Colorimetric detection of oligonucleotides using a polydiacetylene vesicle sensor

A new system for the colorimetric detection of oligonucleotides was developed using polydiacetylene vesicles, which play the dual role of an indicator of color transition and an amplification tag. The results are of significance in understanding the mechanism of color transition of biological recognition in polydiacetylene systems and in designing new biosensors.     

聚联乙炔囊泡负载的Bola型两亲分子识别三聚氰胺过程中Chaotrope促进型显色机制及热力学

用聚联乙炔囊泡为载体,将bola型两亲分子1,12-二乳清酸十二胺盐(DDO)对三聚氰胺的分子识别作用用肉眼可见的颜色变化显示出来.通过比较不同碳链长度的聚联乙炔囊泡对分子识别过程的反映,发现二十三烷基-2.4-二炔酸(TCDA)囊泡的显色灵敏度较高.研究表明,TCDA肉眼可见的颜色变化来自于DDO与三聚氰胺多重氢键的形成以及溶液环境中水结构的变化.为了更好地理解显色机理,用差示扫描量热(DSC)仪详细研究了分子识别过程中聚联乙炔囊泡的相变行为及热力学参数.结果表明:TCDA囊泡和带有识别分子的DDO/TCDA囊泡在三聚氰胺存在下,相变温度Tm均向高温方向移动,并且,随三聚氰胺浓度的增加,Tm值逐渐增大直至囊泡瓦解;但是Tm值的变化没有与囊泡变色必然关联,仅仅DDO/TCDA囊泡具有变色现象,而且,只有当三聚氰胺的浓度超过分子识别氢键形成所需理论量时,肉眼才能可见明显的由蓝到红的颜色变化.为了理解溶液中过量的三聚氰胺对囊泡变色的作用,选用蔗糖和尿素作为典型的水结构促进剂和水结构破坏剂(chaotrope),详细研究了它们对聚联乙炔囊泡反映分子识别过程中相变温度的影响及显色规律.结果表明,过量的三聚氰胺在溶液中起到类似尿素水结构破坏剂的作用.这种作用和分子识别过程中多重氢键的形成对聚联乙炔囊泡的变色缺一不可.本研究首次揭示了由水结构破坏剂参与的聚联乙炔囊泡变色机理,有助于理解共轭聚合物热相变过程中的Hofmeister效应.     

Colorimetric detection and fingerprinting of bacteria by glass-supported lipid/polydiacetylene films

Glass-supported films of lipids and polydiacetylene were applied for visual detection and colorimetric fingerprinting of bacteria. The sensor films comprise polydiacetylene domains serving as the chromatic reporter interspersed within lipid monolayers that function as a biomimetic membrane platform. The detection schemes are based on either visible blue-red transitions or fluorescence transformations of polydiacetylene, induced by amphiphilic molecules secreted by proliferating bacteria. An important feature of the new film platform is the feasibility of either naked-eye detection of bacteria or color analysis using conventional scanners. Furthermore, we find that the degrees of bacterially induced color transformations depend both on the bacterial strains examined and the lipid compositions of the films. Accordingly, bacterial fingerprinting can be achieved through pattern recognition obtained by recording the chromatic transformations in an array of lipid/PDA films having different lipid components.     

糖脂功能化聚二乙炔Langmuir-Schaefer薄膜与大肠杆菌的分子识别及动力学过程研究

在气液界面上研究了α-D-甘露糖苷-十六烷(MC₁₆)与10,12-二十五碳双炔酸混合单分子膜行为,二者具有较好的互溶性.在疏水的玻璃衬底上用Langmuir-Schaefer(LS)薄膜技术制备单层MC₁₆/PDA薄膜,研究了这种仿生薄膜与大肠杆菌jm109的相互作用.大肠杆菌jm109对MC₁₆修饰的聚二乙炔LS薄膜的吸附,使薄膜颜色由蓝色变为红色,用紫外-可见吸收光谱可进行定量检测.动力学研究显示比色响应值随时间的增加而增加,3min内即有显著变化,15min后趋于饱和,20min后CR值达到28%,进一步探讨了分子识别的动力学过程.     

Copper-catalyzed azide-alkyne cycloaddition in the synthesis of polydiacetylene: "click glycoliposome" as biosensors for the specific detection of lectins

Supramolecular self-assembly of conjugated diacetylenic amphiphile-tethered ligands photopolymerize to afford polydiacetylene (PDA) functional liposomes. Upon specific interaction with a variety of biological analytes in aqueous solution, PDA exhibits rapid colorimetric transitions. The PDA nanoassemblies, which are excellent membrane mimics, include an ene-yne polymeric reporter responsible for the chromatic transitions and the molecular recognition elements that are responsible for selective and specific binding to the biological target. A bottleneck in the fabrication of these colorimetric biosensors is the preparation of the diacetylenic monomer embedded with the recognition element of choice. In the present work, we make use of copper-catalyzed azide-alkyne cycloaddition (CuAAC) as key step in the preparation of sugar-coated liposome biosensors. The regioselective click ligation of the triacetylenic N-(2-propynyl)pentacosa-10,12-diynamide (NPPCDAM) with a variety of mannose- and lactose-tethered azides afforded chemo- and regioselectively the corresponding 1,2,3-triazole. The obtained diacetylenic monomers were incorporated efficiently into vesicles to afford functional mannose- and lactose-coated glycoliposomes. The obtained PDA-based click glycoliposomes have been characterized by using transmission electronic microscopy (TEM), dynamic light scattering (DLS), and UV/Vis spectroscopy. The efficiency of the reported approach was demonstrated by the rapid optimization of the hydrophilic spacer between the lipidic matrix and the mannose head group for the colorimetric detection of Concavalin A.     

Clonality characterization of natural epitope-specific antibodies against the tumor-related antigen topoisomerase IIa by peptide chip and proteome analysis: a pilot study with colorectal carcinoma patient samples

Patient-specific sequential epitopes were identified by peptide chip analysis using 15mer peptides immobilized on glass slides that covered the topoisomerase IIa protein with a frameshift of five amino acids. Binding specificities of serum antibodies against sequential epitopes were confirmed as being mono-specific by peptide chip re-analysis of epitope-affinity-purified antibody pools. These results demonstrate that serum samples from colon carcinoma patients contain antibodies against sequential epitopes from the topoisomerase IIa antigen. Interactions of patients’ antibodies with sequential epitopes displayed by peptides on glass surfaces may thus mirror disease-specific immune situations. Consequently, these data suggest epitope–antibody reactivities on peptide chips as potential diagnostic readouts of individual immune response characteristics, especially because monospecific antibodies can be interrogated. Subsequently, the clonality of the antibodies present in the mono-specific antibody pools was characterized by 2D gel electrophoresis. This analysis suggested that the affinity-purified antibodies were oligoclonal. Similarly to large-scale screening approaches for specific antigen–antibody interactions in order to improve disease diagnostic, we suggest that “protein-wide” screening for specific epitope–paratope interactions may help to develop novel assays for monitoring of personalized therapies, since individual properties of antigen–antibody interactions remain distinguishable.     

Antigenic and immunogenic phage displayed mimotopes as substitute antigens: applications and limitations

The most exciting potential of phage displayed peptide libraries is to obtain small peptide molecules that mimic an antigen, at least with respect to a particular epitope. In addition to their interest as research tools, such mimotopes could in principle be useful as diagnostic tools or for eliciting antibodies to a predefined epitope. However, the reduction of the phage insert sequence to a short peptide that can compete with the antigenic and in particular with the immunogenic properties of the natural antigen faces considerable difficulties. This review assesses critically the antigenicity of phage displayed peptides as free peptides and in different molecular environments. The difficulties to use mimotopes to induce antibodies that bind to the natural antigen (crossreactive immunogenicity) and the considerable discrepancy between antigenicity and immunogenicity of phage-derived peptides are discussed. Peptides selected with antibodies from phage displayed random peptide libraries have raised considerable expectations as low molecular weight substitutes of the natural antigen. This review will focus on the results of phage displayed random peptide libraries screened with antibodies specific for proteins, carbohydrates and nucleic acids and critically examine how the above expectations have been met.     

Effect of amphiphilic molecules upon chromatic transitions of polydiacetylene vesicles in aqueous solutions

Effect of amphiphilic molecules upon the chromatic transitions of polymerized 10,12-pentacosadiynoic acid (PCDA) vesicles in aqueous solutions was reported. The colorimetric response of polymerized PCDA vesicles for 1-pentanol is higher than that for ethanol due to more hydrophobic property of 1-pentanol. The colorimetric response of polymerized PCDA vesicles for sodium dodecyl sulfate (SDS) and Triton X-100 is lower than that for cetyltrimethylammonium bromide (CTAB). The strong ability of CTAB to induce chromatic transition of the vesicles is related to the positively charged headgroups of CTAB, which favors approach of CTAB to the negatively charged carboxylate groups at the vesicle surface. The insertion of alkyl chain of CTAB into the hydrophobic domain perturbs the conformation of the conjugated polymer backbone and induces color change of polydiacetylene vesicles. For a series of alkylamine hydrochloric salts, the longer the alkyl chain, the stronger the ability of alkylamine to induce chromatic transition of polydiacetylene vesicles.     

High-density synthetic peptide microarrays: emerging tools for functional genomics and proteomics

New approaches for manufacturing and application of peptide arrays on planar surfaces are emerging, thereby opening advanced opportunities to probe the expression and function of the proteome. In complementing DNA and protein array analyses, peptide fragment screening directly addresses functional protein interaction sites, leading to a detailed insight into the discovered molecular recognition events, placing them in the context of the whole genome, and even allowing rapid determination of the chemical nature of these interactions. This information can then be transferred into powerful small peptide tools that interfere with these interactions in vivo and help to link targets with phenotypes. With the spreading of new peptide array tools, peptide screening will extend its impact on modern genome-driven molecular biology. This will advance the systematic discovery and validation of new pharmaceutical targets as well as the development of potent molecular diagnostics for medical and ecological monitoring.     

Effect of phospholipid insertion on arrayed polydiacetylene biosensors

Micro-arrayed polydiacetylene (PDA) vesicles mixed with phospholipids on glass slides were prepared for label-free detection of Escherichia coli. When E. coli bound to its antibodies chemically attached to polydiacetylene, the fluorescence of the vesicles was dramatically increased. The insertion of dimyristoyl phosphatidylcholine (DMPC) in the vesicles drastically reduced the response time for the fluorescence changes. Vesicles with 20-30% DMPC provided optimal results for bacterial detection. Fourier transform infrared (FTIR) spectra analysis suggested that DMPC insertion decreased the strength of hydrogen bonding among the amide and carboxylic acid groups of the polydiacetylene vesicles. Reduced bonding strength resulted in less rigid structure of the polydiacetylene polymer, allowing more rapid detection upon molecular recognition.     

Immunochemical characterisation of structure and allergenicity of peanut 2S albumins using different formats of immunoassays

Proteins of the 2S albumin family, such as Ara h2 and Ara h6, are most frequently involved in peanut allergy. We have developed a reverse enzyme allergo-sorbent test (EAST) in which total serum IgE antibodies are first captured by immobilised anti-human IgE monoclonal antibodies, and then the binding of the anti-Ara h2 and anti-Ara h6 specific IgE to the corresponding labelled allergens is measured. This reverse immunoassay was used either as a direct EAST or as an EAST inhibition assay to study the interactions of whole peanut protein extract and purified Ara h2 and Ara h6 with IgE antibodies from peanut-allergic patients. Finally, we identified some IgE-binding epitopes on Ara h6 using a format of EAST in which the protein is immobilised in a particular, well defined, manner through interactions with specific monoclonal antibodies (mAbs) coated on the micro-plates. The fine specificity of those mAbs has been characterised at the epitope level, and their binding to the allergen thus masks a known particular epitope and makes it unavailable for recognition by IgE antibodies. The reverse EAST increased the ratio specific signal/background. It avoids interferences with competitors such as anti-peanut protein IgG antibodies and allows the study of the specificity and/or affinity of the interactions between IgE antibodies and Ara h2 or Ara h6 with a higher sensitivity and accuracy than the conventional EAST. The EAST results obtained when the allergens are presented by specific mAbs suggest that the homologous molecular domain(s) in peanut 2S albumins encompass major IgE epitope(s) and are strongly involved in peanut allergenicity.     

A Proximity-Induced Fluorogenic Reaction Triggered by Antibody–Antigen Interactions with Adjacent Epitopes

Proximity-induced chemical reactions are site-specific and rapid by taking advantage of their high affinity and highly selective interactions with the template. However, reactions induced solely by antibody–antigen interactions have not been developed. Herein, we propose a biepitopic antigen-templated chemical reaction (BATER) as a novel template reaction. In BATER, reactive functional groups are conjugated to two antibodies that interact with two epitopes of the same antigen to accelerate the reaction. We developed a method for visualizing the progress of BATER using fluorogenic click chemistry for optimal antibody selection and linker design. The reaction is accelerated in the presence of a specific antigen in a linker length-dependent manner. The choice of the antibody epitope is important for a rapid reaction. This design will lead to various applications of BATER in living systems.     

Recognition of peptides by antibodies and investigations of affinity using biosensor technology

The study of peptide-antibody interactions has many applications in biology and medicine. Synthetic peptides corresponding to single protein epitopes are used instead of intact proteins as reagents for the diagnosis of viral and autoimmune diseases. Furthermore, antibodies raised against peptides are useful reagents for isolating and characterizing gene products. In this review, methods for analysing the molecular basis of peptide-antibody interactions are described, such as amino acid replacement studies, X-ray crystallography of peptide-antibody complexes and biosensor technology based on surface plasmon resonance. The importance of peptide conformation in antibody recognition is discussed, and the antigenic reactivity of epitopes in synthetic peptides and in cognate, intact proteins is compared.     

Size effect of polydiacetylene vesicles functionalized with glycolipids on their colorimetric detection ability

In this paper, the size effect of the polydiacetylene vesicles functionalized with glycolipids on their colorimetric detection ability has been studied. Polydiacetylene vesicles in which were incorporated glycolipids acted as a model system for the affinochromatic property. Visible color changes from blue to red could be observed to the naked eye owing to Con A binding to the sugar moiety and be detected quantitatively by the visible absorption spectrum. In the experiment, small and uniform vesicles were obtained after extrusion through membranes with different pore sizes. The morphology and mean size distribution of the extruded vesicles were studied by transmission electron microscopy (TEM) and dynamic light scattering (DLS), respectively. Our work shows that the smaller the vesicles are, the stronger is the effect, making the detection of Con A easier. The results may apply to the sensitivity enhancement of polydiacetylene biosensors for the recognition of other biomolecules.     

Cross-linking strategy for molecular recognition and fluorescent sensing of a multi-phosphorylated peptide in aqueous solution

In the research field of molecular recognition, selective recognition and sensing of phosphorylated protein surfaces is strongly desirable both for elucidation of protein-protein recognition at the molecular level and for regulation of signal transduction through protein surfaces. Here we describe a new strategy for molecular recognition of a multi-phosphorylated peptide using intrapeptide cross-linking on the basis of coordination chemistry. The present artificial receptor can selectively bind to doubly phosphorylated peptide through multiple-point interactions and fluorescently sense the binding event with an association constant of more than 106 M-1 in neutral aqueous solution.     

Color fingerprinting of proteins by calixarenes embedded in lipid/polydiacetylene vesicles

"Naked eye" color detection of proteins was achieved by embedding calixarene receptors within vesicles comprising phospholipids and the chromatic polymer polydiacetylene. Dramatic visible absorbance changes were induced through electrostatic interactions between the protein surface and the vesicle-incorporated hosts. The colorimetric responses could be induced by micromolar protein concentrations, and furthermore, specific protein fingerprints could be obtained by incorporating different receptors within the vesicles. Fluorescence and circular dichroism experiments confirmed the relationship between the colorimetric phenomena and protein docking on the surface of the chromatic vesicles. The colorimetric assay constitutes a generic platform for high-sensitivity detection of soluble proteins and for evaluation of protein surface charge distribution.     

Direct colorimetric study on the interaction of Escherichia coli with mannose in polydiacetylene Langmuir–Blodgett films

The membranes of polydiacetylene backbone decorated with mannose assembled by Langmuir–Blodgett technology can interact with Escherichia coli. The interactions lead to the color transition of the membranes which was readily visible to the naked eyes and could be quantified by visible absorption spectroscopy. To understand the mechanism of the chromatic transition, the affinochromism properties of polydiacetylene were examined by resonance Raman spectroscopy. The results demonstrated that the side chains of polymer backbone performed rearrangement, and the electronic structure in the polymer backbone changed from acetylene to butatriene form when the chromatic transformation from blue to red. The direct colorimetric detection by polydiacetylene membranes not only opens a new path for the use of these membranes in the area of biosensor development but also offers new possibilities for diagnostic applications and screening for binding ligand.     

A Binary Bivalent Supramolecular Assembly Platform Based on Cucurbit[8]uril and Dimeric Adapter Protein 14-3-3

Interactions between proteins frequently involve recognition sequences based on multivalent binding events. Dimeric 14-3-3 adapter proteins are a prominent example and typically bind partner proteins in a phosphorylation-dependent mono- or bivalent manner. Herein we describe the development of a cucurbit[8]uril (Q8)-based supramolecular system, which in conjunction with the 14-3-3 protein dimer acts as a binary and bivalent protein assembly platform. We fused the phenylalanine–glycine–glycine (FGG) tripeptide motif to the N-terminus of the 14-3-3-binding epitope of the estrogen receptor α (ERα) for selective binding to Q8. Q8-induced dimerization of the ERα epitope augmented its affinity towards 14-3-3 through a binary bivalent binding mode. The crystal structure of the Q8-induced ternary complex revealed molecular insight into the multiple supramolecular interactions between the protein, the peptide, and Q8.     

The antigenic determinants on HIV p24 for CD4+ T cell inhibiting antibodies as determined by limited proteolysis, chemical modification, and mass spectrometry

In the last decade, mass spectrometry has been employed by more and more researchers for identifying the proteins in a macromolecular complex as well as for defining the surfaces of their binding interfaces. This characterization of protein-protein interfaces usually involves at least one of several different methodologies in addition to the actual mass spectrometry. For example, limited proteolysis is often used as a first step in defining regions of a protein that are protected from proteolysis when the protein of interest is part of a macromolecular complex. Other techniques used in conjunction with mass spectrometry for determining regions of a protein involved in protein-protein interactions include chemical modification, such as covalent cross-linking, acetylation of lysines, hydrogen-deuterium exchange, or other forms of modification. In this report, both limited proteolysis and chemical modification were combined with several mass spectrometric techniques in efforts to define the protein surface on the HIV core protein, p24, recognized by two different monoclonal human antibodies that were isolated from HIV+ patients. One of these antibodies, 1571, strongly inhibits the CD4+ T cell proliferative response to a known epitope (PEVIPMFSALSEGATP), while the other antibody, 241-D, does not inhibit as strongly. The epitopes for both of these antibodies were determined to be discontinuous and localized to the N-terminus of p24. Interestingly, the epitope recognized by the strongly inhibiting antibody, 1571, completely overlaps the T cell epitope PEVIPMFSALSEGATP, while the antibody 241-D binds to a region adjacent to the region of p24 recognized by the antibody 1571. These results suggest that, possibly due to epitope competition, antibodies produced during HIV infection can negatively affect CD4+ T cell-mediated immunity against the virus.     

Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses

Due to the COVID-19 pandemic, researchers have attempted to identify complex structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (S-protein) with angiotensin-converting enzyme 2 (ACE2) or a blocking antibody. However, the molecular recognition mechanism—critical information for drug and antibody design—has not been fully clarified at the amino acid residue level. Elucidating such a microscopic mechanism in detail requires a more accurate molecular interpretation that includes quantum mechanics to quantitatively evaluate hydrogen bonds, XH/π interactions (X = N, O, and C), and salt bridges. In this study, we applied the fragment molecular orbital (FMO) method to characterize the SARS-CoV-2 S-protein binding interactions with not only ACE2 but also the B38 Fab antibody involved in ACE2-inhibitory binding. By analyzing FMO-based interaction energies along a wide range of binding interfaces carefully, we identified amino acid residues critical for molecular recognition between S-protein and ACE2 or B38 Fab antibody. Importantly, hydrophobic residues that are involved in weak interactions such as CH–O hydrogen bond and XH/π interactions, as well as polar residues that construct conspicuous hydrogen bonds, play important roles in molecular recognition and binding ability. Moreover, through these FMO-based analyses, we also clarified novel hot spots and epitopes that had been overlooked in previous studies by structural and molecular mechanical approaches. Altogether, these hot spots/epitopes identified between S-protein and ACE2/B38 Fab antibody may provide useful information for future antibody design, evaluation of the binding property of the SARS-CoV-2 variants including its N501Y, and small or medium drug design against the SARS-CoV-2.

Quantum chemical calculations investigated molecular recognition of SARS-CoV-2 spike glycoproteins including its N501Y variant for ACE2 and antibody. Hot spot and epitope analyses revealed key residues to design drugs and antibodies against COVID-19.