Screening of DNA Signaling Aptamer from Multiple Candidates Obtained from SELEX with Next-generation Sequencing

Programming DNA Nanoassemblies into Polyvalent Lysosomal Degraders for Potent Degradation of Pathogenic Membrane Proteins

Lysosome-targeting chimera (LYTAC) shows great promise for protein-based therapeutics by targeted degradation of disease-associated membrane or extracellular proteins, yet its efficiency is constrained by the limited binding affinity between LYTAC reagents and designated proteins. Here, we established a programmable and multivalent LYTAC system by tandem assembly of DNA into a high-affinity protein degrader, a heterodimer aptamer nanostructure targeting both pathogenic membrane protein and lysosome-targeting receptor (insulin-like growth factor 2 receptor, IGF2R) with adjustable spatial distribution or organization pattern. The DNA-based multivalent LYTACs showed enhanced efficacy in removing immune-checkpoint protein programmable death-ligand 1 (PD-L1) and vascular endothelial growth factor receptor 2 (VEGFR2) in tumor cell membrane that respectively motivated a significant increase in T cell activity and a potent effect on cancer cell growth inhibition. With high programmability and versatility, this multivalent LYTAC system holds considerable promise for realizing protein therapeutics with enhanced activity.

Efficient Screening of Pesticide Diazinon-Binding Aptamers Using the Sol-Gel-Coated Nanoporous Membrane-Assisted SELEX Process and Next-Generation Sequencing

Aptamer-based methods for detecting pesticides are more efficient than antibody-based methods by high thermal stability, low molecular weight, easy modification, and low cost. In this study, the systematic evolution of ligands by exponential enrichment (SELEX) process, combined with next-generation sequencing (NGS), was performed to select aptamers specific to the pesticide, diazinon, which was fixed on a sol-gel-coated nanoporous-anodized aluminum oxide membrane to overcome the immobilization effect of general method and simplify the elution step. The frequency of specific nucleotide sequences obtained after SELEX rounds was directly analyzed using NGS to eliminate the time-consuming cloning process used in the general SELEX methods. Nine sequences with the highest frequency after SELEX round 10 followed by NGS were selected and tested to derive their binding affinity with the target, diazinon, through circular dichroism (CD) spectrophotometry. The CD signal difference of the aptamer candidates ranged from 0.13 to 2.242 mdeg between diazinon-only treated and diazinon-aptamer-treated samples at a wavelength near 270 nm. Aptamer D-4, which had the highest binding affinity from CD spectrophotometry analysis, showed no cross-reactivity with non-target pesticides, such as baycarb, bifenthrin, and pyridaben, but interacted with the other pesticides, fipronil and 2-phenylphenol. Therefore, an aptamer was effectively screened by selection of high-frequency candidates after SELEX-NGS followed by CD analysis with the highest difference signal. A follow-up study is needed to confirm whether the proposed SELEX process combined with NGS for the discovery of aptamers for new targets can further shorten the SELEX cycle by reducing the number of SELEX rounds to 10 or less.

Using a Biosensor Based on Surface-Enhanced Raman Scattering to Identify Influenza Viruses in Biological Fluids

Biosensors based on the effect of surface-enhanced Raman scattering obtained on silver nanoclusters modified with DNA aptamers allow viruses to be detected with high sensitivity. However, measurements in biological media are complicated by the nonspecific sorption of biomolecules on silver. Conditions for preparing samples of biological fluids that allow the nonspecific sorption of biomolecules to be nullified are studied.

Design strategy of antidote sequence for bivalent aptamer: Rapid neutralization of high-anticoagulant thrombin-binding bivalent DNA aptamer-linked M08 with HD22

Background

Bivalent thrombin-binding aptamers (TBAs) have great potential for the treatment of thrombosis because they exhibit high anticoagulant activity, and their complementary single-stranded DNA (ssDNA) sequences work as an antidote. However, a design strategy for antidote sequences against bivalent aptamers has not been established.

Objectives

To develop bivalent TBAs using M08, which exhibits higher anticoagulant activity than the previously reported exosite Ⅰ-binding DNA aptamers, such as HD1, an exosite Ⅱ-binding DNA aptamer (HD22) was linked to M08 with various types of linkers. In addition, short-length complementary ssDNAs were designed to neutralize the optimized bivalent aptamer effectively and rapidly.

Results

Among the bivalent aptamers of M08 linked to HD22 with various types of linkers, M08-T15-HD22 possessed approximately 5-fold higher anticoagulant activity than previously reported bivalent aptamers. To neutralize the activity of the 87-meric M08-T15-HD22, complementary ssDNA sequences with different lengths and hybridization segments were designed. The complementary sequence against the M08 moiety played a more important role in neutralizing than that against the HD22 moiety. Hybridization of the T15 linker in the M08-T15-HD22 with the A15 sequence in the antidote accelerated neutralization due to toehold-mediated strand displacement. Interestingly, some shorter-length antidotes showed higher neutralizing activity than the full complementary 87-meric antidote, and the shortest, 34-meric antidote, neutralized most effectively.

Conclusions

A pair comprising an 87-meric bivalent TBA containing M08 and a 34-meric short-length antidote with high anticoagulant and rapid neutralizing activities was developed. This design strategy of the DNA sequence can be used for other bivalent DNA aptamers and their antidotes.

Novel Approach to Overcome Defects of Cell-SELEX in Developing Aptamers against Aspartate β-Hydroxylase

Cell-based aptamer selection (Cell-SELEX) against predefined protein targets that benefits using the native form of the targets is the most promising approach to achieve aptamer probes capable of recognizing targets under both in vitro and in vivo conditions. The major disadvantages in Cell-SELEX are the imperfectness of the negative selection step and the lengthy procedure of selection. Here, we introduced the Counter-SELEX as part of our modified Cell-SELEX and implemented deep sequencing to overcome these shortcomings in developing aptamers against aspartate β-hydroxylase (ASPH) as a known tumor marker. In parallel with the conventional Cell-SELEX, five consecutive cycles of counter selection were accomplished using sequences bound to negative cells (the Counter-SELEX) to detect oligos that are not specific for ASPH. After high-throughput sequencing, the representative of each promising achieved family was subjected to further confirmatory analysis via flow cytometry, followed by the fluorescence immunostaining of histopathological sections. Implementing our innovative complementary method, annoying mis-selected sequences in Cell-SELEX enriched pools were effectively identified and removed. According to the affinity assay on the cells displaying ASPH, three aptamers, AP-Cell 1, AP-Cell 2, and AP-Cell 3, with K _d values of 47.51, 39.38, and 65.23 nM, respectively, were obtained, while AP-Cell 1 and 3 could then successfully spot ASPH displayed on the tissues. Our study showed that the Counter-SELEX could be considered as a complementary method for Cell-SELEX to overcome the imperfectness of the negative selection step. Moreover, high-throughput nucleotide sequencing could help to shorten the overall process.

Graphene-Based FRET Aptasensors

Graphene-based FRET aptasensors can be realized only by unique combinations of aptamer that can be freely functionalized by chemical modification, and graphene/graphene oxide that works as an excellent fluorescence acceptor at the same time as aptamer adsorbates. This review describes the principles of the sensor, several applications to microchannel devices, improvement of the sensing performance by molecular design of the aptamer and remarks on future prospects based on an introduction of recent works and achievements, including the author's paper. The sensor employs DNA modified with graphene/graphene oxide at the terminal as the molecular probe. This system is supported by the excellent property of DNA that does not lose the molecular recognition ability even due to a chemical modification at the terminal. I hope that this review will be useful for developing research on higher performance of graphene aptasensors in the future.

Selection and characterization of DNA aptamers for constructing colorimetric biosensor for detection of PBP2a

Rapid and accurate diagnosis of methicillin-resistant staphylococcus aureus (MRSA) is vital for patient treatment, control of infection and monitoring epidemiology. Penicillin binding proteins (PBP2a), as an important marker protein of MRSA, has been proposed as the screening test target for tolerant bacteria of MRSA. However, current technologies based on PBP2a activity or PBP2a immunoassays were suboptimal specificity and sensitivity. In this report, the selection and characterization of DNA aptamers that binds to PBP2a was described. The DNA aptamer is with high affinity and selectivity to binding with PBP2a. Furthermore, utilizing the switched mimicking peroxidase for gold nanoparticles loaded graphene oxide (GO/Au) nanomaterials based on the effect between GO/Au and DNA, a powerful strategy was set out for designing aptamer-based colorimetric biosensor for detection of PBP2a. In this strategy, the employment of biosensor based on GO/Au and PBP2a aptamer greatly improved the detection sensitivity and selectivity with limit of detection as low as 20 nM. Accordingly, the reversible nanozyme inhibition/activation approach may be universally applicable for the biomedical diagnosis.