Structural optimization, characterization, and evaluation of binding mechanism of aptamers against bovine pregnancy-associated glycoproteins and their application in establishment of a colorimetric aptasensor using Fe-based metal-organic framework as peroxidase mimic tags.
Binding mechanism
Colorimetric aptasensor
Metal–organic frameworks
Molecular dynamics
Pregnancy-associated glycoproteins
Journal
Mikrochimica acta
ISSN: 1436-5073
Titre abrégé: Mikrochim Acta
Pays: Austria
ID NLM: 7808782
Informations de publication
Date de publication:
29 10 2024
29 10 2024
Historique:
received:
09
05
2024
accepted:
12
10
2024
medline:
29
10
2024
pubmed:
29
10
2024
entrez:
29
10
2024
Statut:
epublish
Résumé
A truncated aptamer (designated A24-3) was identified that specifically binds to bovine pregnancy-associated glycoproteins (bPAG9) with a low dissociation constant (2.04 nM) through two truncation approaches. Circular dichroism spectroscopy indicated that A24-3 formed parallel G-quadruplexes, which was subsequently confirmed using nuclear magnetic resonance (NMR) spectroscopy. Furthermore, a molecular dynamics simulation was employed to investigate the recognition mechanism of A24-3 and bPAG9. Interaction analysis showed that A24-3 folded into a parallel G-quadruplex structure with three G-tetrads, primarily through numerous hydrogen bonds and hydrophobic and π-π interactions. Finally, a novel colorimetric aptasensor was developed for detecting bPAG9 using A24-3 and an Fe-based metal-organic framework as target recognition elements and enzyme mimics, respectively. The method demonstrated a broad detection range from 0.5 to 50 ng/mL, with a low detection limit of 0.03 ng mL
Identifiants
pubmed: 39470834
doi: 10.1007/s00604-024-06775-6
pii: 10.1007/s00604-024-06775-6
doi:
Substances chimiques
Aptamers, Nucleotide
0
Metal-Organic Frameworks
0
Iron
E1UOL152H7
Glycoproteins
0
Peroxidase
EC 1.11.1.7
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
713Subventions
Organisme : science and technology planning project
ID : 2023AB009-01
Organisme : National Natural Science Foundation of China
ID : 31860647
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.
Références
Wooding FB (1992) Current topic: The synepitheliochorial placenta of ruminants: binucleate cell fusions and hormone production. Placenta 13:101–113. https://doi.org/10.1016/0143-4004(92)90025-O
doi: 10.1016/0143-4004(92)90025-O
pubmed: 1631024
Karen A, Sousa NMD, Beckers JF, Bajcsy ÁC, Tibold J, Mádl I, Szenci O (2015) Comparison of a commercial bovine pregnancy-associated glycoprotein ELISA test and a pregnancy-associated glycoprotein radiomimmunoassay test for early pregnancy diagnosis in dairycattle. Anim Reprod Sci 159:31–37. https://doi.org/10.1016/j.anireprosci.2015.05.005
doi: 10.1016/j.anireprosci.2015.05.005
pubmed: 26059776
Nagappan M, Michael M, Robert S (2009) Methods for early detection of pregnancy in cows. Monsanto Technology LLC, assignee. US Pat No 7:604, 950 B2
Chaves CDMES, Costa RLDD, Duarte KMR, Machado DC, Beltrame RT (2017) Visual ELISA for detection of pregnancy-associated glycoproteins (PAGs) in ewe serum. Theriogenology 97:78–82. https://doi.org/10.1016/j.theriogenology.2017.04.026
doi: 10.1016/j.theriogenology.2017.04.026
Mayo LM, Moore SG, Poock SE, Silvia WJ, Lucy MC (2016) Technical note: Validation of a chemical pregnancy test in dairy cows that uses whole blood, shortened incubation times, and visual readout. J Dairy Sci 99:7634–7641. https://doi.org/10.3168/jds.2016-11224
doi: 10.3168/jds.2016-11224
pubmed: 27394956
pmcid: 5772973
Kim YS, Raston NHA, Gu MB (2016) Aptamer-based nanobiosensors. Biosens Bioelectron 76:2–19. https://doi.org/10.1016/j.bios.2015.06.040
doi: 10.1016/j.bios.2015.06.040
pubmed: 26139320
AlmenhaliAZ ES (2024) Aptamer-based biosensors for the detection of neonicotinoid insecticides in environmental samples: A systematic review. Talanta 275:126190. https://doi.org/10.1016/j.talanta.2024.126190
doi: 10.1016/j.talanta.2024.126190
Lu CX, Liu CB, Shi GQ (2020) Colorimetric enzyme-linked aptamer assay utilizing hybridization chain reaction for determination of bovine pregnancy-associated glycoproteins. Microchim Acta 187:316–324. https://doi.org/10.1007/s00604-020-04301-y
doi: 10.1007/s00604-020-04301-y
Liu CB, Lu CX, Shi GQ (2020) Selection, identification and application of DNA aptamers against bovine pregnancy-associated glycoproteins 4. Anal Bioanal Chem 412:4235–4243. https://doi.org/10.1007/s00216-020-02666-w
doi: 10.1007/s00216-020-02666-w
pubmed: 32561948
Cowperthwaite MC, Ellington AD (2008) Bioinformatic analysis of the contribution of primer sequences to aptamer structures. J Mol Evolution 67:95–102. https://doi.org/10.1007/s00239-008-9130-4
doi: 10.1007/s00239-008-9130-4
Li P, Yu Q, Zhou L, Zhou LL, Dong DX, Wei SN, Ya HZ, Chen B, Qin QW (2018) Probing and characterizing the high specific sequences of ss DNA aptamer against SGIV-infected cells. Virus Res 246:46–54. https://doi.org/10.1016/j.virusres.2018.01.006
doi: 10.1016/j.virusres.2018.01.006
pubmed: 29341876
Kwon YS, Raston NHA, Gu MB (2014) An ultra-sensitive colorimetric detection of tetracyclines using the shortest aptamer with highly enhanced affinity. Chem Commun 50:40–42. https://doi.org/10.1039/c3cc47108j
doi: 10.1039/c3cc47108j
Gao SX, Wei H, Zheng X, Cai S, Wu JH (2019) Functionalized aptamer with an antiparallel G-quadruplex: Structural remodeling, recognition mechanism, and diagnostic applications targeting CTGF. Biosens Bioelectron 142:111475. https://doi.org/10.1016/j.bios.2019.111475
doi: 10.1016/j.bios.2019.111475
pubmed: 31288216
Wang F, Liu Y, Cao L, Hu H, Yao X, Zheng J, Liu H (2023) A label-free plasmonic nanosensor driven by horseradish peroxidase-assisted tetramethylbenzidine redox catalysis for colorimetric sensing H2O2 and cholesterol. Sens Actuators, B Chem 389:133893. https://doi.org/10.1016/j.snb.2023.133893
doi: 10.1016/j.snb.2023.133893
Zeng YJ, Wang MH, Sun ZW, Sha LJ, Yang J, Li GX (2022) Colorimetric immunosensor constructed using 2D metal-organic framework nanosheets as enzyme mimics for the detection of protein biomarkers. J Mater Chem B 10:450. https://doi.org/10.1039/D1TB02192C
doi: 10.1039/D1TB02192C
pubmed: 34981801
Wang LM, Liu GJ, Ren YX, Feng YH, Zhao XY, Zhu YQ, Chen M, Zhu FW, Liu Q, Chen XQ (2020) Integrating target-triggered aptamer-capped HRP@metal-organic frameworks with a colorimeter readout for on-site sensitive detection of antibiotics. Anal Chem 92:14259–14266. https://doi.org/10.1021/acs.analchem.0c03723
doi: 10.1021/acs.analchem.0c03723
pubmed: 32998507
Li J, Yu CF, Wu YN, Zhu YJ, Xu JJ, Wang Y, Wang HT, Guo MT, Li FT (2019) Novel sensing platform based on gold nanoparticle-aptamer and Fe-metal organic frame work for multiple antibiotic detection and signal amplification. Environ Int 125:135–141. https://doi.org/10.1016/j.envint.2019.01.033
doi: 10.1016/j.envint.2019.01.033
pubmed: 30716573
Zhang JW, Zhang HT, Du ZY, Wang XQ, Yu SH, Jiang HL (2014) Water-stable metal-organic frameworks with intrinsic peroxidase-like catalytic activity as acolorimetric biosensing platform. Chem Commun 50:1092–1094. https://doi.org/10.1039/C3CC48398C
doi: 10.1039/C3CC48398C
Li LL, Chen DM, Li B, Yang DQ, Zhao JC, Ma DH, Jiang L, Yang YP, Li YZ, Wang JQ (2019) MOFzyme: Enzyme Mimics of Fe/Fe-MIL-101. J Biosci Med 7:213–221. https://doi.org/10.4236/jbm.2019.75023
doi: 10.4236/jbm.2019.75023
Zhang YD, Ren HX, Miao YB (2019) Visualization and colorimetric determination of clenbuterol in pork by using magnetic beads modified with aptamer and complementary DNA as capture probes, and G-quadruplex/hemin and DNA antibody on the metal-organic framework MIL-101(Fe) acting as a peroxidase mimic. Microchim Acta 186:515. https://doi.org/10.1007/s00604-019-3604-5
doi: 10.1007/s00604-019-3604-5
Huang PP, Chang Q, Jiang GD, Wang X, Zhu HP, Liu QQ (2023) Rapidly and ultra-sensitive colorimetric detection of H2O2 and glucose based on ferrous-metal organic framework with enhanced peroxidase-mimicking activity. Spectrochimica Acta A 285:121943. https://doi.org/10.1016/j.saa.2022.121943
doi: 10.1016/j.saa.2022.121943
Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A (2016) Comparative protein structure modeling using modeller. Curr protoc Bioinform 05, Unit–5.6. https://doi.org/10.1002/cpbi.3
Yan YM, Zhang D, Zhou P, Li BT, Huang SY (2017) HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy. Nucleic Acids Res 45:W365–W373. https://doi.org/10.1093/nar/gkx407
doi: 10.1093/nar/gkx407
pubmed: 28521030
pmcid: 5793843
Skobelev IY, Sorokin AB, Kovalenko KA, Fedin VP, Kholdeeva OA (2013) Solvent-free allylic oxidation of alkenes with O2 mediated by Fe- and Cr-MIL-101. J Catal 298:61–69. https://doi.org/10.1016/j.jcat.2012.11.003
doi: 10.1016/j.jcat.2012.11.003
Duan N, Chen XW, Lin XF, Ying DC, Wang ZP, Yuan WB (2023) Paper-based fluorometric sensing of malachite green using synergistic recognition of aptamer-molecularly imprinted polymers and luminescent metal–organic frameworks. Sensor Actuat B-Chem 384:133665. https://doi.org/10.1016/j.snb.2023.133665
doi: 10.1016/j.snb.2023.133665
Shrivastava A, Gupta VB (2011) Methods for the determination of limit of detection and limit of quantitation of the analytical methods. Chron Young Sci 2:15–21. https://doi.org/10.4103/2229-5186.79345
doi: 10.4103/2229-5186.79345
Paré J, Audet-Grenier MH, Rouillier P, Sirard MA (2008) Evaluation of the DG29 test for early detection of pregnancy in cattle. Can Vet J 49:1119–1121. https://doi.org/10.1186/1746-6148-4-43
doi: 10.1186/1746-6148-4-43
pubmed: 19183736
pmcid: 2572099
Lam EYN, Beraldi D, Tannahill D, Balasubramanian S (2013) G-quadruplex structures are stable and detectable in human genomic DNA. Nat Commun 4:1796. https://doi.org/10.1038/ncomms2792
doi: 10.1038/ncomms2792
pubmed: 23653208
Kypr J, Kejnovska I, Renčiuk D, Vorlíčkova M (2009) Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res 37:1713–1725. https://doi.org/10.1093/nar/gkp026
doi: 10.1093/nar/gkp026
pubmed: 19190094
pmcid: 2665218
Guruprasad K, Blundell TL, Xie S, Green J, Szafranska B, Nagel RJ, McDowell K, Baker CB, Roberts RM (1996) Comparative modelling and analysis of amino acid substitution suggests that the family of pregnancy-associated glycoproteins includes both active and inactive aspartic proteinases. Protein Eng 9:849–856. https://doi.org/10.1093/protein/9.10.849
doi: 10.1093/protein/9.10.849
pubmed: 8931124
Li XH, Guo WL, Liu ZH, Wang RQ, Liu H (2016) Fe-based MOFs for efficient adsorption and degradation of acid orange7 in aqueous solution via persulfate activation. Appl Surface Sci 369:130–136. https://doi.org/10.1016/j.apsusc.2016.02.037
doi: 10.1016/j.apsusc.2016.02.037
Liu YL, Zhao XJ, Yang XX, Li YF (2013) A nanosized metal-organic framework of Fe-MIL-88NH2 as a novel peroxidase mimic used for colorimetric detection of glucose. Analyst 138:4526–4531. https://doi.org/10.1039/C3AN00560G
doi: 10.1039/C3AN00560G
pubmed: 23775015
Liu L, Shi Y, YangY LM, Long Y, Huang Y, Zheng H (2016) Fluorescein as an artificial enzyme to mimic peroxidase. Chem Commun 52:13912–13915. https://doi.org/10.1039/C6CC07896F
doi: 10.1039/C6CC07896F
Valekar AH, Batule BS, Kim MI, Cho KH, Hong DY, Lee UH, Chang JS, Park HG, Hwang YK (2018) Novel amine-functionalized iron trimesates with enhanced peroxidase-like activity and their applications for the fluorescent assay of choline and acetylcholine. Biosens Bioelectron 100:161–168. https://doi.org/10.1016/j.bios.2017.08.056
doi: 10.1016/j.bios.2017.08.056
pubmed: 28888178
Gao L, Zhuang J, Nie L, Zhang JB, Yan XY (2007) Intrinsic peroxidase-like activity of ferromagnetic nanoparticles. Nat Nanotechnol 2:577. https://doi.org/10.1038/nnano.2007.260
doi: 10.1038/nnano.2007.260
pubmed: 18654371
Green JA, Xie S, Quan X, Bao B, Gan X, Mathialagan N, Beckers JF, Roberts RM (2000) Pregnancy-associated bovine and ovine glycoproteins exhibit spatially and temporally distinct expression patterns during pregnancy. Biol Reprod 62:1624–1631. https://doi.org/10.1095/biolreprod62.6.1624
doi: 10.1095/biolreprod62.6.1624
pubmed: 10819764
Commun L, Velek K, Barbry JB, Pun S, Rice A, Mestek A, Egli C, Leterme S (2016) Detection of pregnancy-associated glycoproteins in milk and blood as a test for early pregnancy in dairy cows. J Vet Diagn Investig 28:207–213. https://doi.org/10.1177/10406387166328
doi: 10.1177/10406387166328
Zoli AP, Guilbault LA, Delabaut P, Ortiz WB, Beckers JF (1992) Radioimmunoassay of a bovine pregnancy-associated glycoproteinin serum: its application for pregnancy diagnosis. Biol Reprod 46:83–92. https://doi.org/10.1095/biolreprod46.1.83
doi: 10.1095/biolreprod46.1.83
pubmed: 1547318
Friedrich M, Holtz W (2010) Establishment of an ELISA for measuring bovine pregnancy-associated glycoprotein in serum or milk and its application for early pregnancy detection. Reprod Domest Anim 45:142–146. https://doi.org/10.1111/j.1439-0531.2008.01287.x
doi: 10.1111/j.1439-0531.2008.01287.x
pubmed: 19032429
Ricci A, Carvalho PD, Amundson MC, Fourdraine RH, Vincenti L, Fricke PM (2015) Factors associated with pregnancy-associated glycoprotein (PAG) levels in plasma and milk of Holstein cows during early pregnancy and their effect on the accuracy of pregnancy diagnosis. J Dairy Sci 98:2502–2514. https://doi.org/10.3168/jds.2014-8974
doi: 10.3168/jds.2014-8974
pubmed: 25660740