G-quadruplex-forming aptamer enhances the peroxidase activity of myoglobin against luminol.

Aptamers can control the biological functions of enzymes, thereby facilitating the development of novel biosensors. While aptamers that inhibit catalytic reactions of enzymes were found and used as signal transducers to sense target molecules in biosensors, no aptamers that amplify enzymatic activity have been identified. In this study, we report G-quadruplex (G4)-forming DNA aptamers that upregulate the peroxidase activity in myoglobin specifically for luminol.

Development of HGF-binding aptamers with the combination of G4 promoter-derived aptamer selection and in silico maturation.

We describe the selection of aptamers based on bioinformatics-based approaches without Systematic Evolution of Ligands by EXponential enrichment (SELEX). SELEX is a potent method; however, it is time intensive and the PCR-amplification step, which is essential step for SELEX, leads to the loss of good aptamers. We have developed an aptamer-screening method, G4 promoter-derived aptamer selection (G4PAS), and an aptamer-improving method, in silico maturation (ISM).

Methods for Improving Aptamer Binding Affinity.

Aptamers are single stranded oligonucleotides that bind a wide range of biological targets. Although aptamers can be isolated from pools of random sequence oligonucleotides using affinity-based selection, aptamers with high affinities are not always obtained. Therefore, further refinement of aptamers is required to achieve desired binding affinities.

Inhibition of an Allergen-Antibody Reaction Related to Japanese Cedar Pollinosis Using DNA Aptamers Against the Cry j 2 Allergen.

Japanese cedar pollinosis is one of the most prevalent allergies in Japan. Reducing the allergen content of pollen plays a major role in the alleviation of allergy symptoms. Aptamers, oligonucleotides with an affinity for specific molecules, have great potential for reducing allergic activity.

Improvement of the VEGF binding ability of DNA aptamers through in silico maturation and multimerization strategy.

Aptamers are mainly selected by in vitro selection using random nucleic acid libraries. These aptamers have often shown insufficient affinity for biomedical applications. We improved DNA aptamer binding affinity for vascular endothelial growth factor (VEGF) through in silico maturation (ISM) and aptamer multimerization.

DNA aptamers against the Cry j 2 allergen of Japanese cedar pollen for biosensing applications.

Sensing pollen allergens is required to prevent allergic disorders such as pollinosis. Aptamers, which bind to specific molecules, offer great potential as useful tools for detecting pollen allergens as measures against allergic disorders. Here, we report the identification of DNA aptamers binding to Cry j 2, one of the major allergens in Japanese cedar pollen, and the histochemical sensing of Cry j 2 in ruptured Japanese cedar pollen.

Selection of DNA aptamers against uropathogenic Escherichia coli NSM59 by quantitative PCR controlled Cell-SELEX.

In order to better control nosocomial infections, and facilitate the most prudent and effective use of antibiotics, improved strategies for the rapid detection and identification of problematic bacterial pathogens are required. DNA aptamers have much potential in the development of diagnostic assays and biosensors to address this important healthcare need, but further development of aptamers targeting common pathogens, and the strategies used to obtain specific aptamers are required. Here we demonstrate the application of a quantitative PCR (qPCR) controlled Cell-SELEX process, coupled with downstream secondary-conformation-based aptamer profiling.

Simultaneous improvement of specificity and affinity of aptamers against Streptococcus mutans by in silico maturation for biosensor development.

In silico evolution with an in vitro system can facilitate the development of functional aptamers with high specificity and affinity. Although a general technique known as systematic evolution of ligand by exponential enrichment (SELEX) is an efficient method for aptamer selection, it sometimes fails to identify aptamers with sufficient binding properties. We have previously developed in silico maturation (ISM) to improve functions of aptamers based on genetic algorithms.

In silico maturation of binding-specificity of DNA aptamers against Proteus mirabilis.

Proteus mirabilis is a prominent cause of catheter-associated urinary tract infections (CAUTIs) among patients undergoing long-term bladder catheterization. There are currently no effective means of preventing P. mirabilis infections, and strategies for prophylaxis and rapid early diagnosis are urgently required.

Development of a novel biosensing system based on the structural change of a polymerized guanine-quadruplex DNA nanostructure.

By inserting an adenosine aptamer into an aptamer that forms a G-quadruplex, we developed an adaptor molecule, named the Gq-switch, which links an electrode with flavin adenine dinucleotide-dependent glucose dehydrogenase (FADGDH) that is capable of transferring electron to a electrode directly. First, we selected an FADGDH-binding aptamer and identified that its sequence is composed of two blocks of consecutive six guanine bases and it forms a polymerized G-quadruplex structure. Then, we inserted a sequence of an adenosine aptamer between the two blocks of consecutive guanine bases, and we found it also bound to adenosine.

Selection of DNA aptamer against prostate specific antigen using a genetic algorithm and application to sensing.

In order to construct an aptasensor, aptamers that show high affinity for target molecules are required. While the systematic evolution of ligands by exponential enrichment (SELEX) is an efficient method for selecting aptamers, it sometimes fails to obtain aptamers with high affinity and so additional improvements are required. We applied a genetic algorithm (GA) to post-SELEX screening as an in silico maturation of aptamers.