DNA-duplex linker for AFM-SELEX of DNA aptamer against human serum albumin

Takenaka, Musashi; Okumura, Yuzo; Amino, Tomokazu; Miyachi, Yusuke; Ogino, Chiaki; Kondo, Akihiko

doi:10.1016/j.bmcl.2016.12.080

Cited by 33 publications

(16 citation statements)

References 12 publications

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“…According to the binding curves shown in Figure , the measured K D s were 20 ± 4, 1.2 ± 0.3, and 19 ± 3 nM by nonlinear fitting of the curves. Even though the inconsistent results existed among these methods, the K D s were all smaller than the previously reported (72 nM) and commercial HSA aptamer (29.1 nM, Base Pair Biotechnologies, Houston, TX) …”

Section: Resultscontrasting

confidence: 64%

Speeding up in Vitro Discovery of Structure-Switching Aptamers via Magnetic Cross-Linking Precipitation

Qiao

et al. 2019

Anal. Chem.

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We report here a modified aptamer selection method, magnetic cross-linking precipitation (MCP)-SELEX, for highly efficient library enrichment and aptamer isolation. MCP-SELEX isolates bound aptamers via highly efficient chemical cross-linking between amino groups of target proteins and activated carboxylic acid groups on magnetic beads (>90% coupling efficiency). Importantly, MCP-SELEX avoids surface interferences in conventional target-fixed methods and substantially minimizes nonspecific binding. The enrichment efficiencies of MCP-SELEX for various proteins (PD-L1, ubiquitin, thrombin, and HSA) were all greatly higher than those of the conventional target-bound magnetic bead based-SELEX (MB-SELEX). Antithrombin aptamer with KD of 33 nM was successfully isolated by four rounds of MCP-SELEX. MCP-SELEX also enabled the efficient aptamer isolation by coupling with MB-SELEX or falling-off-SELEX. We identified structure-switching aptamers (SSAs) that specifically bind to HSA with low nanomolar dissociation constant via three rounds of MCP-SELEX and 1 round of falling-off-SELEX. Our HSA SSAs also have ∼3-fold higher specificity against streptavidin relative to thrombin SSAs discovered through falling-off-SELEX only. The enriched library has ∼78-fold higher signal-to-noise ratio (the number of DNAs eluted by 50 nM HSA divided by the number of DNAs self-dissociated in blank buffer) than that obtained by 4 rounds of direct falling-off-SELEX. We finally demonstrated the application of the selected SSA in fluorescent detection of HSA in urine with diagnostic required sensitivity and dynamic range. We expect that MCP-SELEX may be coupled with other selection methods to substantially accelerate aptamer discovery.

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Section: Resultscontrasting

confidence: 64%

Speeding up in Vitro Discovery of Structure-Switching Aptamers via Magnetic Cross-Linking Precipitation

Qiao

et al. 2019

Anal. Chem.

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“…AFM-SELEX approach utilizing AFM dynamic affinity force measurement has been developed recently to obtain aptamers with increased affinity [62]. Furthermore, AFM-SELEX has been also successfully applied to develop aptamers against human serum albumin recently [63]. In this study, aptamers against human serum albumin could be selected in the fourth round, based on the measuring of the DNA-duplex interactions by AFM [63].…”

Section: Generation Of Aptamersmentioning

confidence: 99%

“…Furthermore, AFM-SELEX has been also successfully applied to develop aptamers against human serum albumin recently [63]. In this study, aptamers against human serum albumin could be selected in the fourth round, based on the measuring of the DNA-duplex interactions by AFM [63].…”

Section: Generation Of Aptamersmentioning

confidence: 99%

Recent Advances in Aptamer Discovery and Applications

2019

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Aptamers are short, single-stranded DNA, RNA, or synthetic XNA molecules that can be developed with high affinity and specificity to interact with any desired targets. They have been widely used in facilitating discoveries in basic research, ensuring food safety and monitoring the environment. Furthermore, aptamers play promising roles as clinical diagnostics and therapeutic agents. This review provides update on the recent advances in this rapidly progressing field of research with particular emphasis on generation of aptamers and their applications in biosensing, biotechnology and medicine. The limitations and future directions of aptamers in target specific delivery and real-time detection are also discussed.

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“… 70 Such a method has been used to select a DNA aptamer against thrombin with very strong affinity ( K D = 200 pM). 71 …”

Section: Aptamer Selection By Selexmentioning

confidence: 99%

Aptamers for Viral Detection and Inhibition

et al. 2022

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Recent times have experienced more than ever the impact of viral infections in humans. Viral infections are known to cause diseases not only in humans but also in plants and animals. Here, we have compiled the literature review of aptamers selected and used for detection and inhibition of viral infections in all three categories: humans, animals, and plants. This review gives an in-depth introduction to aptamers, different types of aptamer selection (SELEX) methodologies, the benefits of using aptamers over commonly used antibody-based strategies, and the structural and functional mechanism of aptasensors for viral detection and therapy. The review is organized based on the different characterization and read-out tools used to detect virus–aptasensor interactions with a detailed index of existing virus-targeting aptamers. Along with addressing recent developments, we also discuss a way forward with aptamers for DNA nanotechnology-based detection and treatment of viral diseases. Overall, this review will serve as a comprehensive resource for aptamer-based strategies in viral diagnostics and treatment.

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DNA-duplex linker for AFM-SELEX of DNA aptamer against human serum albumin

Cited by 33 publications

References 12 publications

Speeding up in Vitro Discovery of Structure-Switching Aptamers via Magnetic Cross-Linking Precipitation

Speeding up in Vitro Discovery of Structure-Switching Aptamers via Magnetic Cross-Linking Precipitation

Recent Advances in Aptamer Discovery and Applications

Aptamers for Viral Detection and Inhibition

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