Improvement of Homogeneity of Analytical Biodevices by Gene Manipulation

Two-Dimensional Protein Nanoarray as a Carrier of Sensing Elements for Gold-Based Immunosensing Systems

Homogeneous and high-density immobilization of proteins on gold-based sensing surface without the loss of protein activity is of great significance for high-performance immunosensing but remains challenging. To realize more sensitive immunosensing, an improved method for protein immobilization on the gold surface is urgently required. Here, we propose a biological and mild approach by combining a genetically encoded SpyTag-SpyCatcher interaction system with a redesigned S-layer of bacteria. This method allows proteins of interest to be covalently linked with the S-layer in a biological manner and arranged orderly in a two-dimensional nanoarray on the gold surface. The activity of African swine fever virus proteins was significantly preserved after immobilization. In addition, our S-layer-based immobilization method exhibited an eightfold increase in detection sensitivity compared with the conventional chemical cross-linking for protein immobilization during serological tests. Together, our S-layer-based immobilization method provides an innovative approach for building a quality gold-based biosensing interface and should greatly contribute to the high-sensitivity sensing for a deeper understanding of pathogen infection and host immunity.

Biomacromolecular nanostructures-based interfacial engineering: from precise assembly to precision biosensing

Biosensors are a type of important biodevice that integrate biological recognition elements, such as enzyme, antibody and DNA, and physical or chemical transducers, which have revolutionized clinical diagnosis especially under the context of point-of-care tests. Since the performance of a biosensor depends largely on the bio–solid interface, design and engineering of the interface play a pivotal role in developing quality biosensors. Along this line, a number of strategies have been developed to improve the homogeneity of the interface or the precision in regulating the interactions between biomolecules and the interface. Especially, intense efforts have been devoted to controlling the surface chemistry, orientation of immobilization, molecular conformation and packing density of surface-confined biomolecular probes (proteins and nucleic acids). By finely tuning these surface properties, through either gene manipulation or self-assembly, one may reduce the heterogeneity of self-assembled monolayers, increase the accessibility of target molecules and decrease the binding energy barrier to realize high sensitivity and specificity. In this review, we summarize recent progress in interfacial engineering of biosensors with particular focus on the use of protein and DNA nanostructures. These biomacromolecular nanostructures with atomistic precision lead to highly regulated interfacial assemblies at the nanoscale. We further describe the potential use of the high-performance biosensors for precision diagnostics.

Mapping the placement of oligonucleotide molecules using scanning probe microscopy

The successful development of novel bio-inspired devices requires the ability to place specific biomolecules on a substrate with nanometre precision, in such a way so that their bioactivity is retained. A method is required that can verify this bio-modification. Scanning probe microscopy (SPM) can image and probe a surface in a liquid environment with nanometre resolution. Using short chain complementary oligonucleotides as the bioactive molecules we have modified continuous and patterned gold substrates and SPM probes. We demonstrated that the attached oligonucleotides retained their biological activity after surface attachment with a hybridization interaction force that varies between 50 and 400pN as measured by SPM force measurements. Finally, the position of the attached oligonucleotides was determined with nanometre resolution. Thus we have demonstrated the capabilities of SPM in the application of the development of substrates and templates suitable for forming the basis of novel and innovative devices.

Seeding-induced self-assembling protein nanowires dramatically increase the sensitivity of immunoassays

Aiming to build a supersensitive and easily operable immunoassay, bifunctional protein nanowires were generated by seeding-induced self-assembling of the yeast amyloid protein Sup35p that genetically fused with protein G and an enzyme (methyl-parathion hydrolase, MPH), respectively. The protein nanowires possessed a high ratio of enzyme molecules to protein G, allowing a dramatic increase of the enzymatic signal when protein G was bound to an antibody target. As a result, a 100-fold enhancement of the sensitivity was obtained when applied in the detection of the Yersinia pestis F1 antigen.

Adhesion forces between Staphylococcus epidermidis and surfaces bearing self-assembled monolayers in the presence of model proteins

Self-assembled monolayers (SAMs) are being developed into coatings to reduce microbial biofilm formation on biomaterials. To test anti-adhesion properties, SAMs can be easily constructed on gold, and used to represent a coated biomaterial. However, coatings that prevent bacterial adhesion must also resist protein adsorption. We explored the competitive effects of bacteria and protein for adsorption to SAMs, choosing fetal bovine serum (FBS) to represent protein non-specific binding, and fibronectin (FN) to evaluate ligand/receptor binding. Staphylococcus epidermidis were immobilized on an atomic force microscope (AFM) tip and used as a force probe to detect the interaction forces between bacteria and gold-coated SAMs. The SAMs tested were alkanethiol molecules terminating in isophthalic acid (IPA) or isophthalic acid with silver (IAG). While S. epidermidis showed weak interactions with FBS, the bacteria showed strong adhesion with FN, due to ligand/receptor binding. Bacterial retention and viability experiments were correlated with the force measurements. S. epidermidis interacting with IAG SAMs showed a loss of viability, due to the mobility of silver ions. For most substrata, there was a link between high adhesion forces with bacteria and a high percentage of dead cells being retained on that substratum (even in the absence of a specific biocidal effect, such as silver). This may suggest that high adhesion forces can cause stress to the bacteria which contributed to their death. The relationship between highly adhesive SAMs and bacterial inactivation may be useful in future biomaterial design. When evaluating coatings for biomaterials, it is important to consider the interplay between bacteria, proteins, and the coating material.

Protein chip for detection of DNA mutations

A large number of human genetic diseases, bacterial drug resistances, and single-nucleotide polymorphisms are caused by gene mutations. Rapid and high-throughput mutation detection methods are urgently demanded. A protein chip method for detection of single-base mismatches and unpaired bases of DNA was developed using a genetic fusion molecular system Trx-His6-(Ser-Gly)6-Strep tagII-(Ser-Gly)6-MutS (THLSLM). The THLSLM coding sequence was constructed by attaching Strep tag II and mutS gene to the vector pET32a (+) sequentially with insertion of a (Ser-Gly)6 coding sequence before and behind Strep tagII gene, respectively. The fusion protein THLSLM was expressed in Escherichia coli AD494 (DE3) and purified using Ni(2+)-chelation affinity resin. The results of bioactivity assay showed that THLSLM both binds to mismatched DNA and interacts with streptavidin. THLSLM was immobilized on the chip matrix coated with the streptavidin through Strep tagII-streptavidin binding reaction. The resulting protein chip was used to detect the mismatched and unpaired mutations in the synthesized oligonucleotides, as well as a single-base mutation in rpoB gene from Mycobacterium tuberculosis, with high specificity. The method could potentially serve as a platform to develop the high-throughput technology for screening and analysis of genetic mutations.

Construction of a high sensitive Escherichia coli alkaline phosphatase reporter system for screening affinity peptides

An enzyme-linker-peptide fusion protein reporter system was constructed for sensitive analysis of affinity of peptide ligands to their receptor. An E. coli alkaline phosphatase (EAP) mutant enzyme with high catalytic activity was selected as the reporter protein. Interaction of affinity peptide and streptavidin was applied as demonstration of the method. Three affinity peptides, strep-tag I (SI), strep-tag II (SII) and streptavidin binding peptide (SBP) were genetically fused to the C-terminal of EAP respectively, with an insertion of a flexible linker peptide in between. The enzyme activity of the EAP fusions showed no obvious change. After expression and purification, the EAP-affinity peptide fusions were applied to the streptavidin modified surface. Binding of the fusions to the surface through interaction of affinity peptides to streptavidin was indicated by color generated from conversion of the substrate by EAP. The relative affinity and specificity of each affinity peptides to the immobilized streptavidin were then evaluated with high sensitivity and broad detection range. This method may be used for effective high-throughput screening of high affinity peptide from the peptide pool.

Reversible immobilization of proteins with streptavidin affinity tags on a surface plasmon resonance biosensor chip

Dissociation of biotin from streptavidin is very difficult due to their high binding affinity. The re-use of streptavidin-modified surfaces is therefore almost impossible, making devices containing them (e.g. surface plasmon resonance (SPR) sensor chips) expensive. This paper describes a new protocol for reversible and site-directed immobilization of proteins with streptavidin affinity tags on the streptavidin-coated SPR biosensor chip (SA chip). Two streptavidin affinity tags, nano-tag and streptavidin-binding peptide (SBP tag), were applied. They both can specifically interact with streptavidin but have weaker binding force compared to the biotin-streptavidin system, thus allowing association and dissociation under controlled conditions. The SA chip surface could be regenerated repeatedly without loss of activity by injection of 50 mM NaOH solution. The fusion construct of a SBP tag and a single-chain antibody to mature bovine prion protein (scFv-Z186-SBP) interacts with the SA chip, resulting in a single-chain-antibody-modified surface. The chip showed kinetic response to the prion antigen with equilibrium dissociation constant K (D) approximately equal to 4.01 x 10(-7). All results indicated that the capture activity of the SA chip has no irreversible loss after repeated immobilization and regeneration cycles. The method should be of great benefit to various biosensors, biochips and immunoassay applications based on the streptavidin capture surface.