Improving the reliability of aptamer-binding data can be achieved by integrating
independent third parties (collaboration partners or other external sources) with
expert knowledge in the use of biophysical methods. Scandals as in the antibody
field about unreliable, unspecific, and compromised antibodies must be avoided.
Consequently, the aptamer community needs to place the reliability of aptamer
binding in the center of an aptamer development project, as well as in the center of
any scientific review.
References
1. Chang AL, McKeague M, Liang JC, Smolke CD (2014) Kinetic and equilibrium binding
characterization of aptamers to small molecules using a label-free, sensitive, and scalable
platform. Anal Chem 86(7):3273–3278
2. Amano R, Takada K, Tanaka Y, Nakamura Y, Kawai G, Kozu T, Sakamoto T (2016) Kinetic
and thermodynamic analyses of interaction between a high-affinity RNA aptamer and its target
protein. Biochemistry 55(45):6221–6229
3. Stoltenburg R, Schubert T, Strehlitz B (2015) In vitro selection and interaction studies of a DNA
aptamer targeting protein A. PLoS One 10:e0134403. https://doi.org/10.1371/journal.pone.
0134403
4. Fülle L et al (2018) RNA aptamers recognizing murine CCL17 inhibit T cell chemotaxis and
reduce contact hypersensitivity in vivo. Mol Ther 26(1):95–104. https://doi.org/10.1016/j.
ymthe.2017.10.005
5. Wochner A, Menger M, Orgel D, Cech B, Rimmele M, Erdmann VA, Glökler J (2008) A DNA
aptamer with high affinity and specificity for therapeutic anthracyclines. Anal Biochem 373
(1):34–42
6. Lou X, Egli M, Yang X (2016) Determining functional aptamer-protein interaction by biolayer
interferometry. Curr Protoc Nucleic Acid Chem 67:7.25.1–7.25.15. https://doi.org/10.1002/
cpnc.18
7. Espiritu CAL, Justo CAC, Rubio MJ, Svobodova M, Bashammakh AS, Alyoubi AO, Rivera
WL, Rollon AP, O’Sullivan CK (2018) Aptamer selection against a trichomonas vaginalis
adhesion protein for diagnostic applications. ACS Infect Dis 4(9):1306–1315. https://doi.org/
10.1021/acsinfecdis.8b00065
8. Sakamoto T, Ennifar E, Nakamura Y (2018) Thermodynamic study of aptamers binding to their
target proteins. Biochimie 145:91–97. https://doi.org/10.1016/j.biochi.2017.10.010
9. Poongavanam MV, Kisley L, Kourentzi K, Landes CF, Willson RC (2016) Ensemble and
single-molecule biophysical characterization of D17.4 DNA aptamer-IgE interactions. Biochim
Biophys Acta 1864(1):154–164. https://doi.org/10.1016/j.bbapap.2015.08.008
10. Geng X et al (2013) Screening interaction between ochratoxin A and aptamers by fluorescence
anisotropy approach. Anal Bioanal Chem 405(8):2443–2449. https://doi.org/10.1007/s00216013-6736-1
11. Sefah K, Shangguan D, Xiong X, O’Donoghue MB, Tan W (2010) Development of DNA
aptamers using cell-SELEX. Nat Protoc 5(6):1169–1185
12. Soundy J, Day D (2017) Selection of DNA aptamers specific for live Pseudomonas aeruginosa.
PLoS One 12(9):e0185385. https://doi.org/10.1371/journal.pone.0185385
13. Jauset Rubio M, Svobodová M, Mairal T, Schubert T, Künne S, Mayer G, O’Sullivan CK
(2016) β-Conglutin dual aptamers binding distinct aptatopes. Anal Bioanal Chem 408
(3):875–884. https://doi.org/10.1007/s00216-015-9179-z
14
M. Plach and T. Schubert
independent third parties (collaboration partners or other external sources) with
expert knowledge in the use of biophysical methods. Scandals as in the antibody
field about unreliable, unspecific, and compromised antibodies must be avoided.
Consequently, the aptamer community needs to place the reliability of aptamer
binding in the center of an aptamer development project, as well as in the center of
any scientific review.
References
1. Chang AL, McKeague M, Liang JC, Smolke CD (2014) Kinetic and equilibrium binding
characterization of aptamers to small molecules using a label-free, sensitive, and scalable
platform. Anal Chem 86(7):3273–3278
2. Amano R, Takada K, Tanaka Y, Nakamura Y, Kawai G, Kozu T, Sakamoto T (2016) Kinetic
and thermodynamic analyses of interaction between a high-affinity RNA aptamer and its target
protein. Biochemistry 55(45):6221–6229
3. Stoltenburg R, Schubert T, Strehlitz B (2015) In vitro selection and interaction studies of a DNA
aptamer targeting protein A. PLoS One 10:e0134403. https://doi.org/10.1371/journal.pone.
0134403
4. Fülle L et al (2018) RNA aptamers recognizing murine CCL17 inhibit T cell chemotaxis and
reduce contact hypersensitivity in vivo. Mol Ther 26(1):95–104. https://doi.org/10.1016/j.
ymthe.2017.10.005
5. Wochner A, Menger M, Orgel D, Cech B, Rimmele M, Erdmann VA, Glökler J (2008) A DNA
aptamer with high affinity and specificity for therapeutic anthracyclines. Anal Biochem 373
(1):34–42
6. Lou X, Egli M, Yang X (2016) Determining functional aptamer-protein interaction by biolayer
interferometry. Curr Protoc Nucleic Acid Chem 67:7.25.1–7.25.15. https://doi.org/10.1002/
cpnc.18
7. Espiritu CAL, Justo CAC, Rubio MJ, Svobodova M, Bashammakh AS, Alyoubi AO, Rivera
WL, Rollon AP, O’Sullivan CK (2018) Aptamer selection against a trichomonas vaginalis
adhesion protein for diagnostic applications. ACS Infect Dis 4(9):1306–1315. https://doi.org/
10.1021/acsinfecdis.8b00065
8. Sakamoto T, Ennifar E, Nakamura Y (2018) Thermodynamic study of aptamers binding to their
target proteins. Biochimie 145:91–97. https://doi.org/10.1016/j.biochi.2017.10.010
9. Poongavanam MV, Kisley L, Kourentzi K, Landes CF, Willson RC (2016) Ensemble and
single-molecule biophysical characterization of D17.4 DNA aptamer-IgE interactions. Biochim
Biophys Acta 1864(1):154–164. https://doi.org/10.1016/j.bbapap.2015.08.008
10. Geng X et al (2013) Screening interaction between ochratoxin A and aptamers by fluorescence
anisotropy approach. Anal Bioanal Chem 405(8):2443–2449. https://doi.org/10.1007/s00216013-6736-1
11. Sefah K, Shangguan D, Xiong X, O’Donoghue MB, Tan W (2010) Development of DNA
aptamers using cell-SELEX. Nat Protoc 5(6):1169–1185
12. Soundy J, Day D (2017) Selection of DNA aptamers specific for live Pseudomonas aeruginosa.
PLoS One 12(9):e0185385. https://doi.org/10.1371/journal.pone.0185385
13. Jauset Rubio M, Svobodová M, Mairal T, Schubert T, Künne S, Mayer G, O’Sullivan CK
(2016) β-Conglutin dual aptamers binding distinct aptatopes. Anal Bioanal Chem 408
(3):875–884. https://doi.org/10.1007/s00216-015-9179-z
14
M. Plach and T. Schubert