, making the nanoassembly a useful platform for biofunctionalization of graphene. The nanoassembly is revealed to comprise a bilayer of phospholipids with a reduced graphene oxide sheet hosting in the hydrophobic interior, thus affording a unique planar mimic of the cellular membrane. By using a fluorescein-labeled phospholipid in this nanoassembly, a fluorescence biosensor is developed for activity assay of phospholipase D. The developed biosensor is demonstrated to have high sensitivity, wide dynamic range, and very low detection limit of 0.010 U/L. Moreover, because of its single-step homogeneous assay format it displays excellent robustness, improved assay simplicity and throughput, as well as intrinsic ability to real-time monitor the reaction kinetics.

Radial basis function network-based transform for a nonlinear support vector machine as optimized by a particle swarm optimization algorithm with application to QSAR studies.

The support vector machine (SVM) has been receiving increasing interest in an area of QSAR study for its ability in function approximation and remarkable generalization performance. However, selection of support vectors and intensive optimization of kernel width of a nonlinear SVM are inclined to get trapped into local optima, leading to an increased risk of underfitting or overfitting. To overcome these problems, a new nonlinear SVM algorithm is proposed using adaptive kernel transform based on a radial basis function network (RBFN) as optimized by particle swarm optimization (PSO). The new algorithm incorporates a nonlinear transform of the original variables to feature space via a RBFN with one input and one hidden layer. Such a transform intrinsically yields a kernel transform of the original variables. A synergetic optimization of all parameters including kernel centers and kernel widths as well as SVM model coefficients using PSO enables the determination of a flexible kernel transform according to the performance of the total model. The implementation of PSO demonstrates a relatively high efficiency in convergence to a desired optimum. Applications of the proposed algorithm to QSAR studies of binding affinity of HIV-1 reverse transcriptase inhibitors and activity of 1-phenylbenzimidazoles reveal that the new algorithm provides superior performance to the backpropagation neural network and a conventional nonlinear SVM, indicating that this algorithm holds great promise in nonlinear SVM learning.

Plasmonic ELISA for the ultrasensitive detection of Treponema pallidum

In this report, we have developed a plasmonic ELISA strategy for the detection of syphilis. Plasmonic ELISA is an enzyme-linked immunoassay combined with enzyme-mediated surface plasmon resonance (SPR) of gold nanoparticles (AuNPs). Immune response of the Treponema pallidum (T. pallidum) antibodies triggers the acetylcholinesterase-catalyzed hydrolysis of acetylthiocholine to produce abundant thiocholine. The positive charged thiol, in turn, alters the surface charge distribution the AuNPs and leads to the agglomeration of the AuNPs. The induced strong localized SPR effect of the agglomerate AuNPs can, thus, allow the quantitative assay of T. pallidum antibodies due to the remarkable color and absorption spectral response changes of the reaction system. The plasmonic ELISA exhibited a quasilinear response to the logarithmic T. pallidum antibody concentrations in the range of 1pg/mL-10ng/mL with a detection limit of 0.98pg/mL. Such a low detection limit was 1000-fold improvements in sensitivity over a conventional ELISA. The results of plasmonic ELISA in syphilis assays of serum specimens from 60 patients agreed with those obtained using a conventional ELISA method. The plasmonic ELISA has characteristics (analyte specific, cost-effective, ease of automatic, low limit of detection) that provide potential for diagnosis and therapeutic monitoring of syphilis.

Enzymatic immuno-assembly of gold nanoparticles for visualized activity screening of histone-modifying enzymes.

Activity screening of histone-modifying enzymes is of paramount importance for epigenetic research as well as clinical diagnostics and therapeutics. A novel biosensing strategy has been developed for sensitive and selective detection of histone-modifying enzymes as well as their inhibitors. This strategy relies on the antibody-mediated assembly of gold nanoparticles (AuNPs) decorated with substrate peptides that are subjected to enzymatic modifications by the histone-modifying enzymes. This design allows a visual and homogeneous assay of the enzyme activity using antibodies without any labels, which circumvents the requirements to prefunctionalize the antibody and affords improved assay simplicity and throughput. Additionally, the use of antibody-based recognition of modified peptides could offer improved specificity as compared with existing techniques based on the enzyme coupled assay. We have demonstrated this strategy using a histone methyltransferase acting on histone H3 (Lys 4) and a histone acetyltransferase acting on histone H3 (Lys 14). The results reveal that the absorption peak characteristic for AuNPs decreases dynamically with increasing activity of the enzymes with concomitant visualizable color attenuation, and subnanomolar detection limits are readily achieved for both enzymes. The developed strategy can thus offer a robust and convenient visualized platform for screening the enzyme activities and their inhibitors with high sensitivity and selectivity.