Rabbit antibody detection with RNA aptamers

Yoshida, Yoshihito; Sakai, Nobuya; Masuda, Hiromi; Furuichi, Makio; Nishikawa, Fumiko; Nishikawa, Satoshi; Mizuno, Hiroshi; Waga, Iwao

doi:10.1016/j.ab.2008.01.005

Cited by 31 publications

(24 citation statements)

References 19 publications

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“…Aptamers are versatile tools that rival antibodies in diagnostic applications. A classic example of this property is evidenced by an RNA aptamer selected against the constant region (Fc) of the rabbit IgG, which is used as a reporter and may be a secondary marker in several assays where rabbit IgG antibodies are used 43 . Unlike antibodies, synthetic aptamers can easily be produced with a high degree of accuracy, reproducibility and purity.…”

Section: Discussionmentioning

confidence: 99%

Prostate-specific RNA aptamer: promising nucleic acid antibody-like cancer detection

Marangoni

Neves

Rocha

et al. 2015

Sci Rep

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We described the selection of a novel nucleic acid antibody-like prostate cancer (PCa) that specifically binds to the single-stranded DNA molecule from a 277-nt fragment that may have been partially paired and bound to the PCA3 RNA conformational structure. PCA3-277 aptamer ligands were obtained, and the best binding molecule, named CG3, was synthesized for validation. Aiming to prove its diagnostic utility, we used an apta-qPCR assay with CG3-aptamer conjugated to magnetic beads to capture PCA3 transcripts, which were amplified 97-fold and 7-fold higher than conventional qPCR in blood and tissue, respectively. Histopathologic analysis of 161 prostate biopsies arranged in a TMA and marked with biotin-labeled CG3-aptamer showed moderate staining in both cytoplasm and nucleus of PCa samples; in contrast, benign prostatic hyperplasia (BPH) samples presented strong nuclear staining (78% of the cases). No staining was observed in stromal cells. In addition, using an apta-qPCR, we demonstrated that CG3-aptamer specifically recognizes the conformational PCA3-277 molecule and at least three other transcript variants, indicating that long non-coding RNA (lncRNA) is processed after transcription. We suggest that CG3-aptamer may be a useful PCa diagnostic tool. In addition, this molecule may be used in drug design and drug delivery for PCa therapy.

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Section: Discussionmentioning

confidence: 99%

Prostate-specific RNA aptamer: promising nucleic acid antibody-like cancer detection

Marangoni

Neves

Rocha

et al. 2015

Sci Rep

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“…In the analyses, we examined two aptamers generated against rabbit IgG [60] and factor IXa [61]. In both cases, biotin-steptavidin-biotin sandwiching was performed to attach the biotinylated aptamers based on the amino surface of the sensing plate as described above, through the attachment of aptamer sequences on the biotin extended with 20-base oligos (dT20).…”

Section: Signal Enhancement For Aptamer-protein Interactionsmentioning

confidence: 99%

“…On these aptamer-attached surfaces, the appropriate target molecules (1 to 1,000 nM) were analyzed to differentiate the effects of chemically modified sensor surfaces. The reaction buffers used for all interactions include NaCl and MgCl 2 or NaCl and CaCl 2 , as originally reported [60,61]. Further, signal enhancement could also be achieved using gold nanoparticle–conjugated biomolecules [17].…”

Section: Signal Enhancement For Aptamer-protein Interactionsmentioning

confidence: 99%

Waveguide-Mode Sensors as Aptasensors

Gopinath

Awazu

Fujimaki

2012

Sensors

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Aptamers are artificial nucleic acid ligands that can be generated by in vitro selection through partition and amplification. Aptamers can be generated against a wide range of biomolecules through the formation of versatile stem-loop structures. Because aptamers are potential substitutes for antibodies and drugs, the development of an aptamer-based sensor (aptasensor) is mandatory for diagnosis. We previously reported that waveguide-mode sensors are useful in the analysis of a wide range of biomolecular interactions, including aptamers. The advantages of the waveguide-mode sensor that we developed include physical and chemical stability and that higher sensitivity can be achieved with ease by perforating the waveguide layer or using colored materials such as dyes or metal nanoparticles as labels. Herein, we provide an overview of the strategies and applications for aptamer-based analyses using waveguide-mode sensors.

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“…The truncation strategy worked very well in some cases such as SPC [9] and rabbit immunoglobulin G [10] aptamers which are based on 96 well based sequencers. At this moment, ValFold does not support large data sets from next-generation sequencing equipments because the current version is computationally slow.…”

Section: Caveat and Future Developmentmentioning

confidence: 99%

ValFold: Program for the aptamer truncation process

Akitomi¹,

Kato²,

Yoshida³

et al. 2011

Bioinformation

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DNA or RNA aptamers have gained attention as the next generation antibody-like molecules for medical or diagnostic use. Conventional secondary structure prediction tools for nucleic acids play an important role to truncate or minimize sequence, or introduce limited chemical modifications without compromising or changing its binding affinity to targets in the design of improved aptamers selected by Systematic Evolution of Ligands by EXponential enrichment (SELEX). We describe a novel software package, ValFold, capable of predicting secondary structures with improved accuracy based on unique aptamer characteristics. ValFold predicts not only the canonical Watson-Crick pairs but also G-G pairs derived from G-quadruplex (known structure for many aptamers) using the stem candidate selection algorithm.AvailabilityThe database is available for free at http://code.google.com/p/valfold/

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Rabbit antibody detection with RNA aptamers

Cited by 31 publications

References 19 publications

Prostate-specific RNA aptamer: promising nucleic acid antibody-like cancer detection

Prostate-specific RNA aptamer: promising nucleic acid antibody-like cancer detection

Waveguide-Mode Sensors as Aptasensors

ValFold: Program for the aptamer truncation process

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