Molecular affinity rulers: systematic evaluation of DNA aptamers for their applicabilities in ELISA

Nucleic Acids Research
Michiko KimotoIchiro Hirao

Abstract

Many nucleic acid aptamers that bind to target molecules have been reported as antibody alternatives. However, while the affinities of aptamers vary widely, little is known about the relationship between the affinities and their applicabilities for practical use. Here, we developed molecular affinity rulers: a series of DNA aptamers with different affinities that bind to the same area of target molecules, to measure the aptamer and its device applicabilities. For the ruler preparation, we used high-affinity DNA aptamers containing a hydrophobic unnatural base (Ds) as the fifth base. By replacing Ds bases with A bases in Ds-DNA aptamers targeting VEGF165 and interferon-γ, we prepared two sets of DNA aptamers with dissociation constants (KD) ranging from 10-12 to 10-8 M. Using these molecular affinity rulers, we evaluated the sensitivity of DNA aptamers in ELISA (enzyme-linked immunosorbent assay), which showed the clear relationship between aptamer affinities and their detection sensitivities. In sandwich-type ELISA using combinations of aptamers and antibodies, aptamers with KD values lower than ∼10-9 M were required for sufficient sensitivities (limit of detection (LOD) < 10 pM) and signal intensities, but optimizations improv...Continue Reading

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Citations

Mar 18, 2020·Chembiochem : a European Journal of Chemical Biology·Sepehr ManochehryYingfu Li
Dec 6, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Michelle BauerSarah Shigdar
Mar 24, 2020·Chembiochem : a European Journal of Chemical Biology·Michiko KimotoIchiro Hirao
Jul 8, 2020·International Journal of Molecular Sciences·Jan P ElskensAnnemieke Madder
Sep 16, 2020·Analytical Methods : Advancing Methods and Applications·Marta Jarczewska, Elżbieta Malinowska
Oct 11, 2020·Medicinal Research Reviews·Claudia RiccardiDaniela Montesarchio
Oct 6, 2020·Chemical Society Reviews·Michiko Kimoto, Ichiro Hirao
Oct 11, 2020·International Journal of Molecular Sciences·Chioma Izzi-EngbeayaWaljit S Dhillo
Nov 3, 2020·Analytical Sciences : the International Journal of the Japan Society for Analytical Chemistry·Shingo Saito
Oct 19, 2020·International Journal of Pharmaceutics·Yuan LiHuile Gao
Jan 20, 2021·Analytica Chimica Acta·Min-Seok BaekDong-Myung Kim
Mar 2, 2021·Chemical Society Reviews·Luke K McKenzieMarcel Hollenstein
Apr 15, 2020·Bioorganic & Medicinal Chemistry·Pascal RöthlisbergerMarcel Hollenstein
Jun 29, 2021·Acta Biochimica Et Biophysica Sinica·Nur Amira Khairil AnwarNoor Fatmawati Mokshtar
Sep 2, 2021·Journal of Neuroscience Methods·Taylor D PobranMari L DeMarco

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Methods Mentioned

BETA
SELEX
enzyme-linked immunosorbent assay
ELISA
enzyme-linked oligonucleotide assay
biosensor
electrophoresis
chips

Software Mentioned

ELONA
BIAevaluation
Biacore
ExSELEX

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